Starting phenix.real_space_refine on Wed Mar 13 08:45:10 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5aj3_2913/03_2024/5aj3_2913_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5aj3_2913/03_2024/5aj3_2913.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5aj3_2913/03_2024/5aj3_2913_neut_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5aj3_2913/03_2024/5aj3_2913_neut_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5aj3_2913/03_2024/5aj3_2913_neut_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5aj3_2913/03_2024/5aj3_2913.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5aj3_2913/03_2024/5aj3_2913.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5aj3_2913/03_2024/5aj3_2913_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5aj3_2913/03_2024/5aj3_2913_neut_updated.pdb" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.020 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 3 6.06 5 P 1100 5.49 5 Mg 144 5.21 5 S 178 5.16 5 C 37995 2.51 5 N 11833 2.21 5 O 15110 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B PHE 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c TYR 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 66363 Number of models: 1 Model: "" Number of chains: 44 Chain: "A" Number of atoms: 20411 Number of conformers: 1 Conformer: "" Number of residues, atoms: 960, 20411 Classifications: {'RNA': 960} Modifications used: {'rna2p_pur': 91, 'rna2p_pyr': 67, 'rna3p_pur': 431, 'rna3p_pyr': 371} Link IDs: {'rna2p': 158, 'rna3p': 801} Chain: "B" Number of atoms: 1762 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1762 Classifications: {'peptide': 220} Link IDs: {'PTRANS': 12, 'TRANS': 207} Chain: "C" Number of atoms: 1075 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1075 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 7, 'TRANS': 124} Chain: "E" Number of atoms: 2621 Number of conformers: 1 Conformer: "" Number of residues, atoms: 328, 2621 Classifications: {'peptide': 328} Link IDs: {'PTRANS': 13, 'TRANS': 314} Chain breaks: 1 Chain: "F" Number of atoms: 990 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 990 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 7, 'TRANS': 115} Chain: "G" Number of atoms: 1721 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1721 Classifications: {'peptide': 208} Link IDs: {'PTRANS': 12, 'TRANS': 195} Chain: "I" Number of atoms: 2498 Number of conformers: 1 Conformer: "" Number of residues, atoms: 311, 2498 Classifications: {'peptide': 311} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 13, 'TRANS': 297} Chain breaks: 1 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 32 Planarities with less than four sites: {'UNK:plan-1': 16} Unresolved non-hydrogen planarities: 16 Chain: "J" Number of atoms: 1067 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1067 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 6, 'TRANS': 122} Chain: "K" Number of atoms: 1001 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1001 Classifications: {'peptide': 136} Link IDs: {'PTRANS': 9, 'TRANS': 126} Chain: "L" Number of atoms: 840 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 840 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 10, 'TRANS': 98} Chain: "N" Number of atoms: 858 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 858 Classifications: {'peptide': 101} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 96} Chain: "O" Number of atoms: 1448 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1448 Classifications: {'peptide': 175} Link IDs: {'PTRANS': 8, 'TRANS': 166} Chain: "P" Number of atoms: 932 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 932 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 7, 'TRANS': 109} Chain: "Q" Number of atoms: 853 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 853 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 6, 'TRANS': 102} Chain: "R" Number of atoms: 784 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 784 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 8, 'TRANS': 88} Chain: "T" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 84 Classifications: {'peptide': 14} Link IDs: {'TRANS': 13} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 28 Planarities with less than four sites: {'UNK:plan-1': 14} Unresolved non-hydrogen planarities: 14 Chain: "U" Number of atoms: 734 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 734 Classifications: {'peptide': 86} Link IDs: {'PTRANS': 2, 'TRANS': 83} Chain: "V" Number of atoms: 1158 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 1158 Classifications: {'RNA': 64} Modifications used: {'5*END': 1, 'rna2p': 5, 'rna3p': 59} Link IDs: {'rna2p': 5, 'rna3p': 58} Chain breaks: 2 Unresolved non-hydrogen bonds: 63 Unresolved non-hydrogen angles: 189 Unresolved non-hydrogen dihedrals: 63 Chain: "X" Number of atoms: 231 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 231 Classifications: {'RNA': 13} Modifications used: {'5*END': 1, 'rna2p': 2, 'rna3p': 11} Link IDs: {'rna2p': 2, 'rna3p': 10} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 12 Chain: "Y" Number of atoms: 1158 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 1158 Classifications: {'RNA': 64} Modifications used: {'5*END': 1, 'rna2p': 6, 'rna3p': 58} Link IDs: {'rna2p': 6, 'rna3p': 57} Chain breaks: 3 Unresolved non-hydrogen bonds: 63 Unresolved non-hydrogen angles: 189 Unresolved non-hydrogen dihedrals: 63 Chain: "a" Number of atoms: 2296 Number of conformers: 1 Conformer: "" Number of residues, atoms: 292, 2296 Classifications: {'peptide': 292} Link IDs: {'PTRANS': 13, 'TRANS': 278} Unresolved non-hydrogen bonds: 48 Unresolved non-hydrogen angles: 96 Planarities with less than four sites: {'UNK:plan-1': 48} Unresolved non-hydrogen planarities: 48 Chain: "b" Number of atoms: 1101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1101 Classifications: {'peptide': 135} Link IDs: {'PTRANS': 7, 'TRANS': 127} Chain: "c" Number of atoms: 1367 Number of conformers: 1 Conformer: "" Number of residues, atoms: 169, 1367 Classifications: {'peptide': 169} Link IDs: {'PTRANS': 11, 'TRANS': 157} Chain: "d" Number of atoms: 1467 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1467 Classifications: {'peptide': 177} Link IDs: {'PTRANS': 7, 'TRANS': 169} Chain: "e" Number of atoms: 2016 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2016 Classifications: {'peptide': 336} Link IDs: {'TRANS': 335} Chain breaks: 4 Unresolved non-hydrogen bonds: 336 Unresolved non-hydrogen angles: 672 Planarities with less than four sites: {'UNK:plan-1': 336} Unresolved non-hydrogen planarities: 336 Chain: "f" Number of atoms: 778 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 778 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 3, 'TRANS': 95} Chain: "g" Number of atoms: 2774 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2774 Classifications: {'peptide': 346} Link IDs: {'PTRANS': 16, 'TRANS': 329} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 36 Planarities with less than four sites: {'UNK:plan-1': 18} Unresolved non-hydrogen planarities: 18 Chain: "h" Number of atoms: 876 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 876 Classifications: {'peptide': 103} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 98} Chain: "i" Number of atoms: 824 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 824 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 4, 'TRANS': 94} Chain: "j" Number of atoms: 1777 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1777 Classifications: {'peptide': 213} Link IDs: {'PTRANS': 15, 'TRANS': 197} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Planarities with less than four sites: {'UNK:plan-1': 7} Unresolved non-hydrogen planarities: 7 Chain: "k" Number of atoms: 2222 Number of conformers: 1 Conformer: "" Number of residues, atoms: 275, 2222 Classifications: {'peptide': 275} Link IDs: {'PTRANS': 17, 'TRANS': 257} Chain: "m" Number of atoms: 930 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 930 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 9, 'TRANS': 106} Chain: "n" Number of atoms: 639 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 639 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 2, 'TRANS': 69} Chain: "o" Number of atoms: 3028 Number of conformers: 1 Conformer: "" Number of residues, atoms: 476, 3028 Classifications: {'peptide': 476} Link IDs: {'PTRANS': 8, 'TRANS': 467} Chain breaks: 26 Unresolved non-hydrogen bonds: 387 Unresolved non-hydrogen angles: 774 Planarities with less than four sites: {'UNK:plan-1': 387} Unresolved non-hydrogen planarities: 387 Chain: "p" Number of atoms: 1551 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1551 Classifications: {'peptide': 188} Link IDs: {'PTRANS': 20, 'TRANS': 167} Chain: "s" Number of atoms: 96 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 96 Classifications: {'peptide': 16} Link IDs: {'TRANS': 15} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 32 Planarities with less than four sites: {'UNK:plan-1': 16} Unresolved non-hydrogen planarities: 16 Chain: "z" Number of atoms: 102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 102 Classifications: {'peptide': 17} Link IDs: {'TRANS': 16} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 34 Planarities with less than four sites: {'UNK:plan-1': 17} Unresolved non-hydrogen planarities: 17 Chain: "A" Number of atoms: 143 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 143 Unusual residues: {' MG': 143} Classifications: {'undetermined': 143} Link IDs: {None: 142} Chain: "R" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "c" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "g" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 29 Unusual residues: {' MG': 1, 'GDP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 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: "A" Number of atoms: 114 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 114 Classifications: {'water': 114} Link IDs: {None: 113} Chain: "g" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 26704 SG CYS F 105 143.390 114.555 35.501 1.00 48.89 S ATOM 38238 SG CYS R 66 141.288 117.605 34.701 1.00 36.13 S ATOM 38260 SG CYS R 69 140.320 114.214 33.599 1.00 57.30 S ATOM 38517 SG CYS R 101 140.214 115.234 37.222 1.00 40.39 S ATOM 36418 SG CYS P 26 139.915 62.082 125.548 1.00 38.00 S ATOM 46764 SG CYS c 139 141.440 59.071 123.813 1.00 59.47 S ATOM 46778 SG CYS c 141 138.222 60.341 122.683 1.00 86.06 S ATOM 46836 SG CYS c 149 138.395 58.722 125.923 1.00134.28 S ATOM 64707 SG CYS p 94 111.619 76.306 123.482 1.00 62.10 S ATOM 64784 SG CYS p 105 112.126 76.402 119.802 1.00 38.96 S ATOM 64805 SG CYS p 108 110.690 73.347 121.400 1.00 59.50 S ATOM 65090 SG CYS p 143 114.366 74.225 121.862 1.00 62.75 S Time building chain proxies: 27.01, per 1000 atoms: 0.41 Number of scatterers: 66363 At special positions: 0 Unit cell: (246.03, 243.25, 184.87, 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 3 29.99 S 178 16.00 P 1100 15.00 Mg 144 11.99 O 15110 8.00 N 11833 7.00 C 37995 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS m 45 " - pdb=" SG CYS m 76 " distance=2.05 Simple disulfide: pdb=" SG CYS m 55 " - pdb=" SG CYS m 66 " distance=2.04 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: 25.47 Conformation dependent library (CDL) restraints added in 6.3 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN R 500 " pdb="ZN ZN R 500 " - pdb=" SG CYS R 101 " pdb="ZN ZN R 500 " - pdb=" SG CYS F 105 " pdb="ZN ZN R 500 " - pdb=" SG CYS R 66 " pdb="ZN ZN R 500 " - pdb=" SG CYS R 69 " pdb=" ZN c 500 " pdb="ZN ZN c 500 " - pdb=" SG CYS c 141 " pdb="ZN ZN c 500 " - pdb=" SG CYS c 149 " pdb="ZN ZN c 500 " - pdb=" SG CYS c 139 " pdb="ZN ZN c 500 " - pdb=" SG CYS P 26 " pdb=" ZN p 500 " pdb="ZN ZN p 500 " - pdb=" SG CYS p 105 " pdb="ZN ZN p 500 " - pdb=" SG CYS p 94 " pdb="ZN ZN p 500 " - pdb=" SG CYS p 108 " pdb="ZN ZN p 500 " - pdb=" SG CYS p 143 " Number of angles added : 18 9198 Ramachandran restraints generated. 4599 Oldfield, 0 Emsley, 4599 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10528 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 223 helices and 31 sheets defined 54.3% alpha, 10.0% beta 262 base pairs and 577 stacking pairs defined. Time for finding SS restraints: 24.17 Creating SS restraints... Processing helix chain 'B' and resid 56 through 67 Proline residue: B 65 - end of helix Processing helix chain 'B' and resid 74 through 77 Processing helix chain 'B' and resid 80 through 85 Processing helix chain 'B' and resid 94 through 96 No H-bonds generated for 'chain 'B' and resid 94 through 96' Processing helix chain 'B' and resid 117 through 136 removed outlier: 3.518A pdb=" N LEU B 126 " --> pdb=" O ALA B 122 " (cutoff:3.500A) Processing helix chain 'B' and resid 151 through 161 removed outlier: 3.630A pdb=" N ASP B 160 " --> pdb=" O THR B 156 " (cutoff:3.500A) Processing helix chain 'B' and resid 178 through 181 No H-bonds generated for 'chain 'B' and resid 178 through 181' Processing helix chain 'B' and resid 206 through 214 Processing helix chain 'B' and resid 242 through 273 Processing helix chain 'C' and resid 59 through 61 No H-bonds generated for 'chain 'C' and resid 59 through 61' Processing helix chain 'C' and resid 73 through 75 No H-bonds generated for 'chain 'C' and resid 73 through 75' Processing helix chain 'C' and resid 82 through 99 Processing helix chain 'C' and resid 129 through 146 Processing helix chain 'E' and resid 95 through 103 Processing helix chain 'E' and resid 162 through 186 removed outlier: 4.031A pdb=" N LYS E 186 " --> pdb=" O ARG E 182 " (cutoff:3.500A) Processing helix chain 'E' and resid 264 through 277 removed outlier: 3.792A pdb=" N HIS E 277 " --> pdb=" O ASN E 273 " (cutoff:3.500A) Processing helix chain 'E' and resid 285 through 287 No H-bonds generated for 'chain 'E' and resid 285 through 287' Processing helix chain 'E' and resid 318 through 327 Processing helix chain 'E' and resid 342 through 354 Processing helix chain 'E' and resid 359 through 366 Processing helix chain 'E' and resid 408 through 414 Processing helix chain 'F' and resid 15 through 32 Processing helix chain 'F' and resid 72 through 84 removed outlier: 3.627A pdb=" N VAL F 75 " --> pdb=" O ALA F 72 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N GLU F 76 " --> pdb=" O THR F 73 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N ARG F 84 " --> pdb=" O HIS F 81 " (cutoff:3.500A) Processing helix chain 'G' and resid 48 through 52 Processing helix chain 'G' and resid 58 through 69 Processing helix chain 'G' and resid 89 through 98 removed outlier: 3.547A pdb=" N MET G 98 " --> pdb=" O PHE G 94 " (cutoff:3.500A) Processing helix chain 'G' and resid 104 through 127 Processing helix chain 'G' and resid 131 through 136 Processing helix chain 'G' and resid 141 through 150 Processing helix chain 'G' and resid 176 through 193 Processing helix chain 'G' and resid 201 through 213 Processing helix chain 'G' and resid 218 through 232 Processing helix chain 'G' and resid 234 through 238 Processing helix chain 'I' and resid 71 through 92 removed outlier: 3.526A pdb=" N MET I 91 " --> pdb=" O HIS I 87 " (cutoff:3.500A) Processing helix chain 'I' and resid 101 through 111 removed outlier: 3.521A pdb=" N ARG I 106 " --> pdb=" O GLU I 102 " (cutoff:3.500A) Processing helix chain 'I' and resid 128 through 131 No H-bonds generated for 'chain 'I' and resid 128 through 131' Processing helix chain 'I' and resid 151 through 153 No H-bonds generated for 'chain 'I' and resid 151 through 153' Processing helix chain 'I' and resid 156 through 175 removed outlier: 3.637A pdb=" N LEU I 161 " --> pdb=" O SER I 157 " (cutoff:3.500A) Processing helix chain 'I' and resid 203 through 209 Processing helix chain 'I' and resid 216 through 230 Processing helix chain 'I' and resid 236 through 244 Processing helix chain 'I' and resid 301 through 304 No H-bonds generated for 'chain 'I' and resid 301 through 304' Processing helix chain 'I' and resid 308 through 321 Proline residue: I 317 - end of helix Processing helix chain 'I' and resid 338 through 352 Processing helix chain 'I' and resid 359 through 368 removed outlier: 4.426A pdb=" N GLU I 363 " --> pdb=" O GLU I 359 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N TRP I 364 " --> pdb=" O ASP I 360 " (cutoff:3.500A) Processing helix chain 'J' and resid 85 through 101 removed outlier: 3.595A pdb=" N GLU J 101 " --> pdb=" O LEU J 97 " (cutoff:3.500A) Processing helix chain 'J' and resid 150 through 163 removed outlier: 3.563A pdb=" N ASN J 163 " --> pdb=" O TYR J 159 " (cutoff:3.500A) Processing helix chain 'K' and resid 123 through 125 No H-bonds generated for 'chain 'K' and resid 123 through 125' Processing helix chain 'K' and resid 127 through 144 removed outlier: 3.520A pdb=" N ALA K 136 " --> pdb=" O THR K 132 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LYS K 144 " --> pdb=" O LYS K 140 " (cutoff:3.500A) Processing helix chain 'K' and resid 160 through 169 removed outlier: 3.533A pdb=" N THR K 168 " --> pdb=" O ILE K 164 " (cutoff:3.500A) Processing helix chain 'L' and resid 33 through 38 Processing helix chain 'N' and resid 32 through 46 Processing helix chain 'N' and resid 48 through 58 removed outlier: 3.797A pdb=" N LEU N 57 " --> pdb=" O ARG N 53 " (cutoff:3.500A) Processing helix chain 'N' and resid 65 through 77 removed outlier: 3.612A pdb=" N VAL N 70 " --> pdb=" O ASP N 66 " (cutoff:3.500A) Processing helix chain 'N' and resid 84 through 86 No H-bonds generated for 'chain 'N' and resid 84 through 86' Processing helix chain 'N' and resid 108 through 117 removed outlier: 3.556A pdb=" N HIS N 117 " --> pdb=" O HIS N 113 " (cutoff:3.500A) Processing helix chain 'O' and resid 75 through 77 No H-bonds generated for 'chain 'O' and resid 75 through 77' Processing helix chain 'O' and resid 88 through 93 Processing helix chain 'O' and resid 96 through 98 No H-bonds generated for 'chain 'O' and resid 96 through 98' Processing helix chain 'O' and resid 101 through 116 Processing helix chain 'O' and resid 126 through 146 removed outlier: 3.539A pdb=" N GLU O 142 " --> pdb=" O ARG O 138 " (cutoff:3.500A) Processing helix chain 'O' and resid 151 through 173 removed outlier: 3.523A pdb=" N ASP O 162 " --> pdb=" O LEU O 158 " (cutoff:3.500A) Processing helix chain 'O' and resid 176 through 185 Processing helix chain 'O' and resid 202 through 238 removed outlier: 3.801A pdb=" N LYS O 220 " --> pdb=" O ARG O 216 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ARG O 229 " --> pdb=" O LYS O 225 " (cutoff:3.500A) Processing helix chain 'P' and resid 70 through 79 Processing helix chain 'P' and resid 85 through 94 Processing helix chain 'P' and resid 101 through 125 Processing helix chain 'R' and resid 78 through 84 removed outlier: 3.758A pdb=" N PHE R 84 " --> pdb=" O LEU R 80 " (cutoff:3.500A) Processing helix chain 'R' and resid 95 through 98 No H-bonds generated for 'chain 'R' and resid 95 through 98' Processing helix chain 'R' and resid 102 through 117 Processing helix chain 'R' and resid 128 through 132 removed outlier: 4.146A pdb=" N LYS R 132 " --> pdb=" O ALA R 129 " (cutoff:3.500A) Processing helix chain 'U' and resid 19 through 33 Processing helix chain 'U' and resid 35 through 43 Processing helix chain 'U' and resid 48 through 79 removed outlier: 3.554A pdb=" N ARG U 54 " --> pdb=" O ARG U 50 " (cutoff:3.500A) removed outlier: 5.030A pdb=" N ARG U 77 " --> pdb=" O ASN U 73 " (cutoff:3.500A) removed outlier: 5.521A pdb=" N LYS U 78 " --> pdb=" O PHE U 74 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ASN U 79 " --> pdb=" O LEU U 75 " (cutoff:3.500A) Processing helix chain 'a' and resid 72 through 82 Processing helix chain 'a' and resid 86 through 89 No H-bonds generated for 'chain 'a' and resid 86 through 89' Processing helix chain 'a' and resid 107 through 125 removed outlier: 3.691A pdb=" N VAL a 123 " --> pdb=" O GLU a 119 " (cutoff:3.500A) Processing helix chain 'a' and resid 145 through 150 removed outlier: 4.229A pdb=" N GLY a 149 " --> pdb=" O LYS a 145 " (cutoff:3.500A) removed outlier: 5.099A pdb=" N THR a 150 " --> pdb=" O ILE a 146 " (cutoff:3.500A) No H-bonds generated for 'chain 'a' and resid 145 through 150' Processing helix chain 'a' and resid 185 through 195 Processing helix chain 'a' and resid 207 through 209 No H-bonds generated for 'chain 'a' and resid 207 through 209' Processing helix chain 'a' and resid 211 through 219 Processing helix chain 'a' and resid 223 through 233 removed outlier: 3.635A pdb=" N VAL a 231 " --> pdb=" O LEU a 227 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ALA a 232 " --> pdb=" O ASN a 228 " (cutoff:3.500A) Processing helix chain 'a' and resid 239 through 254 Processing helix chain 'a' and resid 258 through 261 Processing helix chain 'a' and resid 267 through 275 Processing helix chain 'a' and resid 281 through 289 Processing helix chain 'a' and resid 293 through 306 Processing helix chain 'a' and resid 311 through 318 Processing helix chain 'a' and resid 323 through 333 Processing helix chain 'a' and resid 338 through 355 removed outlier: 3.735A pdb=" N UNK a 349 " --> pdb=" O UNK a 345 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N UNK a 355 " --> pdb=" O UNK a 351 " (cutoff:3.500A) Processing helix chain 'b' and resid 12 through 21 Processing helix chain 'b' and resid 30 through 37 Processing helix chain 'b' and resid 66 through 77 removed outlier: 4.009A pdb=" N LYS b 73 " --> pdb=" O ARG b 69 " (cutoff:3.500A) Processing helix chain 'b' and resid 95 through 107 Processing helix chain 'b' and resid 114 through 127 Processing helix chain 'c' and resid 8 through 11 Processing helix chain 'c' and resid 14 through 18 Processing helix chain 'c' and resid 42 through 49 removed outlier: 3.527A pdb=" N LYS c 46 " --> pdb=" O GLU c 42 " (cutoff:3.500A) Processing helix chain 'c' and resid 51 through 58 removed outlier: 3.752A pdb=" N TYR c 57 " --> pdb=" O PRO c 53 " (cutoff:3.500A) Processing helix chain 'c' and resid 95 through 105 Processing helix chain 'c' and resid 110 through 123 removed outlier: 4.256A pdb=" N LEU c 123 " --> pdb=" O GLU c 119 " (cutoff:3.500A) Processing helix chain 'c' and resid 157 through 159 No H-bonds generated for 'chain 'c' and resid 157 through 159' Processing helix chain 'c' and resid 161 through 169 Processing helix chain 'd' and resid 36 through 39 No H-bonds generated for 'chain 'd' and resid 36 through 39' Processing helix chain 'd' and resid 50 through 86 removed outlier: 3.521A pdb=" N LEU d 72 " --> pdb=" O ARG d 68 " (cutoff:3.500A) Processing helix chain 'd' and resid 89 through 165 removed outlier: 4.267A pdb=" N LYS d 165 " --> pdb=" O GLN d 161 " (cutoff:3.500A) Processing helix chain 'd' and resid 173 through 182 removed outlier: 3.699A pdb=" N GLU d 178 " --> pdb=" O GLU d 174 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ASP d 182 " --> pdb=" O GLU d 178 " (cutoff:3.500A) Processing helix chain 'e' and resid 29 through 42 Processing helix chain 'e' and resid 50 through 62 Processing helix chain 'e' and resid 70 through 81 removed outlier: 4.970A pdb=" N UNK e 81 " --> pdb=" O UNK e 77 " (cutoff:3.500A) Processing helix chain 'e' and resid 86 through 97 removed outlier: 4.032A pdb=" N UNK e 90 " --> pdb=" O UNK e 86 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N UNK e 91 " --> pdb=" O UNK e 87 " (cutoff:3.500A) Processing helix chain 'e' and resid 105 through 117 Processing helix chain 'e' and resid 121 through 133 Processing helix chain 'e' and resid 140 through 152 Processing helix chain 'e' and resid 156 through 168 Processing helix chain 'e' and resid 175 through 191 removed outlier: 3.952A pdb=" N UNK e 190 " --> pdb=" O UNK e 186 " (cutoff:3.500A) Processing helix chain 'e' and resid 197 through 210 removed outlier: 3.808A pdb=" N UNK e 208 " --> pdb=" O UNK e 204 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N UNK e 209 " --> pdb=" O UNK e 205 " (cutoff:3.500A) removed outlier: 5.183A pdb=" N UNK e 210 " --> pdb=" O UNK e 206 " (cutoff:3.500A) Processing helix chain 'e' and resid 214 through 228 removed outlier: 3.584A pdb=" N UNK e 227 " --> pdb=" O UNK e 223 " (cutoff:3.500A) Processing helix chain 'e' and resid 233 through 236 No H-bonds generated for 'chain 'e' and resid 233 through 236' Processing helix chain 'e' and resid 248 through 260 removed outlier: 3.651A pdb=" N UNK e 253 " --> pdb=" O UNK e 249 " (cutoff:3.500A) Processing helix chain 'e' and resid 274 through 290 removed outlier: 5.301A pdb=" N UNK e 279 " --> pdb=" O UNK e 275 " (cutoff:3.500A) removed outlier: 5.221A pdb=" N UNK e 280 " --> pdb=" O UNK e 276 " (cutoff:3.500A) Processing helix chain 'e' and resid 295 through 307 Processing helix chain 'e' and resid 355 through 363 Processing helix chain 'e' and resid 367 through 380 removed outlier: 3.697A pdb=" N UNK e 373 " --> pdb=" O UNK e 369 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N UNK e 377 " --> pdb=" O UNK e 373 " (cutoff:3.500A) Processing helix chain 'e' and resid 383 through 405 removed outlier: 3.722A pdb=" N UNK e 392 " --> pdb=" O UNK e 388 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N UNK e 397 " --> pdb=" O UNK e 393 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N UNK e 400 " --> pdb=" O UNK e 396 " (cutoff:3.500A) Processing helix chain 'f' and resid 81 through 86 Processing helix chain 'f' and resid 89 through 92 No H-bonds generated for 'chain 'f' and resid 89 through 92' Processing helix chain 'f' and resid 132 through 134 No H-bonds generated for 'chain 'f' and resid 132 through 134' Processing helix chain 'g' and resid 71 through 77 Processing helix chain 'g' and resid 84 through 93 Processing helix chain 'g' and resid 102 through 112 Processing helix chain 'g' and resid 135 through 146 removed outlier: 4.409A pdb=" N ILE g 140 " --> pdb=" O SER g 136 " (cutoff:3.500A) Processing helix chain 'g' and resid 157 through 161 Processing helix chain 'g' and resid 180 through 193 removed outlier: 4.023A pdb=" N THR g 192 " --> pdb=" O LYS g 188 " (cutoff:3.500A) Processing helix chain 'g' and resid 196 through 200 removed outlier: 3.795A pdb=" N GLN g 200 " --> pdb=" O HIS g 196 " (cutoff:3.500A) No H-bonds generated for 'chain 'g' and resid 196 through 200' Processing helix chain 'g' and resid 221 through 230 Processing helix chain 'g' and resid 235 through 251 removed outlier: 4.338A pdb=" N SER g 251 " --> pdb=" O LYS g 247 " (cutoff:3.500A) Processing helix chain 'g' and resid 264 through 268 removed outlier: 3.657A pdb=" N TRP g 268 " --> pdb=" O ASN g 265 " (cutoff:3.500A) Processing helix chain 'g' and resid 287 through 295 removed outlier: 3.784A pdb=" N LYS g 294 " --> pdb=" O HIS g 290 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N MET g 295 " --> pdb=" O ASN g 291 " (cutoff:3.500A) Processing helix chain 'g' and resid 324 through 336 removed outlier: 6.097A pdb=" N LYS g 330 " --> pdb=" O GLU g 326 " (cutoff:3.500A) removed outlier: 8.523A pdb=" N GLU g 331 " --> pdb=" O LEU g 327 " (cutoff:3.500A) Processing helix chain 'g' and resid 349 through 361 Processing helix chain 'g' and resid 368 through 371 removed outlier: 4.075A pdb=" N HIS g 371 " --> pdb=" O GLU g 368 " (cutoff:3.500A) No H-bonds generated for 'chain 'g' and resid 368 through 371' Processing helix chain 'g' and resid 373 through 383 Processing helix chain 'g' and resid 387 through 395 Processing helix chain 'h' and resid 289 through 299 Processing helix chain 'h' and resid 315 through 317 No H-bonds generated for 'chain 'h' and resid 315 through 317' Processing helix chain 'h' and resid 320 through 322 No H-bonds generated for 'chain 'h' and resid 320 through 322' Processing helix chain 'h' and resid 327 through 330 Processing helix chain 'h' and resid 338 through 351 Processing helix chain 'h' and resid 358 through 374 Processing helix chain 'h' and resid 377 through 382 Processing helix chain 'i' and resid 6 through 19 Processing helix chain 'i' and resid 30 through 37 Processing helix chain 'i' and resid 42 through 44 No H-bonds generated for 'chain 'i' and resid 42 through 44' Processing helix chain 'i' and resid 46 through 49 No H-bonds generated for 'chain 'i' and resid 46 through 49' Processing helix chain 'i' and resid 55 through 67 Processing helix chain 'i' and resid 74 through 88 Processing helix chain 'j' and resid 11 through 26 removed outlier: 3.513A pdb=" N ALA j 15 " --> pdb=" O ILE j 11 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N ARG j 16 " --> pdb=" O ALA j 12 " (cutoff:3.500A) Processing helix chain 'j' and resid 30 through 33 No H-bonds generated for 'chain 'j' and resid 30 through 33' Processing helix chain 'j' and resid 55 through 60 Processing helix chain 'j' and resid 64 through 67 No H-bonds generated for 'chain 'j' and resid 64 through 67' Processing helix chain 'j' and resid 83 through 88 Processing helix chain 'j' and resid 146 through 150 removed outlier: 3.618A pdb=" N PHE j 150 " --> pdb=" O GLU j 147 " (cutoff:3.500A) Processing helix chain 'j' and resid 168 through 181 Processing helix chain 'k' and resid 68 through 71 No H-bonds generated for 'chain 'k' and resid 68 through 71' Processing helix chain 'k' and resid 105 through 108 No H-bonds generated for 'chain 'k' and resid 105 through 108' Processing helix chain 'k' and resid 114 through 116 No H-bonds generated for 'chain 'k' and resid 114 through 116' Processing helix chain 'k' and resid 118 through 128 Processing helix chain 'k' and resid 137 through 140 Processing helix chain 'k' and resid 142 through 148 Processing helix chain 'k' and resid 168 through 171 removed outlier: 3.524A pdb=" N ARG k 171 " --> pdb=" O PRO k 168 " (cutoff:3.500A) No H-bonds generated for 'chain 'k' and resid 168 through 171' Processing helix chain 'k' and resid 179 through 181 No H-bonds generated for 'chain 'k' and resid 179 through 181' Processing helix chain 'k' and resid 186 through 199 removed outlier: 6.822A pdb=" N ASP k 198 " --> pdb=" O LYS k 194 " (cutoff:3.500A) removed outlier: 7.792A pdb=" N ARG k 199 " --> pdb=" O LEU k 195 " (cutoff:3.500A) Processing helix chain 'k' and resid 217 through 235 Processing helix chain 'k' and resid 240 through 243 No H-bonds generated for 'chain 'k' and resid 240 through 243' Processing helix chain 'k' and resid 259 through 275 Processing helix chain 'k' and resid 282 through 287 Processing helix chain 'k' and resid 289 through 303 Processing helix chain 'k' and resid 308 through 322 Processing helix chain 'm' and resid 46 through 58 Processing helix chain 'm' and resid 68 through 92 removed outlier: 4.802A pdb=" N GLU m 91 " --> pdb=" O ARG m 87 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N ASN m 92 " --> pdb=" O SER m 88 " (cutoff:3.500A) Processing helix chain 'm' and resid 101 through 110 Processing helix chain 'n' and resid 129 through 149 removed outlier: 4.175A pdb=" N ARG n 134 " --> pdb=" O LEU n 131 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N LYS n 142 " --> pdb=" O ASN n 139 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N LYS n 145 " --> pdb=" O LYS n 142 " (cutoff:3.500A) Processing helix chain 'n' and resid 151 through 180 removed outlier: 3.668A pdb=" N VAL n 167 " --> pdb=" O ARG n 163 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ILE n 176 " --> pdb=" O ASP n 172 " (cutoff:3.500A) Processing helix chain 'o' and resid 67 through 75 removed outlier: 3.872A pdb=" N ILE o 70 " --> pdb=" O LYS o 67 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ALA o 73 " --> pdb=" O ILE o 70 " (cutoff:3.500A) Processing helix chain 'o' and resid 100 through 123 Processing helix chain 'o' and resid 138 through 140 No H-bonds generated for 'chain 'o' and resid 138 through 140' Processing helix chain 'o' and resid 154 through 163 Processing helix chain 'o' and resid 168 through 179 Processing helix chain 'o' and resid 186 through 197 Processing helix chain 'o' and resid 201 through 214 Processing helix chain 'o' and resid 221 through 233 Processing helix chain 'o' and resid 239 through 248 Processing helix chain 'o' and resid 261 through 274 Processing helix chain 'o' and resid 278 through 290 Processing helix chain 'o' and resid 296 through 308 Processing helix chain 'o' and resid 316 through 328 Processing helix chain 'o' and resid 337 through 348 Processing helix chain 'o' and resid 356 through 367 Processing helix chain 'o' and resid 372 through 384 Processing helix chain 'o' and resid 391 through 404 Processing helix chain 'o' and resid 411 through 429 Processing helix chain 'o' and resid 434 through 445 Processing helix chain 'o' and resid 458 through 468 Processing helix chain 'o' and resid 476 through 488 Processing helix chain 'o' and resid 493 through 505 Processing helix chain 'o' and resid 511 through 523 Processing helix chain 'o' and resid 532 through 540 Processing helix chain 'o' and resid 547 through 558 Processing helix chain 'o' and resid 576 through 584 Processing helix chain 'o' and resid 594 through 605 Processing helix chain 'o' and resid 652 through 659 Processing helix chain 'o' and resid 667 through 675 Processing helix chain 'p' and resid 56 through 60 Processing helix chain 'p' and resid 62 through 67 Processing helix chain 'p' and resid 106 through 109 No H-bonds generated for 'chain 'p' and resid 106 through 109' Processing helix chain 'p' and resid 120 through 126 removed outlier: 4.240A pdb=" N GLN p 125 " --> pdb=" O LYS p 121 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N PHE p 126 " --> pdb=" O LEU p 122 " (cutoff:3.500A) Processing helix chain 'p' and resid 137 through 140 No H-bonds generated for 'chain 'p' and resid 137 through 140' Processing helix chain 'p' and resid 144 through 159 Processing helix chain 'p' and resid 191 through 194 No H-bonds generated for 'chain 'p' and resid 191 through 194' Processing helix chain 'p' and resid 210 through 219 Processing helix chain 's' and resid 2361 through 2373 Processing helix chain 'z' and resid 699 through 707 Processing sheet with id= A, first strand: chain 'B' and resid 164 through 166 removed outlier: 6.819A pdb=" N LEU B 191 " --> pdb=" O LEU B 142 " (cutoff:3.500A) removed outlier: 7.864A pdb=" N VAL B 144 " --> pdb=" O LEU B 191 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N ILE B 193 " --> pdb=" O VAL B 144 " (cutoff:3.500A) removed outlier: 7.864A pdb=" N PHE B 194 " --> pdb=" O PRO B 217 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N VAL B 219 " --> pdb=" O PHE B 194 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N TYR B 233 " --> pdb=" O GLY B 220 " (cutoff:3.500A) removed outlier: 7.163A pdb=" N VAL B 222 " --> pdb=" O TYR B 233 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N VAL B 235 " --> pdb=" O VAL B 222 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 105 through 109 removed outlier: 6.795A pdb=" N ILE B 114 " --> pdb=" O PHE B 106 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N SER B 108 " --> pdb=" O GLN B 112 " (cutoff:3.500A) removed outlier: 6.037A pdb=" N GLN B 112 " --> pdb=" O SER B 108 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'C' and resid 109 through 113 Processing sheet with id= D, first strand: chain 'E' and resid 254 through 261 removed outlier: 6.524A pdb=" N ALA E 246 " --> pdb=" O ILE E 222 " (cutoff:3.500A) removed outlier: 5.414A pdb=" N ILE E 222 " --> pdb=" O ALA E 246 " (cutoff:3.500A) removed outlier: 7.262A pdb=" N GLY E 248 " --> pdb=" O THR E 220 " (cutoff:3.500A) removed outlier: 5.492A pdb=" N THR E 220 " --> pdb=" O GLY E 248 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'E' and resid 294 through 298 Processing sheet with id= F, first strand: chain 'E' and resid 370 through 373 removed outlier: 5.846A pdb=" N GLU E 372 " --> pdb=" O VAL E 383 " (cutoff:3.500A) removed outlier: 5.365A pdb=" N VAL E 383 " --> pdb=" O GLU E 372 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'F' and resid 43 through 46 removed outlier: 3.924A pdb=" N GLY F 43 " --> pdb=" O TYR F 63 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'F' and resid 51 through 53 Processing sheet with id= I, first strand: chain 'F' and resid 35 through 41 removed outlier: 6.731A pdb=" N ASP F 67 " --> pdb=" O ARG F 37 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N LEU F 39 " --> pdb=" O LEU F 65 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N LEU F 65 " --> pdb=" O LEU F 39 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'G' and resid 156 through 163 Processing sheet with id= K, first strand: chain 'I' and resid 198 through 200 Processing sheet with id= L, first strand: chain 'I' and resid 270 through 277 Processing sheet with id= M, first strand: chain 'J' and resid 106 through 109 removed outlier: 4.788A pdb=" N LEU J 72 " --> pdb=" O LEU J 177 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N THR J 175 " --> pdb=" O LYS J 74 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N LEU J 76 " --> pdb=" O THR J 173 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N THR J 173 " --> pdb=" O LEU J 76 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N VAL J 78 " --> pdb=" O GLU J 171 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N GLU J 171 " --> pdb=" O VAL J 78 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N VAL J 80 " --> pdb=" O ALA J 169 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N ALA J 169 " --> pdb=" O VAL J 80 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'J' and resid 114 through 121 Processing sheet with id= O, first strand: chain 'K' and resid 173 through 179 removed outlier: 6.978A pdb=" N VAL K 151 " --> pdb=" O ILE K 175 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N ILE K 177 " --> pdb=" O VAL K 151 " (cutoff:3.500A) removed outlier: 7.288A pdb=" N VAL K 153 " --> pdb=" O ILE K 177 " (cutoff:3.500A) removed outlier: 4.956A pdb=" N ASP K 179 " --> pdb=" O VAL K 153 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'L' and resid 107 through 111 Processing sheet with id= Q, first strand: chain 'L' and resid 65 through 68 Processing sheet with id= R, first strand: chain 'P' and resid 17 through 22 removed outlier: 6.047A pdb=" N ALA P 36 " --> pdb=" O GLN P 50 " (cutoff:3.500A) removed outlier: 5.429A pdb=" N GLN P 50 " --> pdb=" O ALA P 36 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'Q' and resid 12 through 16 removed outlier: 8.712A pdb=" N LYS Q 78 " --> pdb=" O THR Q 48 " (cutoff:3.500A) removed outlier: 8.301A pdb=" N PHE Q 50 " --> pdb=" O LYS Q 78 " (cutoff:3.500A) removed outlier: 5.786A pdb=" N GLU Q 80 " --> pdb=" O PHE Q 50 " (cutoff:3.500A) removed outlier: 5.635A pdb=" N HIS Q 52 " --> pdb=" O GLU Q 80 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N ARG Q 29 " --> pdb=" O VAL Q 17 " (cutoff:3.500A) removed outlier: 5.587A pdb=" N VAL Q 17 " --> pdb=" O ARG Q 29 " (cutoff:3.500A) removed outlier: 7.543A pdb=" N THR Q 31 " --> pdb=" O GLY Q 15 " (cutoff:3.500A) removed outlier: 7.457A pdb=" N GLY Q 15 " --> pdb=" O THR Q 31 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'Q' and resid 63 through 65 removed outlier: 6.299A pdb=" N LEU Q 65 " --> pdb=" O ILE Q 84 " (cutoff:3.500A) removed outlier: 5.743A pdb=" N ILE Q 84 " --> pdb=" O LEU Q 65 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'a' and resid 155 through 158 removed outlier: 3.623A pdb=" N ALA a 142 " --> pdb=" O LEU a 180 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N LYS a 182 " --> pdb=" O VAL a 140 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N VAL a 140 " --> pdb=" O LYS a 182 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'c' and resid 63 through 68 Processing sheet with id= W, first strand: chain 'f' and resid 123 through 126 removed outlier: 3.741A pdb=" N HIS f 107 " --> pdb=" O TYR f 114 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N ASP f 116 " --> pdb=" O ILE f 105 " (cutoff:3.500A) removed outlier: 5.278A pdb=" N ILE f 105 " --> pdb=" O ASP f 116 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N ASP f 167 " --> pdb=" O LEU f 146 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'g' and resid 66 through 69 removed outlier: 4.358A pdb=" N ALA g 96 " --> pdb=" O UNK g 69 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'g' and resid 340 through 344 removed outlier: 4.149A pdb=" N VAL g 121 " --> pdb=" O GLY g 303 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N LEU g 257 " --> pdb=" O ALA g 304 " (cutoff:3.500A) removed outlier: 7.398A pdb=" N VAL g 306 " --> pdb=" O LEU g 257 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N VAL g 259 " --> pdb=" O VAL g 306 " (cutoff:3.500A) removed outlier: 7.937A pdb=" N THR g 308 " --> pdb=" O VAL g 259 " (cutoff:3.500A) removed outlier: 7.305A pdb=" N VAL g 261 " --> pdb=" O THR g 308 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N LEU g 150 " --> pdb=" O LEU g 258 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N ALA g 260 " --> pdb=" O LEU g 150 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N LEU g 152 " --> pdb=" O ALA g 260 " (cutoff:3.500A) removed outlier: 7.364A pdb=" N ASP g 262 " --> pdb=" O LEU g 152 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N ILE g 154 " --> pdb=" O ASP g 262 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'g' and resid 168 through 170 Processing sheet with id= AA, first strand: chain 'g' and resid 206 through 208 Processing sheet with id= AB, first strand: chain 'j' and resid 80 through 82 Processing sheet with id= AC, first strand: chain 'j' and resid 123 through 125 removed outlier: 4.115A pdb=" N HIS j 111 " --> pdb=" O ASP j 103 " (cutoff:3.500A) removed outlier: 5.573A pdb=" N ILE j 117 " --> pdb=" O LEU j 97 " (cutoff:3.500A) removed outlier: 5.417A pdb=" N LEU j 97 " --> pdb=" O ILE j 117 " (cutoff:3.500A) removed outlier: 7.162A pdb=" N THR j 119 " --> pdb=" O TRP j 95 " (cutoff:3.500A) removed outlier: 4.928A pdb=" N TRP j 95 " --> pdb=" O THR j 119 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'j' and resid 163 through 165 Processing sheet with id= AE, first strand: chain 'k' and resid 151 through 155 1847 hydrogen bonds defined for protein. 5316 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 640 hydrogen bonds 1146 hydrogen bond angles 0 basepair planarities 262 basepair parallelities 577 stacking parallelities Total time for adding SS restraints: 28.77 Time building geometry restraints manager: 27.70 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.35: 18593 1.35 - 1.49: 26322 1.49 - 1.64: 24433 1.64 - 1.79: 33 1.79 - 1.93: 251 Bond restraints: 69632 Sorted by residual: bond pdb=" C1' Y5P V 21 " pdb=" N1 Y5P V 21 " ideal model delta sigma weight residual 1.480 1.610 -0.130 1.50e-02 4.44e+03 7.50e+01 bond pdb=" C1' Y5P Y 37 " pdb=" N1 Y5P Y 37 " ideal model delta sigma weight residual 1.480 1.608 -0.128 1.50e-02 4.44e+03 7.29e+01 bond pdb=" C5 Y5P X 16 " pdb=" C6 Y5P X 16 " ideal model delta sigma weight residual 1.493 1.323 0.170 2.00e-02 2.50e+03 7.21e+01 bond pdb=" N3 Y5P V 41 " pdb=" C4 Y5P V 41 " ideal model delta sigma weight residual 1.488 1.319 0.169 2.00e-02 2.50e+03 7.10e+01 bond pdb=" C5 Y5P X 17 " pdb=" C6 Y5P X 17 " ideal model delta sigma weight residual 1.493 1.328 0.165 2.00e-02 2.50e+03 6.84e+01 ... (remaining 69627 not shown) Histogram of bond angle deviations from ideal: 96.07 - 104.00: 4365 104.00 - 111.94: 36376 111.94 - 119.88: 27699 119.88 - 127.81: 28402 127.81 - 135.75: 2059 Bond angle restraints: 98901 Sorted by residual: angle pdb=" C ASP Q 36 " pdb=" N PRO Q 37 " pdb=" CA PRO Q 37 " ideal model delta sigma weight residual 119.19 129.67 -10.48 1.06e+00 8.90e-01 9.77e+01 angle pdb=" C GLU p 54 " pdb=" N PRO p 55 " pdb=" CA PRO p 55 " ideal model delta sigma weight residual 119.84 131.28 -11.44 1.25e+00 6.40e-01 8.38e+01 angle pdb=" C PRO p 230 " pdb=" N PRO p 231 " pdb=" CA PRO p 231 " ideal model delta sigma weight residual 120.38 129.38 -9.00 1.03e+00 9.43e-01 7.63e+01 angle pdb=" C ALA k 76 " pdb=" N PRO k 77 " pdb=" CA PRO k 77 " ideal model delta sigma weight residual 119.82 128.27 -8.45 9.80e-01 1.04e+00 7.43e+01 angle pdb=" C PRO b 39 " pdb=" N PRO b 40 " pdb=" CA PRO b 40 " ideal model delta sigma weight residual 120.21 128.47 -8.26 9.60e-01 1.09e+00 7.41e+01 ... (remaining 98896 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.94: 39308 34.94 - 69.87: 3540 69.87 - 104.81: 349 104.81 - 139.75: 22 139.75 - 174.68: 9 Dihedral angle restraints: 43228 sinusoidal: 27080 harmonic: 16148 Sorted by residual: dihedral pdb=" CA ARG K 194 " pdb=" C ARG K 194 " pdb=" N ARG K 195 " pdb=" CA ARG K 195 " ideal model delta harmonic sigma weight residual 180.00 122.21 57.79 0 5.00e+00 4.00e-02 1.34e+02 dihedral pdb=" O4' U A 505 " pdb=" C1' U A 505 " pdb=" N1 U A 505 " pdb=" C2 U A 505 " ideal model delta sinusoidal sigma weight residual 232.00 58.81 173.19 1 1.70e+01 3.46e-03 6.62e+01 dihedral pdb=" O4' C A 372 " pdb=" C1' C A 372 " pdb=" N1 C A 372 " pdb=" C2 C A 372 " ideal model delta sinusoidal sigma weight residual -128.00 43.73 -171.73 1 1.70e+01 3.46e-03 6.61e+01 ... (remaining 43225 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.070: 9820 0.070 - 0.140: 1302 0.140 - 0.211: 124 0.211 - 0.281: 11 0.281 - 0.351: 1 Chirality restraints: 11258 Sorted by residual: chirality pdb=" C4' A A 900 " pdb=" C5' A A 900 " pdb=" O4' A A 900 " pdb=" C3' A A 900 " both_signs ideal model delta sigma weight residual False -2.50 -2.15 -0.35 2.00e-01 2.50e+01 3.08e+00 chirality pdb=" CA ARG K 194 " pdb=" N ARG K 194 " pdb=" C ARG K 194 " pdb=" CB ARG K 194 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.52e+00 chirality pdb=" P A A 317 " pdb=" OP1 A A 317 " pdb=" OP2 A A 317 " pdb=" O5' A A 317 " both_signs ideal model delta sigma weight residual True 2.41 -2.65 -0.24 2.00e-01 2.50e+01 1.46e+00 ... (remaining 11255 not shown) Planarity restraints: 8814 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C5' Y5P Y 38 " -0.083 2.00e-02 2.50e+03 6.51e-01 9.55e+03 pdb=" C4' Y5P Y 38 " -0.464 2.00e-02 2.50e+03 pdb=" O4' Y5P Y 38 " -0.712 2.00e-02 2.50e+03 pdb=" C3' Y5P Y 38 " 0.600 2.00e-02 2.50e+03 pdb=" O3' Y5P Y 38 " 0.754 2.00e-02 2.50e+03 pdb=" C2' Y5P Y 38 " 0.152 2.00e-02 2.50e+03 pdb=" O2' Y5P Y 38 " -1.020 2.00e-02 2.50e+03 pdb=" C1' Y5P Y 38 " -0.245 2.00e-02 2.50e+03 pdb=" N1 Y5P Y 38 " 1.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' Y5P V 29 " 0.083 2.00e-02 2.50e+03 6.35e-01 9.08e+03 pdb=" C4' Y5P V 29 " 0.431 2.00e-02 2.50e+03 pdb=" O4' Y5P V 29 " 0.651 2.00e-02 2.50e+03 pdb=" C3' Y5P V 29 " -0.609 2.00e-02 2.50e+03 pdb=" O3' Y5P V 29 " -0.717 2.00e-02 2.50e+03 pdb=" C2' Y5P V 29 " -0.135 2.00e-02 2.50e+03 pdb=" O2' Y5P V 29 " 1.034 2.00e-02 2.50e+03 pdb=" C1' Y5P V 29 " 0.253 2.00e-02 2.50e+03 pdb=" N1 Y5P V 29 " -0.991 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' Y5P V 63 " 0.073 2.00e-02 2.50e+03 6.35e-01 9.07e+03 pdb=" C4' Y5P V 63 " 0.449 2.00e-02 2.50e+03 pdb=" O4' Y5P V 63 " 0.680 2.00e-02 2.50e+03 pdb=" C3' Y5P V 63 " -0.600 2.00e-02 2.50e+03 pdb=" O3' Y5P V 63 " -0.720 2.00e-02 2.50e+03 pdb=" C2' Y5P V 63 " -0.153 2.00e-02 2.50e+03 pdb=" O2' Y5P V 63 " 1.009 2.00e-02 2.50e+03 pdb=" C1' Y5P V 63 " 0.249 2.00e-02 2.50e+03 pdb=" N1 Y5P V 63 " -0.987 2.00e-02 2.50e+03 ... (remaining 8811 not shown) Histogram of nonbonded interaction distances: 1.84 - 2.46: 453 2.46 - 3.07: 42485 3.07 - 3.68: 109505 3.68 - 4.29: 166112 4.29 - 4.90: 242980 Nonbonded interactions: 561535 Sorted by model distance: nonbonded pdb=" O2 U A 112 " pdb="MG MG A5005 " model vdw 1.844 2.170 nonbonded pdb=" OP2 G A 691 " pdb="MG MG A5045 " model vdw 1.911 2.170 nonbonded pdb=" OP2 A A 72 " pdb="MG MG A5021 " model vdw 1.915 2.170 nonbonded pdb=" NZ LYS a 88 " pdb=" O LEU a 260 " model vdw 1.939 2.520 nonbonded pdb=" NH1 ARG d 59 " pdb=" O TRP p 202 " model vdw 1.944 2.520 ... (remaining 561530 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'T' selection = (chain 's' and resid 2362 through 2375) } ncs_group { reference = chain 'V' selection = chain 'Y' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.590 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: 5.000 Check model and map are aligned: 0.760 Set scattering table: 0.460 Process input model: 169.660 Find NCS groups from input model: 1.640 Set up NCS constraints: 0.240 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: 0.010 Load rotamer database and sin/cos tables:3.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 181.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8492 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 : 0.018 0.170 69632 Z= 1.132 Angle : 1.284 25.338 98901 Z= 0.766 Chirality : 0.047 0.351 11258 Planarity : 0.073 0.651 8814 Dihedral : 21.862 174.682 32694 Min Nonbonded Distance : 1.844 Molprobity Statistics. All-atom Clashscore : 24.00 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.87 % Favored : 96.02 % Rotamer: Outliers : 10.71 % Allowed : 11.35 % Favored : 77.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.39 % Cis-general : 0.00 % Twisted Proline : 0.39 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.65 (0.09), residues: 4599 helix: -3.13 (0.08), residues: 1934 sheet: -1.24 (0.20), residues: 457 loop : -1.87 (0.11), residues: 2208 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP h 296 HIS 0.011 0.002 HIS m 32 PHE 0.035 0.003 PHE B 150 TYR 0.028 0.002 TYR G 64 ARG 0.006 0.001 ARG g 165 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9198 Ramachandran restraints generated. 4599 Oldfield, 0 Emsley, 4599 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9198 Ramachandran restraints generated. 4599 Oldfield, 0 Emsley, 4599 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1896 residues out of total 4072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 436 poor density : 1460 time to evaluate : 4.202 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 57 LEU cc_start: 0.7638 (OUTLIER) cc_final: 0.7345 (mm) REVERT: B 63 SER cc_start: 0.9406 (t) cc_final: 0.9133 (t) REVERT: B 115 ILE cc_start: 0.9246 (OUTLIER) cc_final: 0.8951 (mm) REVERT: B 141 ILE cc_start: 0.9037 (OUTLIER) cc_final: 0.8357 (mm) REVERT: B 159 ARG cc_start: 0.8693 (OUTLIER) cc_final: 0.8280 (ttp-170) REVERT: B 177 ASN cc_start: 0.9006 (t160) cc_final: 0.8802 (t0) REVERT: C 37 ASN cc_start: 0.8203 (OUTLIER) cc_final: 0.7846 (m-40) REVERT: C 38 ARG cc_start: 0.8459 (OUTLIER) cc_final: 0.8254 (mmt-90) REVERT: C 66 LYS cc_start: 0.9267 (tttt) cc_final: 0.8984 (mtpt) REVERT: C 89 ASP cc_start: 0.8670 (t0) cc_final: 0.8210 (t0) REVERT: C 112 ARG cc_start: 0.8985 (OUTLIER) cc_final: 0.8367 (mtm-85) REVERT: C 122 LEU cc_start: 0.8783 (OUTLIER) cc_final: 0.8568 (mm) REVERT: C 125 ARG cc_start: 0.7334 (OUTLIER) cc_final: 0.6539 (mtt180) REVERT: C 141 THR cc_start: 0.9285 (m) cc_final: 0.9049 (p) REVERT: C 157 THR cc_start: 0.8664 (m) cc_final: 0.8451 (p) REVERT: E 130 GLN cc_start: 0.8344 (mt0) cc_final: 0.8137 (mt0) REVERT: E 146 ILE cc_start: 0.7179 (OUTLIER) cc_final: 0.6830 (pt) REVERT: E 226 ARG cc_start: 0.8719 (OUTLIER) cc_final: 0.8127 (ttt90) REVERT: E 231 MET cc_start: 0.9092 (tpp) cc_final: 0.8780 (tpt) REVERT: E 282 ILE cc_start: 0.9340 (mm) cc_final: 0.9108 (mm) REVERT: E 339 SER cc_start: 0.8959 (t) cc_final: 0.8725 (p) REVERT: E 346 THR cc_start: 0.9184 (OUTLIER) cc_final: 0.8823 (m) REVERT: E 404 ILE cc_start: 0.8356 (OUTLIER) cc_final: 0.8127 (mt) REVERT: F 14 GLN cc_start: 0.8647 (mm-40) cc_final: 0.8420 (mm-40) REVERT: F 23 LYS cc_start: 0.8979 (tttt) cc_final: 0.8763 (tttt) REVERT: F 27 GLU cc_start: 0.8600 (mt-10) cc_final: 0.8325 (mt-10) REVERT: F 85 ASP cc_start: 0.9081 (t70) cc_final: 0.8830 (t70) REVERT: F 88 VAL cc_start: 0.9323 (t) cc_final: 0.8793 (m) REVERT: F 94 VAL cc_start: 0.9140 (t) cc_final: 0.8878 (m) REVERT: F 109 VAL cc_start: 0.8330 (t) cc_final: 0.8058 (p) REVERT: F 121 LYS cc_start: 0.8526 (mttt) cc_final: 0.7844 (mmmt) REVERT: G 37 TYR cc_start: 0.8809 (m-80) cc_final: 0.8477 (m-10) REVERT: G 45 GLN cc_start: 0.8220 (tt0) cc_final: 0.7870 (tt0) REVERT: G 50 TYR cc_start: 0.7976 (t80) cc_final: 0.6779 (t80) REVERT: G 57 GLU cc_start: 0.6834 (mm-30) cc_final: 0.6335 (tp30) REVERT: G 74 ILE cc_start: 0.9371 (mm) cc_final: 0.9115 (mm) REVERT: G 99 MET cc_start: 0.9055 (ttp) cc_final: 0.8732 (ptp) REVERT: G 103 ASN cc_start: 0.9172 (OUTLIER) cc_final: 0.8777 (m-40) REVERT: G 113 GLN cc_start: 0.8874 (mt0) cc_final: 0.8644 (mt0) REVERT: G 126 TYR cc_start: 0.8538 (t80) cc_final: 0.8280 (t80) REVERT: G 139 ARG cc_start: 0.7084 (OUTLIER) cc_final: 0.6586 (mmt90) REVERT: G 143 THR cc_start: 0.9245 (t) cc_final: 0.8824 (t) REVERT: G 147 GLN cc_start: 0.8152 (tp40) cc_final: 0.7800 (tp40) REVERT: G 185 LYS cc_start: 0.8942 (tptt) cc_final: 0.8677 (tttm) REVERT: G 201 MET cc_start: 0.8891 (tpt) cc_final: 0.8200 (tpt) REVERT: G 205 LEU cc_start: 0.9406 (OUTLIER) cc_final: 0.9143 (tt) REVERT: G 214 HIS cc_start: 0.8784 (m-70) cc_final: 0.8514 (m-70) REVERT: G 224 HIS cc_start: 0.9081 (OUTLIER) cc_final: 0.8833 (m90) REVERT: I 73 PHE cc_start: 0.7172 (m-80) cc_final: 0.6954 (t80) REVERT: I 75 LYS cc_start: 0.8941 (mttt) cc_final: 0.8473 (tppp) REVERT: I 76 LYS cc_start: 0.8876 (mttt) cc_final: 0.8419 (mtpp) REVERT: I 99 PHE cc_start: 0.6587 (OUTLIER) cc_final: 0.5657 (m-80) REVERT: I 129 GLU cc_start: 0.8235 (pt0) cc_final: 0.7966 (pt0) REVERT: I 170 LEU cc_start: 0.8215 (tp) cc_final: 0.7924 (tp) REVERT: I 209 MET cc_start: 0.7847 (OUTLIER) cc_final: 0.7568 (ttt) REVERT: I 215 SER cc_start: 0.8997 (OUTLIER) cc_final: 0.8797 (t) REVERT: I 217 GLN cc_start: 0.8300 (OUTLIER) cc_final: 0.7957 (mt0) REVERT: I 237 THR cc_start: 0.6271 (OUTLIER) cc_final: 0.6016 (t) REVERT: I 241 PHE cc_start: 0.8913 (t80) cc_final: 0.8572 (t80) REVERT: I 243 ASN cc_start: 0.8281 (m-40) cc_final: 0.8038 (m110) REVERT: I 300 ASP cc_start: 0.8560 (m-30) cc_final: 0.8318 (t0) REVERT: I 303 LEU cc_start: 0.8771 (OUTLIER) cc_final: 0.8565 (mt) REVERT: I 308 THR cc_start: 0.8558 (m) cc_final: 0.8055 (t) REVERT: I 329 MET cc_start: 0.7961 (ptp) cc_final: 0.7651 (ptp) REVERT: I 366 ARG cc_start: 0.7400 (ttm170) cc_final: 0.7152 (ttt-90) REVERT: J 62 GLU cc_start: 0.7344 (mt-10) cc_final: 0.6881 (tt0) REVERT: J 81 LYS cc_start: 0.9098 (mttt) cc_final: 0.8821 (mtmm) REVERT: J 85 LYS cc_start: 0.8989 (tttt) cc_final: 0.8789 (tptt) REVERT: J 101 GLU cc_start: 0.8376 (mm-30) cc_final: 0.8071 (mt-10) REVERT: J 122 LYS cc_start: 0.9181 (tttt) cc_final: 0.8894 (tttt) REVERT: J 135 GLU cc_start: 0.8545 (mt-10) cc_final: 0.8185 (mt-10) REVERT: J 136 MET cc_start: 0.8444 (OUTLIER) cc_final: 0.8136 (mtt) REVERT: K 98 GLN cc_start: 0.8596 (OUTLIER) cc_final: 0.8127 (pt0) REVERT: K 165 LYS cc_start: 0.8650 (tttt) cc_final: 0.8092 (ttmm) REVERT: K 180 ASN cc_start: 0.8516 (t0) cc_final: 0.8302 (t0) REVERT: L 32 THR cc_start: 0.9396 (OUTLIER) cc_final: 0.9134 (p) REVERT: L 46 PRO cc_start: 0.8452 (Cg_exo) cc_final: 0.8030 (Cg_endo) REVERT: L 63 LEU cc_start: 0.9030 (mt) cc_final: 0.7845 (mp) REVERT: L 71 LYS cc_start: 0.9077 (mtpt) cc_final: 0.8779 (ttmm) REVERT: L 77 ASN cc_start: 0.7721 (OUTLIER) cc_final: 0.7300 (p0) REVERT: L 127 ARG cc_start: 0.8018 (OUTLIER) cc_final: 0.7561 (tpp-160) REVERT: N 37 ASP cc_start: 0.8705 (OUTLIER) cc_final: 0.8080 (t70) REVERT: N 65 LYS cc_start: 0.8827 (mttt) cc_final: 0.8480 (tptp) REVERT: N 70 VAL cc_start: 0.8348 (t) cc_final: 0.7654 (p) REVERT: N 98 ARG cc_start: 0.8424 (mtt180) cc_final: 0.8131 (mtt90) REVERT: O 72 MET cc_start: 0.8976 (OUTLIER) cc_final: 0.8355 (tpp) REVERT: O 78 GLN cc_start: 0.8067 (tp40) cc_final: 0.7633 (mt0) REVERT: O 100 ASN cc_start: 0.8298 (t0) cc_final: 0.7954 (t0) REVERT: O 112 LEU cc_start: 0.8935 (tp) cc_final: 0.8729 (tp) REVERT: O 122 ASP cc_start: 0.7727 (m-30) cc_final: 0.7427 (p0) REVERT: O 127 GLU cc_start: 0.8895 (mt-10) cc_final: 0.8650 (mp0) REVERT: O 133 LEU cc_start: 0.9020 (mt) cc_final: 0.8631 (mp) REVERT: O 141 GLU cc_start: 0.8585 (mm-30) cc_final: 0.8379 (mm-30) REVERT: O 176 TYR cc_start: 0.9148 (t80) cc_final: 0.8922 (t80) REVERT: P 16 HIS cc_start: 0.9001 (OUTLIER) cc_final: 0.8743 (p-80) REVERT: P 44 ASP cc_start: 0.8408 (m-30) cc_final: 0.8162 (m-30) REVERT: P 90 LEU cc_start: 0.9334 (OUTLIER) cc_final: 0.8916 (mp) REVERT: Q 38 TYR cc_start: 0.9123 (t80) cc_final: 0.8852 (t80) REVERT: Q 59 THR cc_start: 0.7921 (OUTLIER) cc_final: 0.7412 (p) REVERT: Q 81 LEU cc_start: 0.9064 (OUTLIER) cc_final: 0.8667 (tt) REVERT: Q 104 THR cc_start: 0.8961 (m) cc_final: 0.8742 (p) REVERT: R 77 ASN cc_start: 0.8714 (OUTLIER) cc_final: 0.8003 (p0) REVERT: R 95 ARG cc_start: 0.8753 (mtt-85) cc_final: 0.8505 (mtt90) REVERT: R 120 PHE cc_start: 0.9427 (OUTLIER) cc_final: 0.8787 (m-80) REVERT: U 8 ILE cc_start: 0.9277 (mt) cc_final: 0.8983 (mm) REVERT: U 12 VAL cc_start: 0.9496 (t) cc_final: 0.9294 (m) REVERT: U 43 ARG cc_start: 0.8751 (ttt180) cc_final: 0.8438 (ttt90) REVERT: U 47 LYS cc_start: 0.9083 (OUTLIER) cc_final: 0.8693 (mmtp) REVERT: U 49 CYS cc_start: 0.9401 (OUTLIER) cc_final: 0.9020 (t) REVERT: U 60 CYS cc_start: 0.8670 (OUTLIER) cc_final: 0.8269 (m) REVERT: U 62 ARG cc_start: 0.8713 (ttm110) cc_final: 0.8236 (ttm-80) REVERT: U 66 MET cc_start: 0.8928 (tpp) cc_final: 0.8578 (mmt) REVERT: U 68 MET cc_start: 0.8999 (tpt) cc_final: 0.8756 (tpp) REVERT: U 70 ARG cc_start: 0.8783 (OUTLIER) cc_final: 0.8554 (ttp80) REVERT: U 80 ARG cc_start: 0.9035 (OUTLIER) cc_final: 0.7194 (ptp-170) REVERT: U 82 ASP cc_start: 0.9127 (OUTLIER) cc_final: 0.8807 (p0) REVERT: a 68 THR cc_start: 0.7619 (m) cc_final: 0.7169 (p) REVERT: a 80 LYS cc_start: 0.8604 (mmmt) cc_final: 0.8345 (tppt) REVERT: a 154 LYS cc_start: 0.8722 (mttt) cc_final: 0.8276 (mtpt) REVERT: a 162 TYR cc_start: 0.8151 (t80) cc_final: 0.7749 (t80) REVERT: a 204 LEU cc_start: 0.8262 (OUTLIER) cc_final: 0.7761 (tp) REVERT: a 228 ASN cc_start: 0.8938 (OUTLIER) cc_final: 0.8142 (m-40) REVERT: a 230 CYS cc_start: 0.8880 (m) cc_final: 0.8562 (t) REVERT: a 258 TYR cc_start: 0.7823 (m-80) cc_final: 0.7427 (m-10) REVERT: a 284 LEU cc_start: 0.8406 (mt) cc_final: 0.8021 (mt) REVERT: a 302 LEU cc_start: 0.9106 (mt) cc_final: 0.8880 (mt) REVERT: b 6 LEU cc_start: 0.9218 (OUTLIER) cc_final: 0.8946 (mt) REVERT: b 30 LEU cc_start: 0.8454 (OUTLIER) cc_final: 0.7891 (mt) REVERT: b 34 ILE cc_start: 0.9597 (mt) cc_final: 0.9378 (mt) REVERT: b 95 THR cc_start: 0.8705 (m) cc_final: 0.8455 (p) REVERT: b 99 PHE cc_start: 0.8778 (t80) cc_final: 0.8382 (t80) REVERT: b 100 VAL cc_start: 0.9160 (t) cc_final: 0.8913 (t) REVERT: b 103 TYR cc_start: 0.8282 (t80) cc_final: 0.8071 (t80) REVERT: b 104 ILE cc_start: 0.8199 (mt) cc_final: 0.7928 (mt) REVERT: b 111 GLU cc_start: 0.6194 (mt-10) cc_final: 0.5857 (tm-30) REVERT: b 126 LEU cc_start: 0.7807 (mt) cc_final: 0.7567 (mt) REVERT: b 134 ARG cc_start: 0.7578 (ttt180) cc_final: 0.7111 (tpp-160) REVERT: c 3 MET cc_start: 0.7973 (OUTLIER) cc_final: 0.7756 (mtp) REVERT: c 20 ASP cc_start: 0.7514 (t0) cc_final: 0.7308 (p0) REVERT: c 31 THR cc_start: 0.8942 (OUTLIER) cc_final: 0.8686 (m) REVERT: c 40 LEU cc_start: 0.8994 (mt) cc_final: 0.8626 (mt) REVERT: c 70 MET cc_start: 0.9150 (OUTLIER) cc_final: 0.8879 (mtp) REVERT: c 71 THR cc_start: 0.9443 (m) cc_final: 0.8991 (p) REVERT: c 73 SER cc_start: 0.9233 (m) cc_final: 0.8843 (p) REVERT: c 152 LEU cc_start: 0.8843 (OUTLIER) cc_final: 0.8614 (mt) REVERT: c 159 MET cc_start: 0.8425 (mmp) cc_final: 0.8065 (mmp) REVERT: d 57 THR cc_start: 0.8502 (m) cc_final: 0.8235 (p) REVERT: d 102 HIS cc_start: 0.8528 (t-90) cc_final: 0.7290 (t70) REVERT: d 141 LEU cc_start: 0.7464 (mt) cc_final: 0.7207 (tp) REVERT: d 155 GLN cc_start: 0.8273 (mt0) cc_final: 0.7967 (tp40) REVERT: d 192 THR cc_start: 0.9085 (m) cc_final: 0.8862 (p) REVERT: f 101 VAL cc_start: 0.8815 (OUTLIER) cc_final: 0.8554 (m) REVERT: f 124 VAL cc_start: 0.8942 (OUTLIER) cc_final: 0.8682 (p) REVERT: f 130 VAL cc_start: 0.8473 (t) cc_final: 0.8060 (p) REVERT: g 99 MET cc_start: 0.7372 (mtp) cc_final: 0.6947 (mmm) REVERT: g 134 THR cc_start: 0.7878 (OUTLIER) cc_final: 0.7655 (m) REVERT: g 139 HIS cc_start: 0.8081 (OUTLIER) cc_final: 0.6689 (t70) REVERT: g 159 ILE cc_start: 0.8823 (mt) cc_final: 0.8552 (tp) REVERT: g 170 SER cc_start: 0.6256 (OUTLIER) cc_final: 0.6039 (p) REVERT: g 186 TRP cc_start: 0.8389 (t60) cc_final: 0.7493 (t60) REVERT: g 188 LYS cc_start: 0.8944 (mttt) cc_final: 0.8730 (tptm) REVERT: g 196 HIS cc_start: 0.8052 (OUTLIER) cc_final: 0.7572 (t-170) REVERT: g 214 SER cc_start: 0.8032 (p) cc_final: 0.7629 (m) REVERT: g 215 THR cc_start: 0.2723 (OUTLIER) cc_final: 0.1266 (m) REVERT: g 277 ASP cc_start: 0.7633 (m-30) cc_final: 0.7321 (p0) REVERT: g 297 LYS cc_start: 0.8755 (mttt) cc_final: 0.8447 (mmmt) REVERT: g 340 ILE cc_start: 0.8767 (mt) cc_final: 0.8512 (mt) REVERT: g 372 THR cc_start: 0.8189 (OUTLIER) cc_final: 0.7808 (p) REVERT: h 308 ASN cc_start: 0.8642 (OUTLIER) cc_final: 0.8319 (p0) REVERT: h 319 GLU cc_start: 0.8966 (mt-10) cc_final: 0.8466 (mt-10) REVERT: h 324 ILE cc_start: 0.9186 (mm) cc_final: 0.8974 (mm) REVERT: h 329 TYR cc_start: 0.7733 (m-80) cc_final: 0.7468 (m-80) REVERT: h 343 MET cc_start: 0.9185 (mmp) cc_final: 0.8597 (mmt) REVERT: h 344 GLU cc_start: 0.8511 (mt-10) cc_final: 0.8196 (mt-10) REVERT: i 6 GLU cc_start: 0.7967 (tt0) cc_final: 0.7420 (pm20) REVERT: i 9 VAL cc_start: 0.9155 (t) cc_final: 0.8921 (t) REVERT: i 10 ARG cc_start: 0.8189 (mmt180) cc_final: 0.7819 (mmt180) REVERT: i 55 HIS cc_start: 0.8832 (OUTLIER) cc_final: 0.7791 (m90) REVERT: i 81 GLU cc_start: 0.8652 (tt0) cc_final: 0.7956 (tt0) REVERT: i 86 LYS cc_start: 0.8236 (tttt) cc_final: 0.8029 (ttmt) REVERT: j 41 MET cc_start: 0.8914 (tpp) cc_final: 0.8659 (tpp) REVERT: j 42 MET cc_start: 0.7854 (tpp) cc_final: 0.7184 (tpp) REVERT: j 48 ASN cc_start: 0.6660 (t0) cc_final: 0.6460 (t0) REVERT: j 88 GLN cc_start: 0.8624 (mm-40) cc_final: 0.8284 (mm-40) REVERT: j 89 HIS cc_start: 0.8434 (m-70) cc_final: 0.8099 (m90) REVERT: j 104 TYR cc_start: 0.7121 (p90) cc_final: 0.6136 (p90) REVERT: j 115 TRP cc_start: 0.7583 (m-10) cc_final: 0.6957 (m-10) REVERT: j 144 LYS cc_start: 0.8395 (mttt) cc_final: 0.7573 (mmmt) REVERT: j 150 PHE cc_start: 0.6258 (OUTLIER) cc_final: 0.5082 (m-10) REVERT: j 164 VAL cc_start: 0.8415 (OUTLIER) cc_final: 0.8209 (p) REVERT: j 180 LYS cc_start: 0.8386 (mmtt) cc_final: 0.7636 (tmmt) REVERT: k 62 MET cc_start: 0.5652 (tpp) cc_final: 0.4826 (tpt) REVERT: k 74 VAL cc_start: 0.9287 (OUTLIER) cc_final: 0.9082 (p) REVERT: k 89 MET cc_start: 0.8398 (OUTLIER) cc_final: 0.7944 (ttt) REVERT: k 106 GLU cc_start: 0.7527 (mm-30) cc_final: 0.7282 (mm-30) REVERT: k 158 TYR cc_start: 0.7641 (m-80) cc_final: 0.7415 (m-80) REVERT: k 192 LEU cc_start: 0.9154 (OUTLIER) cc_final: 0.8918 (tt) REVERT: k 200 TYR cc_start: 0.8494 (t80) cc_final: 0.7663 (t80) REVERT: k 204 THR cc_start: 0.9063 (OUTLIER) cc_final: 0.8768 (p) REVERT: k 205 ASP cc_start: 0.8305 (m-30) cc_final: 0.7837 (m-30) REVERT: k 254 ILE cc_start: 0.8900 (mt) cc_final: 0.8546 (pt) REVERT: k 259 THR cc_start: 0.8298 (m) cc_final: 0.7910 (m) REVERT: k 306 ASP cc_start: 0.7122 (OUTLIER) cc_final: 0.6830 (m-30) REVERT: k 309 ASN cc_start: 0.8518 (OUTLIER) cc_final: 0.8004 (m-40) REVERT: m 22 LYS cc_start: 0.8955 (mttt) cc_final: 0.8503 (mttp) REVERT: m 25 LYS cc_start: 0.9135 (mttt) cc_final: 0.8793 (mtpp) REVERT: m 28 ILE cc_start: 0.8971 (OUTLIER) cc_final: 0.8589 (mt) REVERT: m 29 LEU cc_start: 0.9305 (OUTLIER) cc_final: 0.9041 (mt) REVERT: m 47 THR cc_start: 0.8860 (m) cc_final: 0.8579 (p) REVERT: m 49 MET cc_start: 0.8049 (tpp) cc_final: 0.7802 (tpt) REVERT: m 60 GLU cc_start: 0.8287 (pt0) cc_final: 0.7971 (tt0) REVERT: m 72 ASP cc_start: 0.8325 (m-30) cc_final: 0.7811 (t0) REVERT: m 87 ARG cc_start: 0.7632 (ptt180) cc_final: 0.7277 (tpm170) REVERT: n 132 LYS cc_start: 0.9334 (mtmt) cc_final: 0.9026 (mttp) REVERT: n 138 MET cc_start: 0.9023 (tpp) cc_final: 0.8806 (tpt) REVERT: n 149 ARG cc_start: 0.8636 (mtt180) cc_final: 0.8217 (mtp-110) REVERT: n 156 LYS cc_start: 0.8479 (mttt) cc_final: 0.8005 (tppp) REVERT: n 159 GLU cc_start: 0.8404 (mt-10) cc_final: 0.7952 (tt0) REVERT: n 170 GLU cc_start: 0.8658 (mm-30) cc_final: 0.8420 (mm-30) REVERT: n 173 LEU cc_start: 0.8971 (OUTLIER) cc_final: 0.8553 (mp) REVERT: n 177 TRP cc_start: 0.7437 (m-10) cc_final: 0.6959 (m-90) REVERT: o 80 ARG cc_start: 0.7613 (ttt180) cc_final: 0.7295 (ttt180) REVERT: o 108 LEU cc_start: 0.9083 (tp) cc_final: 0.8851 (tp) REVERT: o 111 LYS cc_start: 0.8902 (mttt) cc_final: 0.8696 (tppt) REVERT: o 129 GLN cc_start: 0.8636 (tp40) cc_final: 0.8246 (tp-100) REVERT: p 110 ASP cc_start: 0.8411 (t0) cc_final: 0.7957 (t0) REVERT: p 111 GLN cc_start: 0.8375 (tp40) cc_final: 0.8020 (tp40) REVERT: p 119 ASN cc_start: 0.8497 (OUTLIER) cc_final: 0.8017 (p0) REVERT: p 124 GLU cc_start: 0.9011 (tp30) cc_final: 0.8381 (pt0) REVERT: p 155 GLN cc_start: 0.8911 (mm-40) cc_final: 0.8376 (mm-40) REVERT: p 177 PHE cc_start: 0.8308 (OUTLIER) cc_final: 0.7323 (p90) REVERT: p 180 THR cc_start: 0.8164 (p) cc_final: 0.7957 (p) REVERT: p 186 SER cc_start: 0.8104 (m) cc_final: 0.7707 (p) REVERT: p 192 THR cc_start: 0.8599 (m) cc_final: 0.8390 (m) REVERT: p 199 TRP cc_start: 0.8657 (OUTLIER) cc_final: 0.7540 (t60) outliers start: 436 outliers final: 130 residues processed: 1754 average time/residue: 0.7901 time to fit residues: 2229.8390 Evaluate side-chains 1115 residues out of total 4072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 204 poor density : 911 time to evaluate : 4.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 57 LEU Chi-restraints excluded: chain B residue 79 SER Chi-restraints excluded: chain B residue 115 ILE Chi-restraints excluded: chain B residue 141 ILE Chi-restraints excluded: chain B residue 152 HIS Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 157 THR Chi-restraints excluded: chain B residue 159 ARG Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 192 ILE Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain B residue 230 LEU Chi-restraints excluded: chain B residue 249 CYS Chi-restraints excluded: chain C residue 37 ASN Chi-restraints excluded: chain C residue 38 ARG Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 71 LEU Chi-restraints excluded: chain C residue 104 LEU Chi-restraints excluded: chain C residue 112 ARG Chi-restraints excluded: chain C residue 115 ASN Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain C residue 125 ARG Chi-restraints excluded: chain E residue 146 ILE Chi-restraints excluded: chain E residue 215 TYR Chi-restraints excluded: chain E residue 225 VAL Chi-restraints excluded: chain E residue 226 ARG Chi-restraints excluded: chain E residue 239 ARG Chi-restraints excluded: chain E residue 258 ILE Chi-restraints excluded: chain E residue 293 ASP Chi-restraints excluded: chain E residue 305 MET Chi-restraints excluded: chain E residue 314 LEU Chi-restraints excluded: chain E residue 336 VAL Chi-restraints excluded: chain E residue 346 THR Chi-restraints excluded: chain E residue 367 SER Chi-restraints excluded: chain E residue 370 VAL Chi-restraints excluded: chain E residue 404 ILE Chi-restraints excluded: chain F residue 9 ILE Chi-restraints excluded: chain F residue 67 ASP Chi-restraints excluded: chain G residue 103 ASN Chi-restraints excluded: chain G residue 109 SER Chi-restraints excluded: chain G residue 114 THR Chi-restraints excluded: chain G residue 139 ARG Chi-restraints excluded: chain G residue 200 LEU Chi-restraints excluded: chain G residue 205 LEU Chi-restraints excluded: chain G residue 219 VAL Chi-restraints excluded: chain G residue 224 HIS Chi-restraints excluded: chain I residue 90 ASN Chi-restraints excluded: chain I residue 99 PHE Chi-restraints excluded: chain I residue 202 ILE Chi-restraints excluded: chain I residue 209 MET Chi-restraints excluded: chain I residue 215 SER Chi-restraints excluded: chain I residue 217 GLN Chi-restraints excluded: chain I residue 226 LEU Chi-restraints excluded: chain I residue 237 THR Chi-restraints excluded: chain I residue 303 LEU Chi-restraints excluded: chain I residue 331 CYS Chi-restraints excluded: chain I residue 353 LEU Chi-restraints excluded: chain I residue 371 LEU Chi-restraints excluded: chain I residue 377 VAL Chi-restraints excluded: chain I residue 393 THR Chi-restraints excluded: chain J residue 136 MET Chi-restraints excluded: chain K residue 65 TYR Chi-restraints excluded: chain K residue 75 LEU Chi-restraints excluded: chain K residue 98 GLN Chi-restraints excluded: chain K residue 142 THR Chi-restraints excluded: chain K residue 152 VAL Chi-restraints excluded: chain K residue 178 THR Chi-restraints excluded: chain L residue 32 THR Chi-restraints excluded: chain L residue 55 ARG Chi-restraints excluded: chain L residue 59 LYS Chi-restraints excluded: chain L residue 75 SER Chi-restraints excluded: chain L residue 77 ASN Chi-restraints excluded: chain L residue 95 ILE Chi-restraints excluded: chain L residue 110 VAL Chi-restraints excluded: chain L residue 127 ARG Chi-restraints excluded: chain N residue 37 ASP Chi-restraints excluded: chain N residue 56 SER Chi-restraints excluded: chain N residue 57 LEU Chi-restraints excluded: chain N residue 85 VAL Chi-restraints excluded: chain N residue 95 SER Chi-restraints excluded: chain N residue 107 SER Chi-restraints excluded: chain N residue 109 ILE Chi-restraints excluded: chain O residue 71 SER Chi-restraints excluded: chain O residue 72 MET Chi-restraints excluded: chain O residue 74 LEU Chi-restraints excluded: chain O residue 130 ILE Chi-restraints excluded: chain O residue 144 MET Chi-restraints excluded: chain O residue 205 VAL Chi-restraints excluded: chain O residue 212 THR Chi-restraints excluded: chain O residue 214 VAL Chi-restraints excluded: chain P residue 16 HIS Chi-restraints excluded: chain P residue 90 LEU Chi-restraints excluded: chain P residue 97 TYR Chi-restraints excluded: chain P residue 110 LEU Chi-restraints excluded: chain Q residue 9 HIS Chi-restraints excluded: chain Q residue 18 ILE Chi-restraints excluded: chain Q residue 59 THR Chi-restraints excluded: chain Q residue 81 LEU Chi-restraints excluded: chain R residue 51 LEU Chi-restraints excluded: chain R residue 53 VAL Chi-restraints excluded: chain R residue 69 CYS Chi-restraints excluded: chain R residue 73 VAL Chi-restraints excluded: chain R residue 77 ASN Chi-restraints excluded: chain R residue 91 CYS Chi-restraints excluded: chain R residue 109 THR Chi-restraints excluded: chain R residue 117 ILE Chi-restraints excluded: chain R residue 120 PHE Chi-restraints excluded: chain U residue 14 VAL Chi-restraints excluded: chain U residue 47 LYS Chi-restraints excluded: chain U residue 49 CYS Chi-restraints excluded: chain U residue 60 CYS Chi-restraints excluded: chain U residue 70 ARG Chi-restraints excluded: chain U residue 80 ARG Chi-restraints excluded: chain U residue 82 ASP Chi-restraints excluded: chain U residue 87 CYS Chi-restraints excluded: chain a residue 160 ILE Chi-restraints excluded: chain a residue 172 VAL Chi-restraints excluded: chain a residue 204 LEU Chi-restraints excluded: chain a residue 228 ASN Chi-restraints excluded: chain a residue 238 SER Chi-restraints excluded: chain b residue 6 LEU Chi-restraints excluded: chain b residue 30 LEU Chi-restraints excluded: chain c residue 3 MET Chi-restraints excluded: chain c residue 25 ASP Chi-restraints excluded: chain c residue 27 VAL Chi-restraints excluded: chain c residue 31 THR Chi-restraints excluded: chain c residue 48 VAL Chi-restraints excluded: chain c residue 59 ASN Chi-restraints excluded: chain c residue 70 MET Chi-restraints excluded: chain c residue 95 ASN Chi-restraints excluded: chain c residue 106 LEU Chi-restraints excluded: chain c residue 152 LEU Chi-restraints excluded: chain d residue 186 SER Chi-restraints excluded: chain d residue 191 ILE Chi-restraints excluded: chain d residue 196 LEU Chi-restraints excluded: chain f residue 101 VAL Chi-restraints excluded: chain f residue 123 CYS Chi-restraints excluded: chain f residue 124 VAL Chi-restraints excluded: chain f residue 141 VAL Chi-restraints excluded: chain f residue 155 LEU Chi-restraints excluded: chain f residue 160 ASP Chi-restraints excluded: chain f residue 161 THR Chi-restraints excluded: chain f residue 162 THR Chi-restraints excluded: chain f residue 169 VAL Chi-restraints excluded: chain g residue 134 THR Chi-restraints excluded: chain g residue 139 HIS Chi-restraints excluded: chain g residue 150 LEU Chi-restraints excluded: chain g residue 170 SER Chi-restraints excluded: chain g residue 178 ASP Chi-restraints excluded: chain g residue 196 HIS Chi-restraints excluded: chain g residue 215 THR Chi-restraints excluded: chain g residue 265 ASN Chi-restraints excluded: chain g residue 296 VAL Chi-restraints excluded: chain g residue 337 ASP Chi-restraints excluded: chain g residue 372 THR Chi-restraints excluded: chain g residue 380 LEU Chi-restraints excluded: chain g residue 397 LEU Chi-restraints excluded: chain h residue 302 LEU Chi-restraints excluded: chain h residue 308 ASN Chi-restraints excluded: chain h residue 348 CYS Chi-restraints excluded: chain i residue 30 SER Chi-restraints excluded: chain i residue 55 HIS Chi-restraints excluded: chain j residue 50 LEU Chi-restraints excluded: chain j residue 80 VAL Chi-restraints excluded: chain j residue 150 PHE Chi-restraints excluded: chain j residue 164 VAL Chi-restraints excluded: chain j residue 178 ARG Chi-restraints excluded: chain k residue 72 TYR Chi-restraints excluded: chain k residue 74 VAL Chi-restraints excluded: chain k residue 79 LYS Chi-restraints excluded: chain k residue 89 MET Chi-restraints excluded: chain k residue 93 VAL Chi-restraints excluded: chain k residue 157 ASP Chi-restraints excluded: chain k residue 165 ILE Chi-restraints excluded: chain k residue 166 ARG Chi-restraints excluded: chain k residue 192 LEU Chi-restraints excluded: chain k residue 204 THR Chi-restraints excluded: chain k residue 298 VAL Chi-restraints excluded: chain k residue 306 ASP Chi-restraints excluded: chain k residue 309 ASN Chi-restraints excluded: chain m residue 13 LEU Chi-restraints excluded: chain m residue 17 ARG Chi-restraints excluded: chain m residue 28 ILE Chi-restraints excluded: chain m residue 29 LEU Chi-restraints excluded: chain m residue 33 VAL Chi-restraints excluded: chain n residue 147 VAL Chi-restraints excluded: chain n residue 173 LEU Chi-restraints excluded: chain n residue 194 ILE Chi-restraints excluded: chain o residue 68 VAL Chi-restraints excluded: chain o residue 77 THR Chi-restraints excluded: chain o residue 96 ILE Chi-restraints excluded: chain o residue 107 LEU Chi-restraints excluded: chain o residue 134 GLU Chi-restraints excluded: chain p residue 80 ASN Chi-restraints excluded: chain p residue 90 THR Chi-restraints excluded: chain p residue 96 ARG Chi-restraints excluded: chain p residue 103 ASN Chi-restraints excluded: chain p residue 108 CYS Chi-restraints excluded: chain p residue 113 LEU Chi-restraints excluded: chain p residue 119 ASN Chi-restraints excluded: chain p residue 167 ILE Chi-restraints excluded: chain p residue 177 PHE Chi-restraints excluded: chain p residue 199 TRP Chi-restraints excluded: chain p residue 202 TRP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 596 random chunks: chunk 503 optimal weight: 7.9990 chunk 451 optimal weight: 5.9990 chunk 250 optimal weight: 0.7980 chunk 154 optimal weight: 0.9990 chunk 304 optimal weight: 5.9990 chunk 241 optimal weight: 5.9990 chunk 467 optimal weight: 6.9990 chunk 180 optimal weight: 5.9990 chunk 284 optimal weight: 1.9990 chunk 347 optimal weight: 3.9990 chunk 541 optimal weight: 5.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 133 HIS B 152 HIS C 72 HIS C 75 ASN C 115 ASN C 145 HIS C 156 GLN ** E 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 288 HIS E 292 HIS E 302 HIS E 317 HIS E 356 GLN E 369 HIS F 41 ASN ** F 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 122 GLN G 146 HIS G 166 HIS G 227 HIS G 233 ASN G 238 HIS I 127 HIS ** I 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 367 GLN J 83 HIS ** K 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 34 ASN L 37 HIS L 77 ASN L 100 HIS O 147 HIS O 153 HIS O 201 HIS O 213 GLN P 28 ASN P 50 GLN P 100 HIS Q 23 GLN R 79 GLN U 3 ASN a 75 GLN a 107 GLN ** a 223 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 246 HIS a 247 HIS a 276 ASN a 307 HIS ** c 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 59 ASN c 63 GLN ** c 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 125 HIS c 146 GLN d 31 HIS d 102 HIS d 109 ASN d 126 GLN g 80 HIS g 115 ASN g 158 HIS g 196 HIS g 290 HIS g 386 ASN h 309 ASN h 323 HIS h 364 HIS ** i 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 263 ASN k 303 ASN ** m 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 129 ASN ** n 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 72 GLN o 129 GLN p 147 HIS Total number of N/Q/H flips: 66 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8411 moved from start: 0.2775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 69632 Z= 0.280 Angle : 1.505 19.019 98901 Z= 0.933 Chirality : 0.040 0.389 11258 Planarity : 0.015 0.136 8814 Dihedral : 23.970 179.488 23197 Min Nonbonded Distance : 1.773 Molprobity Statistics. All-atom Clashscore : 16.34 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.22 % Favored : 96.74 % Rotamer: Outliers : 7.22 % Allowed : 18.52 % Favored : 74.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.39 % Cis-general : 0.00 % Twisted Proline : 0.39 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.45 (0.11), residues: 4599 helix: -0.69 (0.10), residues: 1959 sheet: -0.67 (0.21), residues: 466 loop : -1.18 (0.12), residues: 2174 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP d 189 HIS 0.011 0.001 HIS C 154 PHE 0.018 0.002 PHE I 222 TYR 0.023 0.002 TYR k 226 ARG 0.006 0.001 ARG J 131 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9198 Ramachandran restraints generated. 4599 Oldfield, 0 Emsley, 4599 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9198 Ramachandran restraints generated. 4599 Oldfield, 0 Emsley, 4599 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1314 residues out of total 4072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 294 poor density : 1020 time to evaluate : 4.318 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 63 SER cc_start: 0.9262 (t) cc_final: 0.8951 (t) REVERT: B 70 ASP cc_start: 0.7893 (t0) cc_final: 0.7602 (t0) REVERT: B 115 ILE cc_start: 0.8912 (OUTLIER) cc_final: 0.8500 (mm) REVERT: B 159 ARG cc_start: 0.8416 (OUTLIER) cc_final: 0.8004 (ttp-170) REVERT: B 270 TYR cc_start: 0.6665 (t80) cc_final: 0.6045 (t80) REVERT: C 49 LYS cc_start: 0.8127 (ttpt) cc_final: 0.7316 (ptmm) REVERT: C 89 ASP cc_start: 0.8644 (t0) cc_final: 0.8341 (t0) REVERT: C 122 LEU cc_start: 0.8738 (OUTLIER) cc_final: 0.8477 (tp) REVERT: C 125 ARG cc_start: 0.7107 (OUTLIER) cc_final: 0.6412 (mtt180) REVERT: C 157 THR cc_start: 0.8659 (m) cc_final: 0.8413 (p) REVERT: E 97 GLU cc_start: 0.8608 (OUTLIER) cc_final: 0.8394 (mm-30) REVERT: E 130 GLN cc_start: 0.8274 (mt0) cc_final: 0.7975 (mt0) REVERT: E 173 VAL cc_start: 0.7699 (t) cc_final: 0.7444 (t) REVERT: E 184 LYS cc_start: 0.7713 (mmtt) cc_final: 0.7171 (pttp) REVERT: E 226 ARG cc_start: 0.8479 (OUTLIER) cc_final: 0.8115 (ttt90) REVERT: E 339 SER cc_start: 0.9107 (t) cc_final: 0.8767 (p) REVERT: E 346 THR cc_start: 0.9057 (OUTLIER) cc_final: 0.8700 (m) REVERT: E 409 GLU cc_start: 0.8413 (mm-30) cc_final: 0.8078 (mp0) REVERT: F 23 LYS cc_start: 0.8866 (tttt) cc_final: 0.8547 (tttt) REVERT: F 27 GLU cc_start: 0.8494 (mt-10) cc_final: 0.8221 (mt-10) REVERT: F 109 VAL cc_start: 0.8225 (t) cc_final: 0.7919 (p) REVERT: F 121 LYS cc_start: 0.8173 (mttt) cc_final: 0.7511 (mmmt) REVERT: G 65 GLU cc_start: 0.8316 (tp30) cc_final: 0.8063 (tp30) REVERT: G 99 MET cc_start: 0.8848 (ttp) cc_final: 0.8516 (ptp) REVERT: G 100 LYS cc_start: 0.8819 (mttt) cc_final: 0.8588 (mmtt) REVERT: G 103 ASN cc_start: 0.8991 (OUTLIER) cc_final: 0.8779 (m-40) REVERT: G 113 GLN cc_start: 0.8786 (mt0) cc_final: 0.8489 (mt0) REVERT: G 126 TYR cc_start: 0.8649 (t80) cc_final: 0.8305 (t80) REVERT: G 139 ARG cc_start: 0.7112 (OUTLIER) cc_final: 0.6611 (mmt90) REVERT: G 147 GLN cc_start: 0.7949 (tp40) cc_final: 0.7715 (tp-100) REVERT: G 185 LYS cc_start: 0.9089 (tptt) cc_final: 0.8815 (tttt) REVERT: G 201 MET cc_start: 0.8789 (tpt) cc_final: 0.8406 (tpt) REVERT: G 205 LEU cc_start: 0.9380 (OUTLIER) cc_final: 0.9022 (tt) REVERT: G 214 HIS cc_start: 0.8749 (m-70) cc_final: 0.8487 (m-70) REVERT: G 220 ILE cc_start: 0.9276 (OUTLIER) cc_final: 0.8970 (mm) REVERT: I 75 LYS cc_start: 0.8888 (mttt) cc_final: 0.8590 (tppp) REVERT: I 79 GLU cc_start: 0.8983 (OUTLIER) cc_final: 0.8710 (mp0) REVERT: I 99 PHE cc_start: 0.6352 (OUTLIER) cc_final: 0.5395 (m-80) REVERT: I 125 MET cc_start: 0.7564 (ttm) cc_final: 0.7229 (tmm) REVERT: I 209 MET cc_start: 0.8183 (OUTLIER) cc_final: 0.7928 (mtp) REVERT: I 217 GLN cc_start: 0.8049 (OUTLIER) cc_final: 0.7792 (mt0) REVERT: I 300 ASP cc_start: 0.8514 (m-30) cc_final: 0.8313 (t0) REVERT: I 308 THR cc_start: 0.8366 (OUTLIER) cc_final: 0.8148 (t) REVERT: I 393 THR cc_start: 0.9146 (m) cc_final: 0.8910 (p) REVERT: J 81 LYS cc_start: 0.9159 (mttt) cc_final: 0.8891 (mttm) REVERT: K 156 LEU cc_start: 0.9179 (OUTLIER) cc_final: 0.8896 (tp) REVERT: K 165 LYS cc_start: 0.8576 (tttt) cc_final: 0.8108 (ttmm) REVERT: L 33 LEU cc_start: 0.9714 (mt) cc_final: 0.9316 (mt) REVERT: L 46 PRO cc_start: 0.8472 (Cg_exo) cc_final: 0.8123 (Cg_endo) REVERT: L 138 LYS cc_start: 0.6299 (pttt) cc_final: 0.5833 (mptt) REVERT: N 37 ASP cc_start: 0.8472 (OUTLIER) cc_final: 0.8100 (t70) REVERT: N 65 LYS cc_start: 0.8773 (mttt) cc_final: 0.8527 (tmtt) REVERT: N 70 VAL cc_start: 0.8428 (t) cc_final: 0.7906 (m) REVERT: O 72 MET cc_start: 0.9045 (OUTLIER) cc_final: 0.8351 (tpp) REVERT: O 78 GLN cc_start: 0.8011 (tp40) cc_final: 0.7713 (mt0) REVERT: O 103 GLU cc_start: 0.8939 (mp0) cc_final: 0.8680 (mp0) REVERT: O 185 GLU cc_start: 0.8752 (mm-30) cc_final: 0.8466 (mt-10) REVERT: O 210 LEU cc_start: 0.9331 (OUTLIER) cc_final: 0.9076 (tp) REVERT: P 44 ASP cc_start: 0.8361 (m-30) cc_final: 0.7990 (m-30) REVERT: P 63 GLU cc_start: 0.6512 (mt-10) cc_final: 0.6223 (mt-10) REVERT: P 74 ARG cc_start: 0.8452 (ptt90) cc_final: 0.8148 (ptt90) REVERT: P 110 LEU cc_start: 0.7395 (OUTLIER) cc_final: 0.7015 (tp) REVERT: P 113 LYS cc_start: 0.9092 (pttp) cc_final: 0.8876 (pttp) REVERT: Q 59 THR cc_start: 0.7990 (OUTLIER) cc_final: 0.7491 (p) REVERT: Q 67 LYS cc_start: 0.8822 (ttpt) cc_final: 0.8503 (ttpt) REVERT: Q 80 GLU cc_start: 0.8742 (pp20) cc_final: 0.8400 (pp20) REVERT: R 77 ASN cc_start: 0.8549 (OUTLIER) cc_final: 0.8216 (p0) REVERT: R 85 ILE cc_start: 0.9072 (tt) cc_final: 0.8779 (pt) REVERT: R 95 ARG cc_start: 0.8657 (mtt-85) cc_final: 0.8450 (mtt90) REVERT: U 8 ILE cc_start: 0.9316 (mt) cc_final: 0.9105 (mt) REVERT: U 43 ARG cc_start: 0.8762 (ttt180) cc_final: 0.8499 (ttt90) REVERT: U 80 ARG cc_start: 0.8895 (OUTLIER) cc_final: 0.6929 (ptp-170) REVERT: a 230 CYS cc_start: 0.8880 (OUTLIER) cc_final: 0.8663 (t) REVERT: a 302 LEU cc_start: 0.9065 (mt) cc_final: 0.8849 (mt) REVERT: b 6 LEU cc_start: 0.8928 (OUTLIER) cc_final: 0.8443 (mt) REVERT: b 27 GLU cc_start: 0.8198 (tp30) cc_final: 0.7765 (tm-30) REVERT: b 86 ASP cc_start: 0.7931 (t0) cc_final: 0.7689 (t0) REVERT: b 99 PHE cc_start: 0.8712 (t80) cc_final: 0.8358 (t80) REVERT: b 100 VAL cc_start: 0.9102 (t) cc_final: 0.8805 (t) REVERT: b 103 TYR cc_start: 0.7946 (t80) cc_final: 0.7634 (t80) REVERT: b 126 LEU cc_start: 0.7879 (mt) cc_final: 0.7489 (mt) REVERT: b 134 ARG cc_start: 0.7683 (ttt180) cc_final: 0.7106 (tpp-160) REVERT: c 3 MET cc_start: 0.7882 (OUTLIER) cc_final: 0.7663 (mtp) REVERT: c 71 THR cc_start: 0.9321 (m) cc_final: 0.8815 (p) REVERT: c 114 GLU cc_start: 0.8122 (OUTLIER) cc_final: 0.7731 (tm-30) REVERT: c 140 MET cc_start: 0.7869 (OUTLIER) cc_final: 0.7542 (ttp) REVERT: c 141 CYS cc_start: 0.8535 (OUTLIER) cc_final: 0.8268 (m) REVERT: c 152 LEU cc_start: 0.8837 (OUTLIER) cc_final: 0.8600 (mt) REVERT: c 159 MET cc_start: 0.8158 (mmp) cc_final: 0.7881 (mmp) REVERT: d 106 MET cc_start: 0.8960 (mmt) cc_final: 0.8584 (mmt) REVERT: d 159 GLN cc_start: 0.8078 (mt0) cc_final: 0.7857 (mt0) REVERT: d 192 THR cc_start: 0.9029 (m) cc_final: 0.8812 (p) REVERT: g 99 MET cc_start: 0.7139 (mtp) cc_final: 0.6760 (mmm) REVERT: g 139 HIS cc_start: 0.7860 (OUTLIER) cc_final: 0.6692 (t-90) REVERT: g 154 ILE cc_start: 0.8906 (mp) cc_final: 0.8367 (tp) REVERT: g 188 LYS cc_start: 0.9039 (mttt) cc_final: 0.8802 (tptm) REVERT: g 196 HIS cc_start: 0.7524 (OUTLIER) cc_final: 0.7163 (t-170) REVERT: g 207 TYR cc_start: 0.6169 (m-80) cc_final: 0.5941 (m-10) REVERT: g 243 LEU cc_start: 0.8335 (OUTLIER) cc_final: 0.8101 (tp) REVERT: g 277 ASP cc_start: 0.7753 (m-30) cc_final: 0.7408 (p0) REVERT: g 389 GLN cc_start: 0.8113 (OUTLIER) cc_final: 0.7783 (tp40) REVERT: h 308 ASN cc_start: 0.8807 (OUTLIER) cc_final: 0.8520 (p0) REVERT: h 371 TYR cc_start: 0.8279 (t80) cc_final: 0.7978 (t80) REVERT: h 381 GLU cc_start: 0.8378 (OUTLIER) cc_final: 0.8091 (mt-10) REVERT: i 50 ASP cc_start: 0.7869 (OUTLIER) cc_final: 0.7095 (t0) REVERT: i 71 TYR cc_start: 0.8147 (t80) cc_final: 0.7845 (t80) REVERT: j 28 PRO cc_start: 0.8725 (Cg_exo) cc_final: 0.8364 (Cg_endo) REVERT: j 89 HIS cc_start: 0.8063 (m-70) cc_final: 0.7050 (m-70) REVERT: j 104 TYR cc_start: 0.6423 (p90) cc_final: 0.6130 (p90) REVERT: j 150 PHE cc_start: 0.6502 (OUTLIER) cc_final: 0.5558 (m-10) REVERT: k 74 VAL cc_start: 0.9227 (OUTLIER) cc_final: 0.8990 (p) REVERT: k 89 MET cc_start: 0.8278 (ttp) cc_final: 0.7905 (ttp) REVERT: k 140 ASP cc_start: 0.8378 (p0) cc_final: 0.8159 (p0) REVERT: k 158 TYR cc_start: 0.7879 (m-80) cc_final: 0.7606 (m-80) REVERT: k 192 LEU cc_start: 0.9179 (OUTLIER) cc_final: 0.8899 (tt) REVERT: k 199 ARG cc_start: 0.8387 (mtt-85) cc_final: 0.8057 (mtt-85) REVERT: k 205 ASP cc_start: 0.8164 (m-30) cc_final: 0.7839 (m-30) REVERT: k 306 ASP cc_start: 0.6863 (OUTLIER) cc_final: 0.6473 (m-30) REVERT: m 25 LYS cc_start: 0.9097 (mttt) cc_final: 0.8840 (mttm) REVERT: m 28 ILE cc_start: 0.8991 (OUTLIER) cc_final: 0.8589 (mt) REVERT: m 39 GLU cc_start: 0.7723 (OUTLIER) cc_final: 0.7032 (pp20) REVERT: m 52 MET cc_start: 0.8680 (ttp) cc_final: 0.8465 (ttp) REVERT: m 56 TRP cc_start: 0.8458 (m-10) cc_final: 0.7865 (m-10) REVERT: m 57 LYS cc_start: 0.8791 (mmtt) cc_final: 0.8544 (mmmt) REVERT: m 71 GLN cc_start: 0.7482 (tp40) cc_final: 0.7138 (tp-100) REVERT: m 72 ASP cc_start: 0.8305 (m-30) cc_final: 0.7777 (t0) REVERT: m 87 ARG cc_start: 0.7653 (ptt180) cc_final: 0.7440 (tpm170) REVERT: n 138 MET cc_start: 0.9114 (tpp) cc_final: 0.8852 (tpt) REVERT: n 149 ARG cc_start: 0.8718 (mtt180) cc_final: 0.8204 (ttp-110) REVERT: n 156 LYS cc_start: 0.8588 (mttt) cc_final: 0.8092 (mtpt) REVERT: n 164 GLN cc_start: 0.8278 (mt0) cc_final: 0.7835 (mt0) REVERT: n 173 LEU cc_start: 0.8683 (OUTLIER) cc_final: 0.8465 (mp) REVERT: n 175 ARG cc_start: 0.8713 (ttp80) cc_final: 0.8357 (tmm-80) REVERT: o 111 LYS cc_start: 0.8782 (mttt) cc_final: 0.8535 (tppt) REVERT: o 119 PHE cc_start: 0.8734 (t80) cc_final: 0.8520 (t80) REVERT: o 129 GLN cc_start: 0.8330 (tp-100) cc_final: 0.7994 (tp-100) REVERT: p 80 ASN cc_start: 0.8204 (OUTLIER) cc_final: 0.7864 (m-40) REVERT: p 111 GLN cc_start: 0.8014 (tp40) cc_final: 0.7678 (tp-100) REVERT: p 124 GLU cc_start: 0.8900 (tp30) cc_final: 0.8270 (pt0) REVERT: p 155 GLN cc_start: 0.8708 (mm-40) cc_final: 0.8417 (mm-40) REVERT: p 177 PHE cc_start: 0.8175 (OUTLIER) cc_final: 0.7247 (p90) REVERT: p 186 SER cc_start: 0.8293 (m) cc_final: 0.7991 (p) REVERT: p 192 THR cc_start: 0.8654 (m) cc_final: 0.8418 (m) REVERT: p 199 TRP cc_start: 0.8421 (OUTLIER) cc_final: 0.7703 (t60) REVERT: p 227 GLU cc_start: 0.8483 (mt-10) cc_final: 0.8201 (pm20) outliers start: 294 outliers final: 139 residues processed: 1224 average time/residue: 0.7078 time to fit residues: 1438.2227 Evaluate side-chains 1020 residues out of total 4072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 187 poor density : 833 time to evaluate : 4.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 67 LYS Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 79 SER Chi-restraints excluded: chain B residue 108 SER Chi-restraints excluded: chain B residue 115 ILE Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 159 ARG Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 192 ILE Chi-restraints excluded: chain B residue 197 THR Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 71 LEU Chi-restraints excluded: chain C residue 77 ASP Chi-restraints excluded: chain C residue 81 HIS Chi-restraints excluded: chain C residue 104 LEU Chi-restraints excluded: chain C residue 115 ASN Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain C residue 125 ARG Chi-restraints excluded: chain C residue 130 HIS Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 97 GLU Chi-restraints excluded: chain E residue 145 ASN Chi-restraints excluded: chain E residue 226 ARG Chi-restraints excluded: chain E residue 242 ARG Chi-restraints excluded: chain E residue 297 LYS Chi-restraints excluded: chain E residue 314 LEU Chi-restraints excluded: chain E residue 336 VAL Chi-restraints excluded: chain E residue 340 VAL Chi-restraints excluded: chain E residue 346 THR Chi-restraints excluded: chain E residue 370 VAL Chi-restraints excluded: chain F residue 67 ASP Chi-restraints excluded: chain F residue 79 MET Chi-restraints excluded: chain G residue 43 ASP Chi-restraints excluded: chain G residue 103 ASN Chi-restraints excluded: chain G residue 109 SER Chi-restraints excluded: chain G residue 139 ARG Chi-restraints excluded: chain G residue 200 LEU Chi-restraints excluded: chain G residue 205 LEU Chi-restraints excluded: chain G residue 219 VAL Chi-restraints excluded: chain G residue 220 ILE Chi-restraints excluded: chain I residue 70 THR Chi-restraints excluded: chain I residue 79 GLU Chi-restraints excluded: chain I residue 90 ASN Chi-restraints excluded: chain I residue 99 PHE Chi-restraints excluded: chain I residue 175 HIS Chi-restraints excluded: chain I residue 202 ILE Chi-restraints excluded: chain I residue 209 MET Chi-restraints excluded: chain I residue 216 ASP Chi-restraints excluded: chain I residue 217 GLN Chi-restraints excluded: chain I residue 226 LEU Chi-restraints excluded: chain I residue 308 THR Chi-restraints excluded: chain I residue 331 CYS Chi-restraints excluded: chain I residue 353 LEU Chi-restraints excluded: chain I residue 371 LEU Chi-restraints excluded: chain J residue 66 SER Chi-restraints excluded: chain J residue 71 THR Chi-restraints excluded: chain J residue 84 ASP Chi-restraints excluded: chain J residue 160 ILE Chi-restraints excluded: chain J residue 173 THR Chi-restraints excluded: chain K residue 65 TYR Chi-restraints excluded: chain K residue 81 LYS Chi-restraints excluded: chain K residue 98 GLN Chi-restraints excluded: chain K residue 142 THR Chi-restraints excluded: chain K residue 146 VAL Chi-restraints excluded: chain K residue 152 VAL Chi-restraints excluded: chain K residue 156 LEU Chi-restraints excluded: chain K residue 161 LEU Chi-restraints excluded: chain K residue 169 MET Chi-restraints excluded: chain K residue 176 SER Chi-restraints excluded: chain K residue 178 THR Chi-restraints excluded: chain L residue 75 SER Chi-restraints excluded: chain N residue 37 ASP Chi-restraints excluded: chain N residue 56 SER Chi-restraints excluded: chain N residue 57 LEU Chi-restraints excluded: chain N residue 95 SER Chi-restraints excluded: chain N residue 109 ILE Chi-restraints excluded: chain N residue 121 SER Chi-restraints excluded: chain O residue 71 SER Chi-restraints excluded: chain O residue 72 MET Chi-restraints excluded: chain O residue 76 ASP Chi-restraints excluded: chain O residue 130 ILE Chi-restraints excluded: chain O residue 171 LEU Chi-restraints excluded: chain O residue 205 VAL Chi-restraints excluded: chain O residue 210 LEU Chi-restraints excluded: chain O residue 212 THR Chi-restraints excluded: chain P residue 97 TYR Chi-restraints excluded: chain P residue 105 THR Chi-restraints excluded: chain P residue 110 LEU Chi-restraints excluded: chain Q residue 59 THR Chi-restraints excluded: chain R residue 51 LEU Chi-restraints excluded: chain R residue 69 CYS Chi-restraints excluded: chain R residue 77 ASN Chi-restraints excluded: chain R residue 112 ILE Chi-restraints excluded: chain R residue 117 ILE Chi-restraints excluded: chain R residue 131 LEU Chi-restraints excluded: chain U residue 14 VAL Chi-restraints excluded: chain U residue 80 ARG Chi-restraints excluded: chain a residue 160 ILE Chi-restraints excluded: chain a residue 172 VAL Chi-restraints excluded: chain a residue 230 CYS Chi-restraints excluded: chain a residue 250 GLU Chi-restraints excluded: chain a residue 254 LYS Chi-restraints excluded: chain b residue 6 LEU Chi-restraints excluded: chain b residue 8 THR Chi-restraints excluded: chain b residue 19 LEU Chi-restraints excluded: chain b residue 30 LEU Chi-restraints excluded: chain c residue 3 MET Chi-restraints excluded: chain c residue 25 ASP Chi-restraints excluded: chain c residue 26 SER Chi-restraints excluded: chain c residue 94 SER Chi-restraints excluded: chain c residue 95 ASN Chi-restraints excluded: chain c residue 106 LEU Chi-restraints excluded: chain c residue 114 GLU Chi-restraints excluded: chain c residue 140 MET Chi-restraints excluded: chain c residue 141 CYS Chi-restraints excluded: chain c residue 152 LEU Chi-restraints excluded: chain d residue 183 SER Chi-restraints excluded: chain d residue 186 SER Chi-restraints excluded: chain d residue 191 ILE Chi-restraints excluded: chain f residue 113 LEU Chi-restraints excluded: chain f residue 123 CYS Chi-restraints excluded: chain f residue 142 ARG Chi-restraints excluded: chain f residue 155 LEU Chi-restraints excluded: chain f residue 159 THR Chi-restraints excluded: chain f residue 160 ASP Chi-restraints excluded: chain f residue 161 THR Chi-restraints excluded: chain f residue 162 THR Chi-restraints excluded: chain g residue 123 TYR Chi-restraints excluded: chain g residue 139 HIS Chi-restraints excluded: chain g residue 150 LEU Chi-restraints excluded: chain g residue 178 ASP Chi-restraints excluded: chain g residue 196 HIS Chi-restraints excluded: chain g residue 243 LEU Chi-restraints excluded: chain g residue 246 LEU Chi-restraints excluded: chain g residue 265 ASN Chi-restraints excluded: chain g residue 296 VAL Chi-restraints excluded: chain g residue 337 ASP Chi-restraints excluded: chain g residue 356 ILE Chi-restraints excluded: chain g residue 380 LEU Chi-restraints excluded: chain g residue 389 GLN Chi-restraints excluded: chain h residue 302 LEU Chi-restraints excluded: chain h residue 308 ASN Chi-restraints excluded: chain h residue 348 CYS Chi-restraints excluded: chain h residue 378 ILE Chi-restraints excluded: chain h residue 381 GLU Chi-restraints excluded: chain h residue 387 ASN Chi-restraints excluded: chain i residue 30 SER Chi-restraints excluded: chain i residue 50 ASP Chi-restraints excluded: chain j residue 93 CYS Chi-restraints excluded: chain j residue 136 TYR Chi-restraints excluded: chain j residue 150 PHE Chi-restraints excluded: chain j residue 187 GLU Chi-restraints excluded: chain k residue 66 GLN Chi-restraints excluded: chain k residue 74 VAL Chi-restraints excluded: chain k residue 79 LYS Chi-restraints excluded: chain k residue 157 ASP Chi-restraints excluded: chain k residue 165 ILE Chi-restraints excluded: chain k residue 166 ARG Chi-restraints excluded: chain k residue 180 SER Chi-restraints excluded: chain k residue 185 ASP Chi-restraints excluded: chain k residue 192 LEU Chi-restraints excluded: chain k residue 306 ASP Chi-restraints excluded: chain m residue 13 LEU Chi-restraints excluded: chain m residue 28 ILE Chi-restraints excluded: chain m residue 33 VAL Chi-restraints excluded: chain m residue 39 GLU Chi-restraints excluded: chain m residue 46 ILE Chi-restraints excluded: chain m residue 63 ASP Chi-restraints excluded: chain n residue 147 VAL Chi-restraints excluded: chain n residue 173 LEU Chi-restraints excluded: chain o residue 57 VAL Chi-restraints excluded: chain o residue 58 VAL Chi-restraints excluded: chain o residue 64 THR Chi-restraints excluded: chain o residue 77 THR Chi-restraints excluded: chain o residue 96 ILE Chi-restraints excluded: chain o residue 107 LEU Chi-restraints excluded: chain o residue 134 GLU Chi-restraints excluded: chain p residue 80 ASN Chi-restraints excluded: chain p residue 103 ASN Chi-restraints excluded: chain p residue 108 CYS Chi-restraints excluded: chain p residue 113 LEU Chi-restraints excluded: chain p residue 167 ILE Chi-restraints excluded: chain p residue 177 PHE Chi-restraints excluded: chain p residue 197 ASP Chi-restraints excluded: chain p residue 199 TRP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 596 random chunks: chunk 300 optimal weight: 0.9980 chunk 167 optimal weight: 5.9990 chunk 450 optimal weight: 5.9990 chunk 368 optimal weight: 30.0000 chunk 149 optimal weight: 4.9990 chunk 542 optimal weight: 8.9990 chunk 585 optimal weight: 0.5980 chunk 482 optimal weight: 8.9990 chunk 537 optimal weight: 0.6980 chunk 184 optimal weight: 10.0000 chunk 434 optimal weight: 30.0000 overall best weight: 2.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 215 ASN C 81 HIS ** C 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 277 HIS E 308 GLN G 72 GLN G 238 HIS I 313 GLN K 98 GLN N 117 HIS Q 23 GLN Q 56 GLN R 83 GLN U 15 GLN U 18 ASN a 228 ASN b 89 ASN ** c 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** j 192 ASN ** k 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8389 moved from start: 0.3520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 69632 Z= 0.250 Angle : 1.398 16.998 98901 Z= 0.887 Chirality : 0.038 0.393 11258 Planarity : 0.015 0.126 8814 Dihedral : 23.355 179.990 23023 Min Nonbonded Distance : 1.825 Molprobity Statistics. All-atom Clashscore : 15.34 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.46 % Favored : 96.50 % Rotamer: Outliers : 6.26 % Allowed : 20.83 % Favored : 72.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.39 % Cis-general : 0.00 % Twisted Proline : 0.39 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.44 (0.12), residues: 4599 helix: 0.39 (0.11), residues: 1962 sheet: -0.37 (0.22), residues: 474 loop : -0.85 (0.13), residues: 2163 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP p 202 HIS 0.011 0.001 HIS C 154 PHE 0.031 0.001 PHE m 73 TYR 0.030 0.002 TYR d 63 ARG 0.010 0.001 ARG b 133 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9198 Ramachandran restraints generated. 4599 Oldfield, 0 Emsley, 4599 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9198 Ramachandran restraints generated. 4599 Oldfield, 0 Emsley, 4599 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1190 residues out of total 4072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 255 poor density : 935 time to evaluate : 4.277 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 58 ARG cc_start: 0.8126 (mmt90) cc_final: 0.7817 (mmt90) REVERT: B 70 ASP cc_start: 0.7471 (t0) cc_final: 0.7166 (t0) REVERT: B 159 ARG cc_start: 0.8453 (OUTLIER) cc_final: 0.8148 (ttp-170) REVERT: C 49 LYS cc_start: 0.8115 (ttpt) cc_final: 0.7596 (ptmm) REVERT: C 89 ASP cc_start: 0.8672 (t0) cc_final: 0.8376 (t0) REVERT: C 125 ARG cc_start: 0.6880 (OUTLIER) cc_final: 0.6205 (mtt180) REVERT: C 140 GLU cc_start: 0.9322 (tm-30) cc_final: 0.9015 (tm-30) REVERT: C 157 THR cc_start: 0.8520 (m) cc_final: 0.8276 (p) REVERT: E 184 LYS cc_start: 0.7720 (mmtt) cc_final: 0.7240 (pttp) REVERT: E 231 MET cc_start: 0.8666 (tpp) cc_final: 0.8312 (mmm) REVERT: E 264 ARG cc_start: 0.8057 (OUTLIER) cc_final: 0.7682 (ttp-110) REVERT: E 339 SER cc_start: 0.9148 (t) cc_final: 0.8836 (p) REVERT: F 76 GLU cc_start: 0.8728 (mp0) cc_final: 0.8457 (tp30) REVERT: F 109 VAL cc_start: 0.8182 (t) cc_final: 0.7860 (p) REVERT: F 121 LYS cc_start: 0.8195 (mttt) cc_final: 0.7831 (mtmt) REVERT: G 50 TYR cc_start: 0.7764 (t80) cc_final: 0.7444 (t80) REVERT: G 64 TYR cc_start: 0.8305 (p90) cc_final: 0.7396 (p90) REVERT: G 68 PHE cc_start: 0.7462 (p90) cc_final: 0.7260 (p90) REVERT: G 99 MET cc_start: 0.8819 (ttp) cc_final: 0.8346 (ptp) REVERT: G 100 LYS cc_start: 0.8826 (mttt) cc_final: 0.8597 (mmtt) REVERT: G 113 GLN cc_start: 0.8740 (mt0) cc_final: 0.8275 (mt0) REVERT: G 133 GLU cc_start: 0.7922 (mp0) cc_final: 0.7542 (mp0) REVERT: G 147 GLN cc_start: 0.8059 (tp40) cc_final: 0.7816 (tp-100) REVERT: G 201 MET cc_start: 0.8723 (tpt) cc_final: 0.8457 (tpt) REVERT: G 214 HIS cc_start: 0.8754 (m-70) cc_final: 0.8497 (m-70) REVERT: I 75 LYS cc_start: 0.8951 (mttt) cc_final: 0.8718 (tppp) REVERT: I 79 GLU cc_start: 0.8902 (OUTLIER) cc_final: 0.8628 (mp0) REVERT: I 125 MET cc_start: 0.7589 (ttm) cc_final: 0.7254 (tmm) REVERT: I 209 MET cc_start: 0.8175 (OUTLIER) cc_final: 0.7951 (ttp) REVERT: I 308 THR cc_start: 0.8247 (OUTLIER) cc_final: 0.7912 (t) REVERT: J 81 LYS cc_start: 0.8970 (mttt) cc_final: 0.8688 (mttm) REVERT: K 165 LYS cc_start: 0.8505 (tttt) cc_final: 0.8035 (ttmm) REVERT: L 46 PRO cc_start: 0.8422 (Cg_exo) cc_final: 0.8078 (Cg_endo) REVERT: L 71 LYS cc_start: 0.8953 (mtpt) cc_final: 0.8627 (ttmm) REVERT: L 138 LYS cc_start: 0.6303 (pttt) cc_final: 0.5745 (mptt) REVERT: N 37 ASP cc_start: 0.8343 (OUTLIER) cc_final: 0.7915 (t70) REVERT: N 43 MET cc_start: 0.8709 (mmm) cc_final: 0.8358 (ttt) REVERT: N 65 LYS cc_start: 0.8807 (mttt) cc_final: 0.8507 (tmtt) REVERT: N 70 VAL cc_start: 0.8315 (t) cc_final: 0.7928 (m) REVERT: O 72 MET cc_start: 0.9076 (OUTLIER) cc_final: 0.8385 (tpp) REVERT: O 78 GLN cc_start: 0.8096 (tp40) cc_final: 0.7684 (mt0) REVERT: O 162 ASP cc_start: 0.7283 (t0) cc_final: 0.6971 (t0) REVERT: P 44 ASP cc_start: 0.8379 (m-30) cc_final: 0.8077 (m-30) REVERT: P 74 ARG cc_start: 0.8495 (ptt90) cc_final: 0.8025 (ptt90) REVERT: P 110 LEU cc_start: 0.7330 (OUTLIER) cc_final: 0.6875 (tp) REVERT: P 113 LYS cc_start: 0.9111 (pttp) cc_final: 0.8900 (pttp) REVERT: Q 59 THR cc_start: 0.8032 (OUTLIER) cc_final: 0.7473 (p) REVERT: Q 67 LYS cc_start: 0.8786 (ttpt) cc_final: 0.8384 (ttpt) REVERT: Q 74 THR cc_start: 0.8506 (OUTLIER) cc_final: 0.8269 (m) REVERT: R 85 ILE cc_start: 0.9105 (tt) cc_final: 0.8860 (pt) REVERT: U 8 ILE cc_start: 0.9290 (OUTLIER) cc_final: 0.9050 (mt) REVERT: U 43 ARG cc_start: 0.8806 (ttt180) cc_final: 0.8523 (ttt90) REVERT: U 62 ARG cc_start: 0.8600 (OUTLIER) cc_final: 0.8118 (ttt90) REVERT: U 80 ARG cc_start: 0.8848 (OUTLIER) cc_final: 0.8572 (ptt-90) REVERT: a 258 TYR cc_start: 0.8242 (OUTLIER) cc_final: 0.7984 (m-10) REVERT: a 302 LEU cc_start: 0.9034 (mt) cc_final: 0.8813 (mt) REVERT: b 27 GLU cc_start: 0.8016 (tp30) cc_final: 0.7755 (tm-30) REVERT: b 46 PHE cc_start: 0.8635 (t80) cc_final: 0.8126 (t80) REVERT: b 99 PHE cc_start: 0.8728 (t80) cc_final: 0.8317 (t80) REVERT: b 103 TYR cc_start: 0.7914 (t80) cc_final: 0.7623 (t80) REVERT: b 134 ARG cc_start: 0.7662 (ttt180) cc_final: 0.6978 (tpp-160) REVERT: c 3 MET cc_start: 0.7638 (mtp) cc_final: 0.7189 (mtp) REVERT: c 71 THR cc_start: 0.9296 (m) cc_final: 0.8734 (p) REVERT: d 106 MET cc_start: 0.8850 (mmt) cc_final: 0.8574 (mmt) REVERT: d 192 THR cc_start: 0.9036 (m) cc_final: 0.8646 (p) REVERT: f 85 LEU cc_start: 0.9251 (OUTLIER) cc_final: 0.8750 (tt) REVERT: f 112 ASP cc_start: 0.8382 (m-30) cc_final: 0.8142 (m-30) REVERT: f 115 ILE cc_start: 0.8919 (mt) cc_final: 0.8659 (mt) REVERT: g 99 MET cc_start: 0.7177 (mtp) cc_final: 0.6892 (mmm) REVERT: g 154 ILE cc_start: 0.9072 (mp) cc_final: 0.8461 (tp) REVERT: g 188 LYS cc_start: 0.9057 (mttt) cc_final: 0.8802 (tptm) REVERT: g 230 MET cc_start: 0.8402 (ppp) cc_final: 0.8104 (tmm) REVERT: g 277 ASP cc_start: 0.7735 (m-30) cc_final: 0.7393 (p0) REVERT: g 295 MET cc_start: 0.8238 (mmm) cc_final: 0.7722 (mmm) REVERT: g 389 GLN cc_start: 0.8142 (OUTLIER) cc_final: 0.7874 (tp40) REVERT: h 308 ASN cc_start: 0.8901 (OUTLIER) cc_final: 0.8626 (p0) REVERT: h 371 TYR cc_start: 0.8353 (t80) cc_final: 0.7994 (t80) REVERT: h 380 LYS cc_start: 0.7493 (pttm) cc_final: 0.7229 (mmtt) REVERT: h 381 GLU cc_start: 0.8338 (OUTLIER) cc_final: 0.7905 (mt-10) REVERT: j 23 GLU cc_start: 0.8674 (tp30) cc_final: 0.8378 (pt0) REVERT: j 88 GLN cc_start: 0.8132 (tt0) cc_final: 0.7714 (tt0) REVERT: j 89 HIS cc_start: 0.7959 (m-70) cc_final: 0.7085 (m-70) REVERT: j 104 TYR cc_start: 0.6384 (p90) cc_final: 0.6128 (p90) REVERT: j 144 LYS cc_start: 0.8356 (mttt) cc_final: 0.7687 (mttp) REVERT: j 150 PHE cc_start: 0.6587 (OUTLIER) cc_final: 0.5571 (m-10) REVERT: k 158 TYR cc_start: 0.7741 (m-80) cc_final: 0.7462 (m-80) REVERT: k 199 ARG cc_start: 0.8329 (mtt-85) cc_final: 0.8029 (mtt-85) REVERT: k 200 TYR cc_start: 0.8535 (t80) cc_final: 0.8033 (t80) REVERT: k 231 LEU cc_start: 0.8987 (mt) cc_final: 0.8751 (mt) REVERT: k 277 ASN cc_start: 0.7160 (m-40) cc_final: 0.6283 (p0) REVERT: m 25 LYS cc_start: 0.9082 (mttt) cc_final: 0.8808 (mttm) REVERT: m 56 TRP cc_start: 0.8614 (m-10) cc_final: 0.8368 (m-10) REVERT: m 57 LYS cc_start: 0.8819 (mmtt) cc_final: 0.8597 (mmmt) REVERT: m 60 GLU cc_start: 0.8398 (tt0) cc_final: 0.8014 (pt0) REVERT: m 71 GLN cc_start: 0.7742 (tp40) cc_final: 0.7440 (tp40) REVERT: m 72 ASP cc_start: 0.8262 (m-30) cc_final: 0.7469 (t0) REVERT: m 75 ASP cc_start: 0.8285 (m-30) cc_final: 0.8028 (m-30) REVERT: m 87 ARG cc_start: 0.7705 (ptt180) cc_final: 0.7454 (tpm170) REVERT: n 156 LYS cc_start: 0.8641 (mttt) cc_final: 0.8200 (mtpt) REVERT: n 175 ARG cc_start: 0.8807 (ttp80) cc_final: 0.8515 (tmm-80) REVERT: o 111 LYS cc_start: 0.8842 (mttt) cc_final: 0.8556 (tppt) REVERT: o 119 PHE cc_start: 0.8801 (t80) cc_final: 0.8547 (t80) REVERT: o 122 ASN cc_start: 0.8913 (m-40) cc_final: 0.8365 (m110) REVERT: o 129 GLN cc_start: 0.8062 (tp-100) cc_final: 0.7816 (tp-100) REVERT: o 141 MET cc_start: 0.9075 (mmm) cc_final: 0.8813 (mmp) REVERT: p 80 ASN cc_start: 0.8180 (OUTLIER) cc_final: 0.7893 (m-40) REVERT: p 103 ASN cc_start: 0.8677 (OUTLIER) cc_final: 0.8382 (p0) REVERT: p 111 GLN cc_start: 0.8000 (tp40) cc_final: 0.7673 (tp-100) REVERT: p 124 GLU cc_start: 0.8895 (tp30) cc_final: 0.8307 (pt0) REVERT: p 177 PHE cc_start: 0.8262 (OUTLIER) cc_final: 0.7286 (p90) REVERT: p 186 SER cc_start: 0.8280 (m) cc_final: 0.7999 (p) REVERT: p 192 THR cc_start: 0.8612 (m) cc_final: 0.8359 (m) REVERT: p 199 TRP cc_start: 0.8333 (OUTLIER) cc_final: 0.7953 (t60) outliers start: 255 outliers final: 148 residues processed: 1114 average time/residue: 0.6738 time to fit residues: 1247.9684 Evaluate side-chains 991 residues out of total 4072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 172 poor density : 819 time to evaluate : 4.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 61 ILE Chi-restraints excluded: chain B residue 67 LYS Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 79 SER Chi-restraints excluded: chain B residue 108 SER Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 154 ILE Chi-restraints excluded: chain B residue 159 ARG Chi-restraints excluded: chain B residue 161 CYS Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 192 ILE Chi-restraints excluded: chain B residue 197 THR Chi-restraints excluded: chain B residue 203 GLU Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 73 THR Chi-restraints excluded: chain C residue 77 ASP Chi-restraints excluded: chain C residue 92 LEU Chi-restraints excluded: chain C residue 115 ASN Chi-restraints excluded: chain C residue 125 ARG Chi-restraints excluded: chain C residue 130 HIS Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 94 THR Chi-restraints excluded: chain E residue 145 ASN Chi-restraints excluded: chain E residue 146 ILE Chi-restraints excluded: chain E residue 239 ARG Chi-restraints excluded: chain E residue 242 ARG Chi-restraints excluded: chain E residue 245 VAL Chi-restraints excluded: chain E residue 264 ARG Chi-restraints excluded: chain E residue 297 LYS Chi-restraints excluded: chain E residue 336 VAL Chi-restraints excluded: chain E residue 340 VAL Chi-restraints excluded: chain E residue 370 VAL Chi-restraints excluded: chain E residue 401 VAL Chi-restraints excluded: chain F residue 13 MET Chi-restraints excluded: chain F residue 25 THR Chi-restraints excluded: chain F residue 67 ASP Chi-restraints excluded: chain F residue 86 ILE Chi-restraints excluded: chain G residue 83 SER Chi-restraints excluded: chain G residue 137 ILE Chi-restraints excluded: chain G residue 139 ARG Chi-restraints excluded: chain G residue 200 LEU Chi-restraints excluded: chain G residue 219 VAL Chi-restraints excluded: chain I residue 79 GLU Chi-restraints excluded: chain I residue 90 ASN Chi-restraints excluded: chain I residue 104 ILE Chi-restraints excluded: chain I residue 175 HIS Chi-restraints excluded: chain I residue 202 ILE Chi-restraints excluded: chain I residue 209 MET Chi-restraints excluded: chain I residue 216 ASP Chi-restraints excluded: chain I residue 226 LEU Chi-restraints excluded: chain I residue 237 THR Chi-restraints excluded: chain I residue 308 THR Chi-restraints excluded: chain I residue 377 VAL Chi-restraints excluded: chain J residue 66 SER Chi-restraints excluded: chain J residue 115 ILE Chi-restraints excluded: chain J residue 132 VAL Chi-restraints excluded: chain J residue 157 LEU Chi-restraints excluded: chain J residue 160 ILE Chi-restraints excluded: chain J residue 172 VAL Chi-restraints excluded: chain K residue 65 TYR Chi-restraints excluded: chain K residue 81 LYS Chi-restraints excluded: chain K residue 98 GLN Chi-restraints excluded: chain K residue 132 THR Chi-restraints excluded: chain K residue 142 THR Chi-restraints excluded: chain K residue 146 VAL Chi-restraints excluded: chain K residue 152 VAL Chi-restraints excluded: chain K residue 161 LEU Chi-restraints excluded: chain K residue 162 SER Chi-restraints excluded: chain K residue 169 MET Chi-restraints excluded: chain K residue 176 SER Chi-restraints excluded: chain K residue 178 THR Chi-restraints excluded: chain L residue 75 SER Chi-restraints excluded: chain N residue 37 ASP Chi-restraints excluded: chain N residue 56 SER Chi-restraints excluded: chain N residue 57 LEU Chi-restraints excluded: chain N residue 61 THR Chi-restraints excluded: chain N residue 121 SER Chi-restraints excluded: chain O residue 72 MET Chi-restraints excluded: chain O residue 76 ASP Chi-restraints excluded: chain O residue 171 LEU Chi-restraints excluded: chain O residue 205 VAL Chi-restraints excluded: chain P residue 97 TYR Chi-restraints excluded: chain P residue 110 LEU Chi-restraints excluded: chain Q residue 59 THR Chi-restraints excluded: chain Q residue 74 THR Chi-restraints excluded: chain Q residue 103 THR Chi-restraints excluded: chain R residue 53 VAL Chi-restraints excluded: chain R residue 69 CYS Chi-restraints excluded: chain R residue 108 ILE Chi-restraints excluded: chain R residue 117 ILE Chi-restraints excluded: chain R residue 131 LEU Chi-restraints excluded: chain R residue 136 VAL Chi-restraints excluded: chain U residue 8 ILE Chi-restraints excluded: chain U residue 14 VAL Chi-restraints excluded: chain U residue 56 SER Chi-restraints excluded: chain U residue 60 CYS Chi-restraints excluded: chain U residue 62 ARG Chi-restraints excluded: chain U residue 80 ARG Chi-restraints excluded: chain a residue 160 ILE Chi-restraints excluded: chain a residue 172 VAL Chi-restraints excluded: chain a residue 205 THR Chi-restraints excluded: chain a residue 250 GLU Chi-restraints excluded: chain a residue 254 LYS Chi-restraints excluded: chain a residue 258 TYR Chi-restraints excluded: chain b residue 94 SER Chi-restraints excluded: chain c residue 25 ASP Chi-restraints excluded: chain c residue 26 SER Chi-restraints excluded: chain c residue 106 LEU Chi-restraints excluded: chain d residue 141 LEU Chi-restraints excluded: chain d residue 183 SER Chi-restraints excluded: chain d residue 191 ILE Chi-restraints excluded: chain f residue 85 LEU Chi-restraints excluded: chain f residue 113 LEU Chi-restraints excluded: chain f residue 123 CYS Chi-restraints excluded: chain f residue 142 ARG Chi-restraints excluded: chain f residue 148 LEU Chi-restraints excluded: chain f residue 155 LEU Chi-restraints excluded: chain f residue 159 THR Chi-restraints excluded: chain f residue 160 ASP Chi-restraints excluded: chain f residue 162 THR Chi-restraints excluded: chain g residue 150 LEU Chi-restraints excluded: chain g residue 178 ASP Chi-restraints excluded: chain g residue 246 LEU Chi-restraints excluded: chain g residue 265 ASN Chi-restraints excluded: chain g residue 296 VAL Chi-restraints excluded: chain g residue 337 ASP Chi-restraints excluded: chain g residue 356 ILE Chi-restraints excluded: chain g residue 380 LEU Chi-restraints excluded: chain g residue 389 GLN Chi-restraints excluded: chain h residue 298 LYS Chi-restraints excluded: chain h residue 302 LEU Chi-restraints excluded: chain h residue 304 GLU Chi-restraints excluded: chain h residue 308 ASN Chi-restraints excluded: chain h residue 329 TYR Chi-restraints excluded: chain h residue 346 VAL Chi-restraints excluded: chain h residue 381 GLU Chi-restraints excluded: chain h residue 387 ASN Chi-restraints excluded: chain j residue 50 LEU Chi-restraints excluded: chain j residue 136 TYR Chi-restraints excluded: chain j residue 150 PHE Chi-restraints excluded: chain j residue 163 SER Chi-restraints excluded: chain j residue 187 GLU Chi-restraints excluded: chain k residue 66 GLN Chi-restraints excluded: chain k residue 71 VAL Chi-restraints excluded: chain k residue 74 VAL Chi-restraints excluded: chain k residue 79 LYS Chi-restraints excluded: chain k residue 165 ILE Chi-restraints excluded: chain k residue 166 ARG Chi-restraints excluded: chain k residue 180 SER Chi-restraints excluded: chain k residue 185 ASP Chi-restraints excluded: chain k residue 198 ASP Chi-restraints excluded: chain k residue 228 LEU Chi-restraints excluded: chain k residue 288 THR Chi-restraints excluded: chain m residue 33 VAL Chi-restraints excluded: chain m residue 46 ILE Chi-restraints excluded: chain m residue 63 ASP Chi-restraints excluded: chain m residue 117 VAL Chi-restraints excluded: chain n residue 194 ILE Chi-restraints excluded: chain o residue 64 THR Chi-restraints excluded: chain o residue 72 GLN Chi-restraints excluded: chain o residue 96 ILE Chi-restraints excluded: chain o residue 107 LEU Chi-restraints excluded: chain o residue 134 GLU Chi-restraints excluded: chain p residue 80 ASN Chi-restraints excluded: chain p residue 103 ASN Chi-restraints excluded: chain p residue 108 CYS Chi-restraints excluded: chain p residue 113 LEU Chi-restraints excluded: chain p residue 140 THR Chi-restraints excluded: chain p residue 177 PHE Chi-restraints excluded: chain p residue 197 ASP Chi-restraints excluded: chain p residue 199 TRP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 596 random chunks: chunk 535 optimal weight: 2.9990 chunk 407 optimal weight: 10.0000 chunk 281 optimal weight: 7.9990 chunk 60 optimal weight: 10.0000 chunk 258 optimal weight: 10.0000 chunk 364 optimal weight: 20.0000 chunk 544 optimal weight: 30.0000 chunk 576 optimal weight: 5.9990 chunk 284 optimal weight: 7.9990 chunk 515 optimal weight: 3.9990 chunk 155 optimal weight: 0.9980 overall best weight: 4.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 177 ASN B 215 ASN C 81 HIS ** C 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 130 GLN ** E 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 71 GLN ** K 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 105 HIS N 119 GLN P 75 HIS a 223 HIS a 245 HIS ** c 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 87 HIS ** g 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** g 196 HIS ** i 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 112 ASN m 15 ASN m 59 ASN ** m 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** p 169 GLN p 221 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8418 moved from start: 0.3952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 69632 Z= 0.320 Angle : 1.401 15.295 98901 Z= 0.887 Chirality : 0.040 0.410 11258 Planarity : 0.015 0.127 8814 Dihedral : 23.061 178.848 22947 Min Nonbonded Distance : 1.808 Molprobity Statistics. All-atom Clashscore : 16.21 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.85 % Favored : 96.11 % Rotamer: Outliers : 6.75 % Allowed : 21.44 % Favored : 71.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.20 (0.12), residues: 4599 helix: 0.63 (0.11), residues: 1959 sheet: -0.33 (0.22), residues: 487 loop : -0.72 (0.13), residues: 2153 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.056 0.002 TRP p 202 HIS 0.010 0.001 HIS I 176 PHE 0.024 0.002 PHE c 129 TYR 0.022 0.002 TYR G 126 ARG 0.011 0.001 ARG d 61 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9198 Ramachandran restraints generated. 4599 Oldfield, 0 Emsley, 4599 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9198 Ramachandran restraints generated. 4599 Oldfield, 0 Emsley, 4599 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1154 residues out of total 4072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 275 poor density : 879 time to evaluate : 4.145 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 58 ARG cc_start: 0.7994 (mmt90) cc_final: 0.7658 (mmt90) REVERT: B 70 ASP cc_start: 0.7585 (t0) cc_final: 0.7353 (t0) REVERT: B 115 ILE cc_start: 0.8891 (OUTLIER) cc_final: 0.8481 (mm) REVERT: B 159 ARG cc_start: 0.8569 (OUTLIER) cc_final: 0.8315 (ttp-170) REVERT: B 163 GLU cc_start: 0.7929 (mm-30) cc_final: 0.7568 (mm-30) REVERT: C 49 LYS cc_start: 0.8351 (ttpt) cc_final: 0.8141 (ptmm) REVERT: C 89 ASP cc_start: 0.8688 (t0) cc_final: 0.8331 (t0) REVERT: C 140 GLU cc_start: 0.9335 (tm-30) cc_final: 0.9061 (tm-30) REVERT: C 157 THR cc_start: 0.8483 (m) cc_final: 0.8065 (p) REVERT: E 184 LYS cc_start: 0.7849 (mmtt) cc_final: 0.7270 (pttp) REVERT: E 231 MET cc_start: 0.8674 (tpp) cc_final: 0.8034 (mmm) REVERT: E 264 ARG cc_start: 0.8078 (OUTLIER) cc_final: 0.7874 (ttp-110) REVERT: F 109 VAL cc_start: 0.8218 (t) cc_final: 0.7907 (p) REVERT: G 84 SER cc_start: 0.8354 (m) cc_final: 0.8150 (p) REVERT: G 113 GLN cc_start: 0.8719 (mt0) cc_final: 0.8406 (mt0) REVERT: G 133 GLU cc_start: 0.8042 (mp0) cc_final: 0.7608 (mp0) REVERT: G 139 ARG cc_start: 0.6880 (OUTLIER) cc_final: 0.6664 (mtm-85) REVERT: G 147 GLN cc_start: 0.8046 (tp40) cc_final: 0.7793 (tp40) REVERT: G 201 MET cc_start: 0.8758 (tpt) cc_final: 0.8416 (tpt) REVERT: G 205 LEU cc_start: 0.9406 (OUTLIER) cc_final: 0.9151 (tt) REVERT: G 214 HIS cc_start: 0.8780 (m-70) cc_final: 0.8556 (m-70) REVERT: G 220 ILE cc_start: 0.9326 (OUTLIER) cc_final: 0.9028 (mm) REVERT: I 75 LYS cc_start: 0.8956 (mttt) cc_final: 0.8744 (tppp) REVERT: I 79 GLU cc_start: 0.8898 (OUTLIER) cc_final: 0.8623 (mp0) REVERT: I 308 THR cc_start: 0.8317 (OUTLIER) cc_final: 0.8074 (t) REVERT: J 81 LYS cc_start: 0.8959 (mttt) cc_final: 0.8725 (mttm) REVERT: K 165 LYS cc_start: 0.8529 (tttt) cc_final: 0.7996 (ttmm) REVERT: L 46 PRO cc_start: 0.8471 (Cg_exo) cc_final: 0.8121 (Cg_endo) REVERT: L 71 LYS cc_start: 0.8893 (mtpt) cc_final: 0.8540 (ttmm) REVERT: L 77 ASN cc_start: 0.7523 (OUTLIER) cc_final: 0.7127 (p0) REVERT: L 138 LYS cc_start: 0.6226 (pttt) cc_final: 0.5926 (mmtt) REVERT: N 37 ASP cc_start: 0.8104 (OUTLIER) cc_final: 0.7456 (t70) REVERT: N 54 ILE cc_start: 0.8678 (OUTLIER) cc_final: 0.8409 (mp) REVERT: N 57 LEU cc_start: 0.8707 (OUTLIER) cc_final: 0.8237 (mt) REVERT: N 65 LYS cc_start: 0.8835 (mttt) cc_final: 0.8487 (tttm) REVERT: O 72 MET cc_start: 0.9059 (OUTLIER) cc_final: 0.8314 (tpp) REVERT: O 77 TYR cc_start: 0.8814 (m-10) cc_final: 0.8388 (m-10) REVERT: O 78 GLN cc_start: 0.8087 (OUTLIER) cc_final: 0.7793 (mt0) REVERT: O 88 ASP cc_start: 0.7947 (m-30) cc_final: 0.7637 (p0) REVERT: O 103 GLU cc_start: 0.8925 (mp0) cc_final: 0.8616 (mp0) REVERT: O 162 ASP cc_start: 0.7471 (t0) cc_final: 0.7070 (t0) REVERT: P 74 ARG cc_start: 0.8494 (ptt90) cc_final: 0.7899 (ptt90) REVERT: P 110 LEU cc_start: 0.7138 (OUTLIER) cc_final: 0.6713 (tp) REVERT: P 113 LYS cc_start: 0.9109 (pttp) cc_final: 0.8894 (pttp) REVERT: Q 59 THR cc_start: 0.8482 (OUTLIER) cc_final: 0.7923 (p) REVERT: Q 67 LYS cc_start: 0.8884 (ttpt) cc_final: 0.8601 (ttpt) REVERT: Q 73 ARG cc_start: 0.8373 (mtt-85) cc_final: 0.8121 (mtp180) REVERT: R 48 ASN cc_start: 0.7638 (t0) cc_final: 0.7399 (t0) REVERT: R 85 ILE cc_start: 0.9045 (tt) cc_final: 0.8741 (pt) REVERT: U 8 ILE cc_start: 0.9265 (OUTLIER) cc_final: 0.8999 (mt) REVERT: U 43 ARG cc_start: 0.8902 (ttt180) cc_final: 0.8624 (ttt90) REVERT: U 68 MET cc_start: 0.8860 (tpt) cc_final: 0.8539 (tpt) REVERT: U 80 ARG cc_start: 0.8940 (OUTLIER) cc_final: 0.8289 (ptt-90) REVERT: a 258 TYR cc_start: 0.8352 (m-10) cc_final: 0.8115 (m-10) REVERT: b 87 LEU cc_start: 0.7522 (OUTLIER) cc_final: 0.7283 (mp) REVERT: b 99 PHE cc_start: 0.8715 (t80) cc_final: 0.8249 (t80) REVERT: b 134 ARG cc_start: 0.7808 (ttt180) cc_final: 0.6999 (tpp-160) REVERT: c 3 MET cc_start: 0.7642 (mtp) cc_final: 0.7241 (mtp) REVERT: c 20 ASP cc_start: 0.7872 (p0) cc_final: 0.7670 (p0) REVERT: c 71 THR cc_start: 0.9346 (m) cc_final: 0.8767 (p) REVERT: d 106 MET cc_start: 0.8869 (mmt) cc_final: 0.8583 (mmt) REVERT: d 192 THR cc_start: 0.8877 (m) cc_final: 0.8517 (p) REVERT: f 85 LEU cc_start: 0.9259 (OUTLIER) cc_final: 0.8780 (tt) REVERT: f 112 ASP cc_start: 0.8467 (m-30) cc_final: 0.8264 (m-30) REVERT: g 99 MET cc_start: 0.7057 (mtp) cc_final: 0.6332 (mmp) REVERT: g 154 ILE cc_start: 0.9162 (mp) cc_final: 0.8453 (tp) REVERT: g 207 TYR cc_start: 0.6065 (m-10) cc_final: 0.5693 (m-10) REVERT: g 262 ASP cc_start: 0.7491 (t0) cc_final: 0.7078 (t70) REVERT: g 277 ASP cc_start: 0.7729 (m-30) cc_final: 0.7325 (p0) REVERT: g 389 GLN cc_start: 0.8158 (OUTLIER) cc_final: 0.7816 (tp40) REVERT: h 308 ASN cc_start: 0.8930 (OUTLIER) cc_final: 0.8628 (p0) REVERT: h 327 ASP cc_start: 0.8448 (p0) cc_final: 0.8103 (p0) REVERT: h 371 TYR cc_start: 0.8459 (t80) cc_final: 0.8053 (t80) REVERT: h 381 GLU cc_start: 0.8395 (OUTLIER) cc_final: 0.7971 (mt-10) REVERT: j 23 GLU cc_start: 0.8761 (tp30) cc_final: 0.8356 (pt0) REVERT: j 88 GLN cc_start: 0.8057 (tt0) cc_final: 0.7776 (tt0) REVERT: j 89 HIS cc_start: 0.7818 (m-70) cc_final: 0.6657 (m-70) REVERT: j 150 PHE cc_start: 0.6557 (OUTLIER) cc_final: 0.5517 (m-10) REVERT: j 166 TYR cc_start: 0.8656 (m-80) cc_final: 0.8381 (m-10) REVERT: k 199 ARG cc_start: 0.8413 (mtt-85) cc_final: 0.8132 (mtt-85) REVERT: k 254 ILE cc_start: 0.9037 (OUTLIER) cc_final: 0.8502 (pt) REVERT: m 25 LYS cc_start: 0.8994 (mttt) cc_final: 0.8757 (mttm) REVERT: m 53 MET cc_start: 0.8830 (mmp) cc_final: 0.8589 (mmp) REVERT: m 56 TRP cc_start: 0.8538 (m-10) cc_final: 0.8077 (m-10) REVERT: m 57 LYS cc_start: 0.8799 (mmtt) cc_final: 0.8565 (mmmt) REVERT: m 59 ASN cc_start: 0.8584 (OUTLIER) cc_final: 0.8056 (t0) REVERT: m 60 GLU cc_start: 0.8452 (tt0) cc_final: 0.8063 (pt0) REVERT: m 72 ASP cc_start: 0.8251 (m-30) cc_final: 0.7846 (t0) REVERT: m 87 ARG cc_start: 0.7765 (ptt180) cc_final: 0.7466 (tpm170) REVERT: n 156 LYS cc_start: 0.8680 (mttt) cc_final: 0.8238 (mtpt) REVERT: n 175 ARG cc_start: 0.8895 (ttp80) cc_final: 0.8609 (tmm-80) REVERT: o 111 LYS cc_start: 0.8815 (mttt) cc_final: 0.8530 (tppt) REVERT: o 122 ASN cc_start: 0.8949 (m-40) cc_final: 0.8401 (m110) REVERT: p 80 ASN cc_start: 0.8139 (OUTLIER) cc_final: 0.7840 (m-40) REVERT: p 103 ASN cc_start: 0.8795 (OUTLIER) cc_final: 0.8466 (p0) REVERT: p 119 ASN cc_start: 0.8300 (OUTLIER) cc_final: 0.7712 (p0) REVERT: p 124 GLU cc_start: 0.8851 (tp30) cc_final: 0.8529 (pt0) REVERT: p 177 PHE cc_start: 0.8372 (OUTLIER) cc_final: 0.7320 (p90) REVERT: p 186 SER cc_start: 0.8345 (m) cc_final: 0.8051 (p) REVERT: p 192 THR cc_start: 0.8645 (m) cc_final: 0.8423 (m) REVERT: p 199 TRP cc_start: 0.8524 (OUTLIER) cc_final: 0.8294 (t60) outliers start: 275 outliers final: 195 residues processed: 1067 average time/residue: 0.6570 time to fit residues: 1166.9395 Evaluate side-chains 1027 residues out of total 4072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 226 poor density : 801 time to evaluate : 4.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 67 LYS Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 108 SER Chi-restraints excluded: chain B residue 115 ILE Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 147 HIS Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 154 ILE Chi-restraints excluded: chain B residue 159 ARG Chi-restraints excluded: chain B residue 161 CYS Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 192 ILE Chi-restraints excluded: chain B residue 197 THR Chi-restraints excluded: chain B residue 270 TYR Chi-restraints excluded: chain C residue 73 THR Chi-restraints excluded: chain C residue 77 ASP Chi-restraints excluded: chain C residue 115 ASN Chi-restraints excluded: chain C residue 130 HIS Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 145 ASN Chi-restraints excluded: chain E residue 146 ILE Chi-restraints excluded: chain E residue 196 ASN Chi-restraints excluded: chain E residue 215 TYR Chi-restraints excluded: chain E residue 217 ASP Chi-restraints excluded: chain E residue 239 ARG Chi-restraints excluded: chain E residue 242 ARG Chi-restraints excluded: chain E residue 245 VAL Chi-restraints excluded: chain E residue 258 ILE Chi-restraints excluded: chain E residue 264 ARG Chi-restraints excluded: chain E residue 276 VAL Chi-restraints excluded: chain E residue 296 LEU Chi-restraints excluded: chain E residue 297 LYS Chi-restraints excluded: chain E residue 336 VAL Chi-restraints excluded: chain E residue 340 VAL Chi-restraints excluded: chain E residue 354 SER Chi-restraints excluded: chain E residue 370 VAL Chi-restraints excluded: chain E residue 401 VAL Chi-restraints excluded: chain E residue 409 GLU Chi-restraints excluded: chain F residue 13 MET Chi-restraints excluded: chain F residue 18 THR Chi-restraints excluded: chain F residue 25 THR Chi-restraints excluded: chain F residue 46 MET Chi-restraints excluded: chain F residue 67 ASP Chi-restraints excluded: chain F residue 88 VAL Chi-restraints excluded: chain G residue 83 SER Chi-restraints excluded: chain G residue 98 MET Chi-restraints excluded: chain G residue 109 SER Chi-restraints excluded: chain G residue 114 THR Chi-restraints excluded: chain G residue 137 ILE Chi-restraints excluded: chain G residue 139 ARG Chi-restraints excluded: chain G residue 155 VAL Chi-restraints excluded: chain G residue 176 ASP Chi-restraints excluded: chain G residue 200 LEU Chi-restraints excluded: chain G residue 205 LEU Chi-restraints excluded: chain G residue 219 VAL Chi-restraints excluded: chain G residue 220 ILE Chi-restraints excluded: chain I residue 70 THR Chi-restraints excluded: chain I residue 79 GLU Chi-restraints excluded: chain I residue 90 ASN Chi-restraints excluded: chain I residue 104 ILE Chi-restraints excluded: chain I residue 175 HIS Chi-restraints excluded: chain I residue 216 ASP Chi-restraints excluded: chain I residue 226 LEU Chi-restraints excluded: chain I residue 229 LEU Chi-restraints excluded: chain I residue 237 THR Chi-restraints excluded: chain I residue 308 THR Chi-restraints excluded: chain I residue 377 VAL Chi-restraints excluded: chain J residue 115 ILE Chi-restraints excluded: chain J residue 132 VAL Chi-restraints excluded: chain J residue 157 LEU Chi-restraints excluded: chain J residue 160 ILE Chi-restraints excluded: chain J residue 172 VAL Chi-restraints excluded: chain K residue 65 TYR Chi-restraints excluded: chain K residue 75 LEU Chi-restraints excluded: chain K residue 98 GLN Chi-restraints excluded: chain K residue 132 THR Chi-restraints excluded: chain K residue 142 THR Chi-restraints excluded: chain K residue 146 VAL Chi-restraints excluded: chain K residue 151 VAL Chi-restraints excluded: chain K residue 152 VAL Chi-restraints excluded: chain K residue 156 LEU Chi-restraints excluded: chain K residue 161 LEU Chi-restraints excluded: chain K residue 162 SER Chi-restraints excluded: chain K residue 169 MET Chi-restraints excluded: chain K residue 176 SER Chi-restraints excluded: chain K residue 178 THR Chi-restraints excluded: chain L residue 75 SER Chi-restraints excluded: chain L residue 77 ASN Chi-restraints excluded: chain L residue 105 HIS Chi-restraints excluded: chain N residue 37 ASP Chi-restraints excluded: chain N residue 54 ILE Chi-restraints excluded: chain N residue 56 SER Chi-restraints excluded: chain N residue 57 LEU Chi-restraints excluded: chain N residue 74 GLU Chi-restraints excluded: chain N residue 109 ILE Chi-restraints excluded: chain O residue 72 MET Chi-restraints excluded: chain O residue 78 GLN Chi-restraints excluded: chain O residue 171 LEU Chi-restraints excluded: chain O residue 205 VAL Chi-restraints excluded: chain O residue 214 VAL Chi-restraints excluded: chain P residue 44 ASP Chi-restraints excluded: chain P residue 53 SER Chi-restraints excluded: chain P residue 83 LEU Chi-restraints excluded: chain P residue 97 TYR Chi-restraints excluded: chain P residue 110 LEU Chi-restraints excluded: chain Q residue 14 VAL Chi-restraints excluded: chain Q residue 30 VAL Chi-restraints excluded: chain Q residue 59 THR Chi-restraints excluded: chain Q residue 103 THR Chi-restraints excluded: chain R residue 53 VAL Chi-restraints excluded: chain R residue 63 LEU Chi-restraints excluded: chain R residue 69 CYS Chi-restraints excluded: chain R residue 108 ILE Chi-restraints excluded: chain R residue 112 ILE Chi-restraints excluded: chain R residue 117 ILE Chi-restraints excluded: chain R residue 131 LEU Chi-restraints excluded: chain R residue 136 VAL Chi-restraints excluded: chain U residue 8 ILE Chi-restraints excluded: chain U residue 14 VAL Chi-restraints excluded: chain U residue 18 ASN Chi-restraints excluded: chain U residue 56 SER Chi-restraints excluded: chain U residue 60 CYS Chi-restraints excluded: chain U residue 62 ARG Chi-restraints excluded: chain U residue 80 ARG Chi-restraints excluded: chain a residue 160 ILE Chi-restraints excluded: chain a residue 172 VAL Chi-restraints excluded: chain a residue 205 THR Chi-restraints excluded: chain a residue 250 GLU Chi-restraints excluded: chain a residue 254 LYS Chi-restraints excluded: chain b residue 60 VAL Chi-restraints excluded: chain b residue 70 ILE Chi-restraints excluded: chain b residue 87 LEU Chi-restraints excluded: chain c residue 25 ASP Chi-restraints excluded: chain c residue 26 SER Chi-restraints excluded: chain c residue 27 VAL Chi-restraints excluded: chain c residue 59 ASN Chi-restraints excluded: chain c residue 106 LEU Chi-restraints excluded: chain c residue 114 GLU Chi-restraints excluded: chain d residue 75 MET Chi-restraints excluded: chain d residue 183 SER Chi-restraints excluded: chain d residue 191 ILE Chi-restraints excluded: chain f residue 85 LEU Chi-restraints excluded: chain f residue 113 LEU Chi-restraints excluded: chain f residue 123 CYS Chi-restraints excluded: chain f residue 148 LEU Chi-restraints excluded: chain f residue 155 LEU Chi-restraints excluded: chain f residue 159 THR Chi-restraints excluded: chain f residue 160 ASP Chi-restraints excluded: chain f residue 162 THR Chi-restraints excluded: chain f residue 169 VAL Chi-restraints excluded: chain g residue 150 LEU Chi-restraints excluded: chain g residue 178 ASP Chi-restraints excluded: chain g residue 208 VAL Chi-restraints excluded: chain g residue 224 VAL Chi-restraints excluded: chain g residue 241 ILE Chi-restraints excluded: chain g residue 246 LEU Chi-restraints excluded: chain g residue 265 ASN Chi-restraints excluded: chain g residue 290 HIS Chi-restraints excluded: chain g residue 296 VAL Chi-restraints excluded: chain g residue 337 ASP Chi-restraints excluded: chain g residue 356 ILE Chi-restraints excluded: chain g residue 380 LEU Chi-restraints excluded: chain g residue 389 GLN Chi-restraints excluded: chain h residue 302 LEU Chi-restraints excluded: chain h residue 308 ASN Chi-restraints excluded: chain h residue 329 TYR Chi-restraints excluded: chain h residue 346 VAL Chi-restraints excluded: chain h residue 381 GLU Chi-restraints excluded: chain h residue 387 ASN Chi-restraints excluded: chain i residue 48 THR Chi-restraints excluded: chain j residue 50 LEU Chi-restraints excluded: chain j residue 80 VAL Chi-restraints excluded: chain j residue 84 SER Chi-restraints excluded: chain j residue 97 LEU Chi-restraints excluded: chain j residue 136 TYR Chi-restraints excluded: chain j residue 150 PHE Chi-restraints excluded: chain j residue 163 SER Chi-restraints excluded: chain j residue 164 VAL Chi-restraints excluded: chain j residue 187 GLU Chi-restraints excluded: chain j residue 199 ASP Chi-restraints excluded: chain k residue 66 GLN Chi-restraints excluded: chain k residue 71 VAL Chi-restraints excluded: chain k residue 74 VAL Chi-restraints excluded: chain k residue 79 LYS Chi-restraints excluded: chain k residue 165 ILE Chi-restraints excluded: chain k residue 166 ARG Chi-restraints excluded: chain k residue 180 SER Chi-restraints excluded: chain k residue 185 ASP Chi-restraints excluded: chain k residue 193 ILE Chi-restraints excluded: chain k residue 198 ASP Chi-restraints excluded: chain k residue 212 ASP Chi-restraints excluded: chain k residue 216 LEU Chi-restraints excluded: chain k residue 226 TYR Chi-restraints excluded: chain k residue 228 LEU Chi-restraints excluded: chain k residue 254 ILE Chi-restraints excluded: chain k residue 288 THR Chi-restraints excluded: chain m residue 15 ASN Chi-restraints excluded: chain m residue 33 VAL Chi-restraints excluded: chain m residue 44 THR Chi-restraints excluded: chain m residue 46 ILE Chi-restraints excluded: chain m residue 59 ASN Chi-restraints excluded: chain m residue 63 ASP Chi-restraints excluded: chain m residue 99 LEU Chi-restraints excluded: chain m residue 117 VAL Chi-restraints excluded: chain n residue 147 VAL Chi-restraints excluded: chain n residue 194 ILE Chi-restraints excluded: chain o residue 57 VAL Chi-restraints excluded: chain o residue 64 THR Chi-restraints excluded: chain o residue 72 GLN Chi-restraints excluded: chain o residue 77 THR Chi-restraints excluded: chain o residue 96 ILE Chi-restraints excluded: chain o residue 107 LEU Chi-restraints excluded: chain o residue 134 GLU Chi-restraints excluded: chain p residue 73 VAL Chi-restraints excluded: chain p residue 80 ASN Chi-restraints excluded: chain p residue 103 ASN Chi-restraints excluded: chain p residue 108 CYS Chi-restraints excluded: chain p residue 113 LEU Chi-restraints excluded: chain p residue 119 ASN Chi-restraints excluded: chain p residue 120 VAL Chi-restraints excluded: chain p residue 140 THR Chi-restraints excluded: chain p residue 163 LEU Chi-restraints excluded: chain p residue 177 PHE Chi-restraints excluded: chain p residue 197 ASP Chi-restraints excluded: chain p residue 199 TRP Chi-restraints excluded: chain p residue 221 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 596 random chunks: chunk 479 optimal weight: 8.9990 chunk 327 optimal weight: 30.0000 chunk 8 optimal weight: 10.0000 chunk 428 optimal weight: 30.0000 chunk 237 optimal weight: 9.9990 chunk 491 optimal weight: 4.9990 chunk 398 optimal weight: 8.9990 chunk 0 optimal weight: 8.9990 chunk 294 optimal weight: 1.9990 chunk 517 optimal weight: 6.9990 chunk 145 optimal weight: 3.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 81 HIS ** E 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 174 GLN ** I 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 313 GLN ** J 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 105 HIS N 119 GLN U 15 GLN a 245 HIS ** c 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 172 ASN g 139 HIS g 142 HIS g 196 HIS ** i 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 112 ASN ** k 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** m 15 ASN ** m 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8432 moved from start: 0.4239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.065 69632 Z= 0.358 Angle : 1.404 15.195 98901 Z= 0.887 Chirality : 0.041 0.404 11258 Planarity : 0.015 0.127 8814 Dihedral : 22.952 178.552 22936 Min Nonbonded Distance : 1.765 Molprobity Statistics. All-atom Clashscore : 16.73 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.52 % Favored : 95.43 % Rotamer: Outliers : 7.66 % Allowed : 21.14 % Favored : 71.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.24 (0.12), residues: 4599 helix: 0.62 (0.11), residues: 1967 sheet: -0.45 (0.22), residues: 490 loop : -0.76 (0.13), residues: 2142 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP p 202 HIS 0.049 0.002 HIS L 105 PHE 0.020 0.002 PHE I 222 TYR 0.026 0.002 TYR i 7 ARG 0.011 0.001 ARG d 61 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9198 Ramachandran restraints generated. 4599 Oldfield, 0 Emsley, 4599 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9198 Ramachandran restraints generated. 4599 Oldfield, 0 Emsley, 4599 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1149 residues out of total 4072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 312 poor density : 837 time to evaluate : 4.139 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 58 ARG cc_start: 0.8034 (mmt90) cc_final: 0.7646 (mmt90) REVERT: B 64 GLU cc_start: 0.8676 (mm-30) cc_final: 0.8411 (mm-30) REVERT: B 70 ASP cc_start: 0.7764 (t0) cc_final: 0.7429 (t0) REVERT: B 115 ILE cc_start: 0.8934 (OUTLIER) cc_final: 0.8489 (mm) REVERT: B 159 ARG cc_start: 0.8605 (OUTLIER) cc_final: 0.8333 (ttp-170) REVERT: B 163 GLU cc_start: 0.7826 (mm-30) cc_final: 0.7544 (mm-30) REVERT: B 246 ARG cc_start: 0.9012 (OUTLIER) cc_final: 0.8195 (mtp85) REVERT: B 273 GLN cc_start: 0.6929 (pt0) cc_final: 0.6708 (pm20) REVERT: C 89 ASP cc_start: 0.8705 (t0) cc_final: 0.8387 (t0) REVERT: C 140 GLU cc_start: 0.9387 (tm-30) cc_final: 0.9083 (tm-30) REVERT: C 157 THR cc_start: 0.8481 (m) cc_final: 0.8079 (p) REVERT: E 184 LYS cc_start: 0.7935 (mmtt) cc_final: 0.7332 (pttp) REVERT: E 185 MET cc_start: 0.7296 (ttm) cc_final: 0.6888 (ttm) REVERT: E 417 MET cc_start: 0.7882 (mmm) cc_final: 0.7119 (tpp) REVERT: F 109 VAL cc_start: 0.8224 (t) cc_final: 0.7920 (p) REVERT: G 113 GLN cc_start: 0.8641 (mt0) cc_final: 0.8359 (mt0) REVERT: G 133 GLU cc_start: 0.8016 (mp0) cc_final: 0.7419 (mp0) REVERT: G 147 GLN cc_start: 0.7605 (tp40) cc_final: 0.7134 (tp40) REVERT: G 201 MET cc_start: 0.8676 (tpt) cc_final: 0.8232 (tpt) REVERT: G 205 LEU cc_start: 0.9504 (OUTLIER) cc_final: 0.9200 (tt) REVERT: G 214 HIS cc_start: 0.8790 (m-70) cc_final: 0.8584 (m-70) REVERT: G 220 ILE cc_start: 0.9292 (OUTLIER) cc_final: 0.8986 (mm) REVERT: I 72 ASP cc_start: 0.7999 (t0) cc_final: 0.7748 (t0) REVERT: I 79 GLU cc_start: 0.8908 (OUTLIER) cc_final: 0.8675 (mp0) REVERT: I 207 GLU cc_start: 0.8408 (tm-30) cc_final: 0.7897 (tm-30) REVERT: I 209 MET cc_start: 0.8244 (ttp) cc_final: 0.7800 (mtp) REVERT: I 308 THR cc_start: 0.8354 (OUTLIER) cc_final: 0.8095 (t) REVERT: J 81 LYS cc_start: 0.9021 (mttt) cc_final: 0.8710 (mttm) REVERT: J 85 LYS cc_start: 0.9068 (tttt) cc_final: 0.8644 (tptt) REVERT: K 165 LYS cc_start: 0.8533 (tttt) cc_final: 0.8027 (ttmm) REVERT: K 189 ARG cc_start: 0.8659 (OUTLIER) cc_final: 0.8376 (ttt180) REVERT: L 71 LYS cc_start: 0.8849 (mtpt) cc_final: 0.8485 (ttmm) REVERT: L 77 ASN cc_start: 0.7588 (OUTLIER) cc_final: 0.7221 (p0) REVERT: N 57 LEU cc_start: 0.8681 (OUTLIER) cc_final: 0.8243 (mt) REVERT: N 65 LYS cc_start: 0.8861 (mttt) cc_final: 0.8439 (tttm) REVERT: N 70 VAL cc_start: 0.8399 (m) cc_final: 0.8004 (p) REVERT: O 72 MET cc_start: 0.8907 (OUTLIER) cc_final: 0.8160 (tpp) REVERT: O 77 TYR cc_start: 0.8777 (m-10) cc_final: 0.8484 (m-10) REVERT: O 78 GLN cc_start: 0.8101 (OUTLIER) cc_final: 0.7721 (mt0) REVERT: O 88 ASP cc_start: 0.8029 (m-30) cc_final: 0.7702 (p0) REVERT: O 158 LEU cc_start: 0.9499 (tp) cc_final: 0.9276 (mt) REVERT: O 162 ASP cc_start: 0.7470 (t0) cc_final: 0.7124 (t0) REVERT: P 74 ARG cc_start: 0.8518 (ptt90) cc_final: 0.7955 (ptt90) REVERT: Q 59 THR cc_start: 0.8530 (OUTLIER) cc_final: 0.7972 (p) REVERT: Q 67 LYS cc_start: 0.8889 (ttpt) cc_final: 0.8580 (ttpt) REVERT: R 85 ILE cc_start: 0.9029 (tt) cc_final: 0.8727 (pt) REVERT: U 8 ILE cc_start: 0.9278 (OUTLIER) cc_final: 0.8980 (mt) REVERT: U 43 ARG cc_start: 0.8921 (ttt180) cc_final: 0.8639 (ttt90) REVERT: U 80 ARG cc_start: 0.8921 (OUTLIER) cc_final: 0.8358 (ptt-90) REVERT: a 152 THR cc_start: 0.8140 (p) cc_final: 0.7750 (p) REVERT: b 6 LEU cc_start: 0.8789 (OUTLIER) cc_final: 0.8382 (mt) REVERT: b 48 ARG cc_start: 0.8273 (OUTLIER) cc_final: 0.7463 (mmt180) REVERT: b 87 LEU cc_start: 0.7696 (OUTLIER) cc_final: 0.7419 (mp) REVERT: b 99 PHE cc_start: 0.8682 (t80) cc_final: 0.8125 (t80) REVERT: b 134 ARG cc_start: 0.7818 (ttt180) cc_final: 0.7005 (tpp-160) REVERT: c 3 MET cc_start: 0.7618 (mtp) cc_final: 0.7225 (mtp) REVERT: c 71 THR cc_start: 0.9357 (m) cc_final: 0.8762 (p) REVERT: d 52 GLU cc_start: 0.8828 (OUTLIER) cc_final: 0.8566 (tp30) REVERT: d 106 MET cc_start: 0.8910 (mmt) cc_final: 0.8582 (mmt) REVERT: d 192 THR cc_start: 0.8896 (m) cc_final: 0.8620 (p) REVERT: f 85 LEU cc_start: 0.9286 (OUTLIER) cc_final: 0.8790 (tt) REVERT: f 112 ASP cc_start: 0.8508 (m-30) cc_final: 0.8265 (m-30) REVERT: g 99 MET cc_start: 0.7046 (mtp) cc_final: 0.6785 (mmm) REVERT: g 186 TRP cc_start: 0.8331 (t60) cc_final: 0.7314 (t60) REVERT: g 207 TYR cc_start: 0.6156 (m-10) cc_final: 0.5706 (m-10) REVERT: g 262 ASP cc_start: 0.7480 (t0) cc_final: 0.7275 (t70) REVERT: g 277 ASP cc_start: 0.7678 (m-30) cc_final: 0.7300 (p0) REVERT: g 378 GLU cc_start: 0.8193 (OUTLIER) cc_final: 0.7806 (mm-30) REVERT: g 389 GLN cc_start: 0.8106 (OUTLIER) cc_final: 0.7737 (tp40) REVERT: h 308 ASN cc_start: 0.9022 (OUTLIER) cc_final: 0.8721 (p0) REVERT: h 329 TYR cc_start: 0.8133 (m-80) cc_final: 0.7718 (m-80) REVERT: h 371 TYR cc_start: 0.8543 (t80) cc_final: 0.8225 (t80) REVERT: j 16 ARG cc_start: 0.7783 (ptm160) cc_final: 0.7580 (ptm-80) REVERT: j 88 GLN cc_start: 0.8092 (tt0) cc_final: 0.7755 (tt0) REVERT: j 89 HIS cc_start: 0.7940 (m-70) cc_final: 0.7010 (m-70) REVERT: j 150 PHE cc_start: 0.6902 (OUTLIER) cc_final: 0.5787 (m-10) REVERT: j 187 GLU cc_start: 0.9053 (OUTLIER) cc_final: 0.8659 (pm20) REVERT: k 89 MET cc_start: 0.8894 (ttt) cc_final: 0.8671 (ttt) REVERT: k 199 ARG cc_start: 0.8437 (mtt-85) cc_final: 0.8142 (mtt-85) REVERT: m 25 LYS cc_start: 0.9065 (mttt) cc_final: 0.8843 (mttm) REVERT: m 39 GLU cc_start: 0.7820 (OUTLIER) cc_final: 0.7084 (pp20) REVERT: m 53 MET cc_start: 0.8812 (mmp) cc_final: 0.8415 (mmp) REVERT: m 56 TRP cc_start: 0.8606 (m-10) cc_final: 0.8263 (m-10) REVERT: m 57 LYS cc_start: 0.8729 (mmtt) cc_final: 0.8474 (mmmt) REVERT: m 59 ASN cc_start: 0.8423 (OUTLIER) cc_final: 0.8195 (t0) REVERT: m 60 GLU cc_start: 0.8373 (tt0) cc_final: 0.8087 (pt0) REVERT: m 62 ARG cc_start: 0.8841 (mtm110) cc_final: 0.8434 (mtm110) REVERT: m 72 ASP cc_start: 0.8305 (m-30) cc_final: 0.7715 (t0) REVERT: m 87 ARG cc_start: 0.7768 (ptt180) cc_final: 0.7455 (tpm170) REVERT: n 156 LYS cc_start: 0.8712 (mttt) cc_final: 0.8267 (mtpt) REVERT: n 175 ARG cc_start: 0.8888 (ttp80) cc_final: 0.8600 (tmm-80) REVERT: o 111 LYS cc_start: 0.8814 (mttt) cc_final: 0.8546 (tppt) REVERT: o 122 ASN cc_start: 0.8980 (m-40) cc_final: 0.8571 (m110) REVERT: p 80 ASN cc_start: 0.8055 (OUTLIER) cc_final: 0.7694 (m-40) REVERT: p 103 ASN cc_start: 0.8844 (OUTLIER) cc_final: 0.8506 (p0) REVERT: p 119 ASN cc_start: 0.8557 (OUTLIER) cc_final: 0.7971 (p0) REVERT: p 124 GLU cc_start: 0.8852 (tp30) cc_final: 0.8532 (pt0) REVERT: p 177 PHE cc_start: 0.8404 (OUTLIER) cc_final: 0.7294 (p90) REVERT: p 186 SER cc_start: 0.8481 (m) cc_final: 0.8206 (p) REVERT: p 220 TYR cc_start: 0.8861 (m-80) cc_final: 0.8484 (m-80) outliers start: 312 outliers final: 229 residues processed: 1050 average time/residue: 0.6568 time to fit residues: 1142.2534 Evaluate side-chains 1050 residues out of total 4072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 260 poor density : 790 time to evaluate : 4.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 61 ILE Chi-restraints excluded: chain B residue 79 SER Chi-restraints excluded: chain B residue 108 SER Chi-restraints excluded: chain B residue 115 ILE Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 147 HIS Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 154 ILE Chi-restraints excluded: chain B residue 159 ARG Chi-restraints excluded: chain B residue 161 CYS Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 192 ILE Chi-restraints excluded: chain B residue 197 THR Chi-restraints excluded: chain B residue 246 ARG Chi-restraints excluded: chain B residue 270 TYR Chi-restraints excluded: chain C residue 71 LEU Chi-restraints excluded: chain C residue 73 THR Chi-restraints excluded: chain C residue 77 ASP Chi-restraints excluded: chain C residue 92 LEU Chi-restraints excluded: chain C residue 115 ASN Chi-restraints excluded: chain C residue 130 HIS Chi-restraints excluded: chain C residue 139 SER Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 145 ASN Chi-restraints excluded: chain E residue 146 ILE Chi-restraints excluded: chain E residue 196 ASN Chi-restraints excluded: chain E residue 215 TYR Chi-restraints excluded: chain E residue 217 ASP Chi-restraints excluded: chain E residue 239 ARG Chi-restraints excluded: chain E residue 242 ARG Chi-restraints excluded: chain E residue 245 VAL Chi-restraints excluded: chain E residue 258 ILE Chi-restraints excluded: chain E residue 276 VAL Chi-restraints excluded: chain E residue 296 LEU Chi-restraints excluded: chain E residue 297 LYS Chi-restraints excluded: chain E residue 323 ILE Chi-restraints excluded: chain E residue 336 VAL Chi-restraints excluded: chain E residue 340 VAL Chi-restraints excluded: chain E residue 354 SER Chi-restraints excluded: chain E residue 367 SER Chi-restraints excluded: chain E residue 370 VAL Chi-restraints excluded: chain E residue 401 VAL Chi-restraints excluded: chain E residue 409 GLU Chi-restraints excluded: chain F residue 13 MET Chi-restraints excluded: chain F residue 18 THR Chi-restraints excluded: chain F residue 25 THR Chi-restraints excluded: chain F residue 46 MET Chi-restraints excluded: chain F residue 67 ASP Chi-restraints excluded: chain F residue 86 ILE Chi-restraints excluded: chain G residue 83 SER Chi-restraints excluded: chain G residue 98 MET Chi-restraints excluded: chain G residue 109 SER Chi-restraints excluded: chain G residue 114 THR Chi-restraints excluded: chain G residue 137 ILE Chi-restraints excluded: chain G residue 139 ARG Chi-restraints excluded: chain G residue 155 VAL Chi-restraints excluded: chain G residue 172 VAL Chi-restraints excluded: chain G residue 176 ASP Chi-restraints excluded: chain G residue 200 LEU Chi-restraints excluded: chain G residue 205 LEU Chi-restraints excluded: chain G residue 219 VAL Chi-restraints excluded: chain G residue 220 ILE Chi-restraints excluded: chain I residue 70 THR Chi-restraints excluded: chain I residue 79 GLU Chi-restraints excluded: chain I residue 90 ASN Chi-restraints excluded: chain I residue 104 ILE Chi-restraints excluded: chain I residue 175 HIS Chi-restraints excluded: chain I residue 202 ILE Chi-restraints excluded: chain I residue 216 ASP Chi-restraints excluded: chain I residue 226 LEU Chi-restraints excluded: chain I residue 229 LEU Chi-restraints excluded: chain I residue 237 THR Chi-restraints excluded: chain I residue 277 ARG Chi-restraints excluded: chain I residue 308 THR Chi-restraints excluded: chain I residue 313 GLN Chi-restraints excluded: chain I residue 322 ASP Chi-restraints excluded: chain I residue 331 CYS Chi-restraints excluded: chain I residue 377 VAL Chi-restraints excluded: chain I residue 393 THR Chi-restraints excluded: chain J residue 106 ILE Chi-restraints excluded: chain J residue 115 ILE Chi-restraints excluded: chain J residue 123 SER Chi-restraints excluded: chain J residue 132 VAL Chi-restraints excluded: chain J residue 143 LEU Chi-restraints excluded: chain J residue 157 LEU Chi-restraints excluded: chain J residue 160 ILE Chi-restraints excluded: chain J residue 166 GLU Chi-restraints excluded: chain J residue 170 MET Chi-restraints excluded: chain J residue 172 VAL Chi-restraints excluded: chain K residue 65 TYR Chi-restraints excluded: chain K residue 75 LEU Chi-restraints excluded: chain K residue 98 GLN Chi-restraints excluded: chain K residue 132 THR Chi-restraints excluded: chain K residue 142 THR Chi-restraints excluded: chain K residue 146 VAL Chi-restraints excluded: chain K residue 151 VAL Chi-restraints excluded: chain K residue 152 VAL Chi-restraints excluded: chain K residue 156 LEU Chi-restraints excluded: chain K residue 161 LEU Chi-restraints excluded: chain K residue 162 SER Chi-restraints excluded: chain K residue 169 MET Chi-restraints excluded: chain K residue 178 THR Chi-restraints excluded: chain K residue 189 ARG Chi-restraints excluded: chain L residue 32 THR Chi-restraints excluded: chain L residue 77 ASN Chi-restraints excluded: chain N residue 56 SER Chi-restraints excluded: chain N residue 57 LEU Chi-restraints excluded: chain N residue 74 GLU Chi-restraints excluded: chain N residue 81 ASP Chi-restraints excluded: chain N residue 107 SER Chi-restraints excluded: chain N residue 109 ILE Chi-restraints excluded: chain N residue 110 VAL Chi-restraints excluded: chain N residue 121 SER Chi-restraints excluded: chain O residue 72 MET Chi-restraints excluded: chain O residue 78 GLN Chi-restraints excluded: chain O residue 89 VAL Chi-restraints excluded: chain O residue 171 LEU Chi-restraints excluded: chain O residue 205 VAL Chi-restraints excluded: chain O residue 214 VAL Chi-restraints excluded: chain P residue 44 ASP Chi-restraints excluded: chain P residue 53 SER Chi-restraints excluded: chain P residue 83 LEU Chi-restraints excluded: chain P residue 84 SER Chi-restraints excluded: chain P residue 97 TYR Chi-restraints excluded: chain P residue 110 LEU Chi-restraints excluded: chain Q residue 14 VAL Chi-restraints excluded: chain Q residue 30 VAL Chi-restraints excluded: chain Q residue 59 THR Chi-restraints excluded: chain Q residue 103 THR Chi-restraints excluded: chain R residue 53 VAL Chi-restraints excluded: chain R residue 63 LEU Chi-restraints excluded: chain R residue 69 CYS Chi-restraints excluded: chain R residue 108 ILE Chi-restraints excluded: chain R residue 112 ILE Chi-restraints excluded: chain R residue 117 ILE Chi-restraints excluded: chain R residue 131 LEU Chi-restraints excluded: chain R residue 136 VAL Chi-restraints excluded: chain U residue 8 ILE Chi-restraints excluded: chain U residue 14 VAL Chi-restraints excluded: chain U residue 18 ASN Chi-restraints excluded: chain U residue 56 SER Chi-restraints excluded: chain U residue 60 CYS Chi-restraints excluded: chain U residue 62 ARG Chi-restraints excluded: chain U residue 80 ARG Chi-restraints excluded: chain a residue 66 LYS Chi-restraints excluded: chain a residue 68 THR Chi-restraints excluded: chain a residue 89 ILE Chi-restraints excluded: chain a residue 145 LYS Chi-restraints excluded: chain a residue 160 ILE Chi-restraints excluded: chain a residue 172 VAL Chi-restraints excluded: chain a residue 205 THR Chi-restraints excluded: chain a residue 238 SER Chi-restraints excluded: chain a residue 250 GLU Chi-restraints excluded: chain a residue 254 LYS Chi-restraints excluded: chain b residue 6 LEU Chi-restraints excluded: chain b residue 12 ILE Chi-restraints excluded: chain b residue 48 ARG Chi-restraints excluded: chain b residue 60 VAL Chi-restraints excluded: chain b residue 70 ILE Chi-restraints excluded: chain b residue 87 LEU Chi-restraints excluded: chain c residue 25 ASP Chi-restraints excluded: chain c residue 26 SER Chi-restraints excluded: chain c residue 27 VAL Chi-restraints excluded: chain c residue 59 ASN Chi-restraints excluded: chain c residue 106 LEU Chi-restraints excluded: chain c residue 114 GLU Chi-restraints excluded: chain c residue 118 GLN Chi-restraints excluded: chain c residue 160 THR Chi-restraints excluded: chain d residue 52 GLU Chi-restraints excluded: chain d residue 75 MET Chi-restraints excluded: chain d residue 191 ILE Chi-restraints excluded: chain f residue 85 LEU Chi-restraints excluded: chain f residue 113 LEU Chi-restraints excluded: chain f residue 123 CYS Chi-restraints excluded: chain f residue 142 ARG Chi-restraints excluded: chain f residue 148 LEU Chi-restraints excluded: chain f residue 155 LEU Chi-restraints excluded: chain f residue 159 THR Chi-restraints excluded: chain f residue 160 ASP Chi-restraints excluded: chain f residue 161 THR Chi-restraints excluded: chain f residue 162 THR Chi-restraints excluded: chain f residue 169 VAL Chi-restraints excluded: chain g residue 122 ARG Chi-restraints excluded: chain g residue 142 HIS Chi-restraints excluded: chain g residue 150 LEU Chi-restraints excluded: chain g residue 178 ASP Chi-restraints excluded: chain g residue 208 VAL Chi-restraints excluded: chain g residue 224 VAL Chi-restraints excluded: chain g residue 246 LEU Chi-restraints excluded: chain g residue 255 PHE Chi-restraints excluded: chain g residue 261 VAL Chi-restraints excluded: chain g residue 265 ASN Chi-restraints excluded: chain g residue 290 HIS Chi-restraints excluded: chain g residue 296 VAL Chi-restraints excluded: chain g residue 337 ASP Chi-restraints excluded: chain g residue 356 ILE Chi-restraints excluded: chain g residue 378 GLU Chi-restraints excluded: chain g residue 380 LEU Chi-restraints excluded: chain g residue 389 GLN Chi-restraints excluded: chain h residue 298 LYS Chi-restraints excluded: chain h residue 302 LEU Chi-restraints excluded: chain h residue 308 ASN Chi-restraints excluded: chain h residue 346 VAL Chi-restraints excluded: chain h residue 387 ASN Chi-restraints excluded: chain i residue 48 THR Chi-restraints excluded: chain j residue 41 MET Chi-restraints excluded: chain j residue 50 LEU Chi-restraints excluded: chain j residue 84 SER Chi-restraints excluded: chain j residue 97 LEU Chi-restraints excluded: chain j residue 136 TYR Chi-restraints excluded: chain j residue 150 PHE Chi-restraints excluded: chain j residue 164 VAL Chi-restraints excluded: chain j residue 187 GLU Chi-restraints excluded: chain j residue 199 ASP Chi-restraints excluded: chain k residue 66 GLN Chi-restraints excluded: chain k residue 74 VAL Chi-restraints excluded: chain k residue 79 LYS Chi-restraints excluded: chain k residue 117 THR Chi-restraints excluded: chain k residue 165 ILE Chi-restraints excluded: chain k residue 166 ARG Chi-restraints excluded: chain k residue 180 SER Chi-restraints excluded: chain k residue 185 ASP Chi-restraints excluded: chain k residue 193 ILE Chi-restraints excluded: chain k residue 198 ASP Chi-restraints excluded: chain k residue 212 ASP Chi-restraints excluded: chain k residue 228 LEU Chi-restraints excluded: chain k residue 230 VAL Chi-restraints excluded: chain k residue 288 THR Chi-restraints excluded: chain k residue 292 GLU Chi-restraints excluded: chain m residue 15 ASN Chi-restraints excluded: chain m residue 33 VAL Chi-restraints excluded: chain m residue 39 GLU Chi-restraints excluded: chain m residue 46 ILE Chi-restraints excluded: chain m residue 59 ASN Chi-restraints excluded: chain m residue 63 ASP Chi-restraints excluded: chain m residue 99 LEU Chi-restraints excluded: chain m residue 117 VAL Chi-restraints excluded: chain n residue 147 VAL Chi-restraints excluded: chain n residue 194 ILE Chi-restraints excluded: chain o residue 57 VAL Chi-restraints excluded: chain o residue 64 THR Chi-restraints excluded: chain o residue 77 THR Chi-restraints excluded: chain o residue 78 VAL Chi-restraints excluded: chain o residue 88 VAL Chi-restraints excluded: chain o residue 96 ILE Chi-restraints excluded: chain o residue 107 LEU Chi-restraints excluded: chain o residue 134 GLU Chi-restraints excluded: chain p residue 63 GLU Chi-restraints excluded: chain p residue 73 VAL Chi-restraints excluded: chain p residue 80 ASN Chi-restraints excluded: chain p residue 96 ARG Chi-restraints excluded: chain p residue 103 ASN Chi-restraints excluded: chain p residue 108 CYS Chi-restraints excluded: chain p residue 113 LEU Chi-restraints excluded: chain p residue 119 ASN Chi-restraints excluded: chain p residue 120 VAL Chi-restraints excluded: chain p residue 140 THR Chi-restraints excluded: chain p residue 163 LEU Chi-restraints excluded: chain p residue 177 PHE Chi-restraints excluded: chain p residue 197 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 596 random chunks: chunk 193 optimal weight: 7.9990 chunk 518 optimal weight: 9.9990 chunk 113 optimal weight: 1.9990 chunk 338 optimal weight: 30.0000 chunk 142 optimal weight: 0.9980 chunk 576 optimal weight: 7.9990 chunk 478 optimal weight: 10.0000 chunk 266 optimal weight: 9.9990 chunk 47 optimal weight: 9.9990 chunk 190 optimal weight: 6.9990 chunk 302 optimal weight: 0.9990 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 152 HIS ** E 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 72 GLN ** I 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 105 HIS N 119 GLN U 15 GLN a 245 HIS ** c 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 117 HIS g 139 HIS ** i 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 108 ASN k 112 ASN ** k 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 15 ASN m 59 ASN ** n 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 72 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8403 moved from start: 0.4485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 69632 Z= 0.277 Angle : 1.383 15.201 98901 Z= 0.880 Chirality : 0.038 0.396 11258 Planarity : 0.015 0.124 8814 Dihedral : 22.850 178.107 22931 Min Nonbonded Distance : 1.815 Molprobity Statistics. All-atom Clashscore : 15.71 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.35 % Favored : 95.61 % Rotamer: Outliers : 7.10 % Allowed : 22.22 % Favored : 70.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.39 % Cis-general : 0.00 % Twisted Proline : 0.39 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.09 (0.12), residues: 4599 helix: 0.82 (0.12), residues: 1951 sheet: -0.48 (0.23), residues: 502 loop : -0.71 (0.13), residues: 2146 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP j 55 HIS 0.022 0.001 HIS g 142 PHE 0.016 0.001 PHE I 222 TYR 0.022 0.002 TYR d 63 ARG 0.006 0.001 ARG B 264 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9198 Ramachandran restraints generated. 4599 Oldfield, 0 Emsley, 4599 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9198 Ramachandran restraints generated. 4599 Oldfield, 0 Emsley, 4599 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1131 residues out of total 4072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 289 poor density : 842 time to evaluate : 4.251 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 58 ARG cc_start: 0.8105 (mmt90) cc_final: 0.7691 (mmt90) REVERT: B 64 GLU cc_start: 0.8652 (mm-30) cc_final: 0.8270 (mm-30) REVERT: B 70 ASP cc_start: 0.7477 (t0) cc_final: 0.7111 (t0) REVERT: B 115 ILE cc_start: 0.8943 (OUTLIER) cc_final: 0.8537 (mm) REVERT: B 163 GLU cc_start: 0.7870 (mm-30) cc_final: 0.7554 (mm-30) REVERT: B 246 ARG cc_start: 0.8989 (OUTLIER) cc_final: 0.8156 (mtp85) REVERT: C 89 ASP cc_start: 0.8667 (t0) cc_final: 0.8382 (t0) REVERT: C 140 GLU cc_start: 0.9376 (tm-30) cc_final: 0.9080 (tm-30) REVERT: C 157 THR cc_start: 0.8509 (m) cc_final: 0.8009 (p) REVERT: E 149 MET cc_start: 0.7570 (mmm) cc_final: 0.7338 (mmm) REVERT: E 184 LYS cc_start: 0.7826 (mmtt) cc_final: 0.7297 (pttp) REVERT: E 231 MET cc_start: 0.8367 (mmm) cc_final: 0.8150 (tpt) REVERT: E 417 MET cc_start: 0.8017 (mmm) cc_final: 0.7341 (tpp) REVERT: F 109 VAL cc_start: 0.8193 (t) cc_final: 0.7892 (p) REVERT: G 113 GLN cc_start: 0.8615 (mt0) cc_final: 0.8318 (mt0) REVERT: G 133 GLU cc_start: 0.8016 (mp0) cc_final: 0.7405 (mp0) REVERT: G 147 GLN cc_start: 0.7521 (tp40) cc_final: 0.7038 (tp40) REVERT: G 162 LEU cc_start: 0.9101 (tp) cc_final: 0.8592 (tt) REVERT: G 163 LYS cc_start: 0.7771 (tptt) cc_final: 0.7548 (mmmt) REVERT: G 201 MET cc_start: 0.8653 (tpt) cc_final: 0.8216 (tpt) REVERT: G 205 LEU cc_start: 0.9525 (OUTLIER) cc_final: 0.9243 (tt) REVERT: G 220 ILE cc_start: 0.9285 (OUTLIER) cc_final: 0.9001 (mm) REVERT: I 79 GLU cc_start: 0.8918 (OUTLIER) cc_final: 0.8659 (mp0) REVERT: I 207 GLU cc_start: 0.8442 (tm-30) cc_final: 0.7915 (tm-30) REVERT: I 209 MET cc_start: 0.8240 (ttp) cc_final: 0.7880 (mtp) REVERT: J 100 LYS cc_start: 0.8864 (mmmt) cc_final: 0.8639 (mmtm) REVERT: J 189 TRP cc_start: 0.4033 (t-100) cc_final: 0.3644 (t-100) REVERT: K 73 ASN cc_start: 0.8087 (t0) cc_final: 0.7541 (p0) REVERT: K 76 ARG cc_start: 0.8966 (mmt-90) cc_final: 0.8238 (mpt180) REVERT: K 165 LYS cc_start: 0.8509 (tttt) cc_final: 0.8015 (ttmm) REVERT: K 189 ARG cc_start: 0.8597 (OUTLIER) cc_final: 0.8347 (ttt180) REVERT: L 71 LYS cc_start: 0.8799 (mtpt) cc_final: 0.8485 (ttmm) REVERT: N 54 ILE cc_start: 0.8774 (OUTLIER) cc_final: 0.8506 (mp) REVERT: N 57 LEU cc_start: 0.8649 (OUTLIER) cc_final: 0.8184 (mt) REVERT: N 65 LYS cc_start: 0.8841 (mttt) cc_final: 0.8447 (tttm) REVERT: O 72 MET cc_start: 0.8927 (OUTLIER) cc_final: 0.8227 (tpp) REVERT: O 78 GLN cc_start: 0.7943 (tp40) cc_final: 0.7664 (mt0) REVERT: O 88 ASP cc_start: 0.8085 (m-30) cc_final: 0.7603 (p0) REVERT: O 112 LEU cc_start: 0.8932 (tp) cc_final: 0.8678 (mt) REVERT: O 162 ASP cc_start: 0.7507 (t0) cc_final: 0.7108 (t0) REVERT: P 74 ARG cc_start: 0.8444 (ptt90) cc_final: 0.7917 (ptt90) REVERT: Q 59 THR cc_start: 0.8572 (OUTLIER) cc_final: 0.8018 (p) REVERT: Q 67 LYS cc_start: 0.8856 (ttpt) cc_final: 0.8376 (ttpt) REVERT: R 49 GLU cc_start: 0.8524 (mm-30) cc_final: 0.8206 (mp0) REVERT: R 85 ILE cc_start: 0.9032 (tt) cc_final: 0.8715 (pt) REVERT: U 8 ILE cc_start: 0.9257 (OUTLIER) cc_final: 0.8928 (mt) REVERT: U 43 ARG cc_start: 0.8884 (ttt180) cc_final: 0.8653 (ttt90) REVERT: U 62 ARG cc_start: 0.8621 (OUTLIER) cc_final: 0.8210 (ttt90) REVERT: U 68 MET cc_start: 0.8739 (tpt) cc_final: 0.8118 (tpt) REVERT: U 80 ARG cc_start: 0.8803 (OUTLIER) cc_final: 0.8407 (ptt-90) REVERT: a 152 THR cc_start: 0.8000 (p) cc_final: 0.7589 (p) REVERT: b 6 LEU cc_start: 0.8757 (OUTLIER) cc_final: 0.8356 (mt) REVERT: b 87 LEU cc_start: 0.7630 (OUTLIER) cc_final: 0.7357 (mp) REVERT: b 99 PHE cc_start: 0.8678 (t80) cc_final: 0.8179 (t80) REVERT: b 134 ARG cc_start: 0.7959 (ttt180) cc_final: 0.7163 (tpp-160) REVERT: c 3 MET cc_start: 0.7627 (mtp) cc_final: 0.7240 (mtp) REVERT: c 71 THR cc_start: 0.9311 (m) cc_final: 0.8883 (p) REVERT: d 106 MET cc_start: 0.8853 (mmt) cc_final: 0.8608 (mmt) REVERT: d 192 THR cc_start: 0.8855 (m) cc_final: 0.8530 (p) REVERT: f 85 LEU cc_start: 0.9265 (OUTLIER) cc_final: 0.8722 (tt) REVERT: g 207 TYR cc_start: 0.6160 (m-10) cc_final: 0.5510 (m-10) REVERT: g 277 ASP cc_start: 0.7684 (m-30) cc_final: 0.7280 (p0) REVERT: g 323 LEU cc_start: 0.7997 (mt) cc_final: 0.7509 (mp) REVERT: g 378 GLU cc_start: 0.8141 (OUTLIER) cc_final: 0.7773 (mm-30) REVERT: h 308 ASN cc_start: 0.9038 (OUTLIER) cc_final: 0.8788 (p0) REVERT: h 371 TYR cc_start: 0.8462 (t80) cc_final: 0.8202 (t80) REVERT: h 381 GLU cc_start: 0.8218 (OUTLIER) cc_final: 0.7901 (mt-10) REVERT: i 79 ARG cc_start: 0.8386 (OUTLIER) cc_final: 0.7607 (mtt-85) REVERT: j 136 TYR cc_start: 0.7520 (OUTLIER) cc_final: 0.4842 (t80) REVERT: j 144 LYS cc_start: 0.8338 (mttt) cc_final: 0.7839 (mttp) REVERT: j 150 PHE cc_start: 0.7286 (OUTLIER) cc_final: 0.6070 (m-10) REVERT: j 187 GLU cc_start: 0.9068 (OUTLIER) cc_final: 0.8675 (pm20) REVERT: j 198 ILE cc_start: 0.7068 (mm) cc_final: 0.6827 (mm) REVERT: k 89 MET cc_start: 0.8861 (ttt) cc_final: 0.8624 (ttt) REVERT: k 199 ARG cc_start: 0.8395 (mtt-85) cc_final: 0.8098 (mtt-85) REVERT: k 223 TYR cc_start: 0.8550 (t80) cc_final: 0.8269 (t80) REVERT: m 39 GLU cc_start: 0.7804 (OUTLIER) cc_final: 0.7075 (pp20) REVERT: m 53 MET cc_start: 0.8729 (mmp) cc_final: 0.8265 (mmp) REVERT: m 56 TRP cc_start: 0.8533 (m-10) cc_final: 0.8130 (m-10) REVERT: m 57 LYS cc_start: 0.8811 (mmtt) cc_final: 0.8524 (mmmt) REVERT: m 59 ASN cc_start: 0.8714 (OUTLIER) cc_final: 0.8358 (t0) REVERT: m 60 GLU cc_start: 0.8358 (tt0) cc_final: 0.8109 (pt0) REVERT: m 72 ASP cc_start: 0.8363 (m-30) cc_final: 0.7663 (t0) REVERT: m 87 ARG cc_start: 0.7744 (ptt180) cc_final: 0.7467 (tpm170) REVERT: n 145 LYS cc_start: 0.8911 (OUTLIER) cc_final: 0.8333 (mtmm) REVERT: n 156 LYS cc_start: 0.8686 (mttt) cc_final: 0.8244 (mtpt) REVERT: o 111 LYS cc_start: 0.8802 (mttt) cc_final: 0.8521 (tppt) REVERT: o 122 ASN cc_start: 0.8970 (m-40) cc_final: 0.8454 (m110) REVERT: o 129 GLN cc_start: 0.8017 (tp-100) cc_final: 0.7754 (tp-100) REVERT: p 80 ASN cc_start: 0.7983 (OUTLIER) cc_final: 0.7673 (m-40) REVERT: p 103 ASN cc_start: 0.8826 (OUTLIER) cc_final: 0.8540 (p0) REVERT: p 119 ASN cc_start: 0.8436 (OUTLIER) cc_final: 0.7839 (p0) REVERT: p 124 GLU cc_start: 0.8723 (tp30) cc_final: 0.8430 (pt0) REVERT: p 174 ASP cc_start: 0.8303 (m-30) cc_final: 0.7799 (m-30) REVERT: p 186 SER cc_start: 0.8489 (m) cc_final: 0.8204 (p) REVERT: p 235 MET cc_start: 0.5944 (OUTLIER) cc_final: 0.5737 (mmm) outliers start: 289 outliers final: 213 residues processed: 1040 average time/residue: 0.6733 time to fit residues: 1164.2439 Evaluate side-chains 1041 residues out of total 4072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 243 poor density : 798 time to evaluate : 4.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 61 ILE Chi-restraints excluded: chain B residue 79 SER Chi-restraints excluded: chain B residue 108 SER Chi-restraints excluded: chain B residue 115 ILE Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 147 HIS Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 161 CYS Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 203 GLU Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain B residue 246 ARG Chi-restraints excluded: chain B residue 270 TYR Chi-restraints excluded: chain C residue 71 LEU Chi-restraints excluded: chain C residue 73 THR Chi-restraints excluded: chain C residue 77 ASP Chi-restraints excluded: chain C residue 92 LEU Chi-restraints excluded: chain C residue 115 ASN Chi-restraints excluded: chain C residue 130 HIS Chi-restraints excluded: chain C residue 139 SER Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 132 ILE Chi-restraints excluded: chain E residue 145 ASN Chi-restraints excluded: chain E residue 146 ILE Chi-restraints excluded: chain E residue 196 ASN Chi-restraints excluded: chain E residue 217 ASP Chi-restraints excluded: chain E residue 227 ASN Chi-restraints excluded: chain E residue 239 ARG Chi-restraints excluded: chain E residue 242 ARG Chi-restraints excluded: chain E residue 245 VAL Chi-restraints excluded: chain E residue 258 ILE Chi-restraints excluded: chain E residue 276 VAL Chi-restraints excluded: chain E residue 296 LEU Chi-restraints excluded: chain E residue 297 LYS Chi-restraints excluded: chain E residue 331 ASP Chi-restraints excluded: chain E residue 336 VAL Chi-restraints excluded: chain E residue 340 VAL Chi-restraints excluded: chain E residue 354 SER Chi-restraints excluded: chain E residue 367 SER Chi-restraints excluded: chain E residue 370 VAL Chi-restraints excluded: chain E residue 401 VAL Chi-restraints excluded: chain E residue 409 GLU Chi-restraints excluded: chain F residue 18 THR Chi-restraints excluded: chain F residue 25 THR Chi-restraints excluded: chain F residue 46 MET Chi-restraints excluded: chain F residue 67 ASP Chi-restraints excluded: chain F residue 86 ILE Chi-restraints excluded: chain F residue 88 VAL Chi-restraints excluded: chain F residue 89 ILE Chi-restraints excluded: chain G residue 43 ASP Chi-restraints excluded: chain G residue 83 SER Chi-restraints excluded: chain G residue 98 MET Chi-restraints excluded: chain G residue 137 ILE Chi-restraints excluded: chain G residue 155 VAL Chi-restraints excluded: chain G residue 176 ASP Chi-restraints excluded: chain G residue 205 LEU Chi-restraints excluded: chain G residue 219 VAL Chi-restraints excluded: chain G residue 220 ILE Chi-restraints excluded: chain I residue 70 THR Chi-restraints excluded: chain I residue 79 GLU Chi-restraints excluded: chain I residue 90 ASN Chi-restraints excluded: chain I residue 104 ILE Chi-restraints excluded: chain I residue 175 HIS Chi-restraints excluded: chain I residue 201 LEU Chi-restraints excluded: chain I residue 202 ILE Chi-restraints excluded: chain I residue 206 LEU Chi-restraints excluded: chain I residue 216 ASP Chi-restraints excluded: chain I residue 226 LEU Chi-restraints excluded: chain I residue 229 LEU Chi-restraints excluded: chain I residue 277 ARG Chi-restraints excluded: chain I residue 322 ASP Chi-restraints excluded: chain I residue 331 CYS Chi-restraints excluded: chain I residue 377 VAL Chi-restraints excluded: chain I residue 393 THR Chi-restraints excluded: chain J residue 106 ILE Chi-restraints excluded: chain J residue 115 ILE Chi-restraints excluded: chain J residue 123 SER Chi-restraints excluded: chain J residue 132 VAL Chi-restraints excluded: chain J residue 160 ILE Chi-restraints excluded: chain J residue 170 MET Chi-restraints excluded: chain J residue 172 VAL Chi-restraints excluded: chain K residue 65 TYR Chi-restraints excluded: chain K residue 75 LEU Chi-restraints excluded: chain K residue 81 LYS Chi-restraints excluded: chain K residue 98 GLN Chi-restraints excluded: chain K residue 132 THR Chi-restraints excluded: chain K residue 142 THR Chi-restraints excluded: chain K residue 146 VAL Chi-restraints excluded: chain K residue 151 VAL Chi-restraints excluded: chain K residue 152 VAL Chi-restraints excluded: chain K residue 156 LEU Chi-restraints excluded: chain K residue 161 LEU Chi-restraints excluded: chain K residue 162 SER Chi-restraints excluded: chain K residue 169 MET Chi-restraints excluded: chain K residue 178 THR Chi-restraints excluded: chain K residue 189 ARG Chi-restraints excluded: chain L residue 59 LYS Chi-restraints excluded: chain N residue 30 VAL Chi-restraints excluded: chain N residue 54 ILE Chi-restraints excluded: chain N residue 56 SER Chi-restraints excluded: chain N residue 57 LEU Chi-restraints excluded: chain N residue 78 LEU Chi-restraints excluded: chain N residue 81 ASP Chi-restraints excluded: chain N residue 109 ILE Chi-restraints excluded: chain N residue 121 SER Chi-restraints excluded: chain O residue 72 MET Chi-restraints excluded: chain O residue 205 VAL Chi-restraints excluded: chain O residue 214 VAL Chi-restraints excluded: chain P residue 44 ASP Chi-restraints excluded: chain P residue 53 SER Chi-restraints excluded: chain P residue 83 LEU Chi-restraints excluded: chain P residue 84 SER Chi-restraints excluded: chain P residue 97 TYR Chi-restraints excluded: chain P residue 110 LEU Chi-restraints excluded: chain Q residue 30 VAL Chi-restraints excluded: chain Q residue 59 THR Chi-restraints excluded: chain Q residue 103 THR Chi-restraints excluded: chain R residue 53 VAL Chi-restraints excluded: chain R residue 63 LEU Chi-restraints excluded: chain R residue 69 CYS Chi-restraints excluded: chain R residue 112 ILE Chi-restraints excluded: chain R residue 117 ILE Chi-restraints excluded: chain R residue 131 LEU Chi-restraints excluded: chain R residue 136 VAL Chi-restraints excluded: chain U residue 8 ILE Chi-restraints excluded: chain U residue 14 VAL Chi-restraints excluded: chain U residue 18 ASN Chi-restraints excluded: chain U residue 56 SER Chi-restraints excluded: chain U residue 60 CYS Chi-restraints excluded: chain U residue 62 ARG Chi-restraints excluded: chain U residue 80 ARG Chi-restraints excluded: chain a residue 66 LYS Chi-restraints excluded: chain a residue 105 MET Chi-restraints excluded: chain a residue 160 ILE Chi-restraints excluded: chain a residue 172 VAL Chi-restraints excluded: chain a residue 205 THR Chi-restraints excluded: chain a residue 250 GLU Chi-restraints excluded: chain a residue 254 LYS Chi-restraints excluded: chain a residue 294 SER Chi-restraints excluded: chain b residue 6 LEU Chi-restraints excluded: chain b residue 12 ILE Chi-restraints excluded: chain b residue 70 ILE Chi-restraints excluded: chain b residue 87 LEU Chi-restraints excluded: chain b residue 94 SER Chi-restraints excluded: chain c residue 25 ASP Chi-restraints excluded: chain c residue 26 SER Chi-restraints excluded: chain c residue 27 VAL Chi-restraints excluded: chain c residue 59 ASN Chi-restraints excluded: chain c residue 106 LEU Chi-restraints excluded: chain c residue 109 ASN Chi-restraints excluded: chain c residue 114 GLU Chi-restraints excluded: chain c residue 123 LEU Chi-restraints excluded: chain d residue 75 MET Chi-restraints excluded: chain d residue 191 ILE Chi-restraints excluded: chain f residue 85 LEU Chi-restraints excluded: chain f residue 113 LEU Chi-restraints excluded: chain f residue 123 CYS Chi-restraints excluded: chain f residue 139 THR Chi-restraints excluded: chain f residue 142 ARG Chi-restraints excluded: chain f residue 148 LEU Chi-restraints excluded: chain f residue 155 LEU Chi-restraints excluded: chain f residue 159 THR Chi-restraints excluded: chain f residue 160 ASP Chi-restraints excluded: chain f residue 161 THR Chi-restraints excluded: chain f residue 162 THR Chi-restraints excluded: chain g residue 150 LEU Chi-restraints excluded: chain g residue 178 ASP Chi-restraints excluded: chain g residue 208 VAL Chi-restraints excluded: chain g residue 224 VAL Chi-restraints excluded: chain g residue 246 LEU Chi-restraints excluded: chain g residue 255 PHE Chi-restraints excluded: chain g residue 265 ASN Chi-restraints excluded: chain g residue 290 HIS Chi-restraints excluded: chain g residue 296 VAL Chi-restraints excluded: chain g residue 337 ASP Chi-restraints excluded: chain g residue 356 ILE Chi-restraints excluded: chain g residue 378 GLU Chi-restraints excluded: chain g residue 380 LEU Chi-restraints excluded: chain h residue 298 LYS Chi-restraints excluded: chain h residue 302 LEU Chi-restraints excluded: chain h residue 308 ASN Chi-restraints excluded: chain h residue 381 GLU Chi-restraints excluded: chain h residue 387 ASN Chi-restraints excluded: chain i residue 48 THR Chi-restraints excluded: chain i residue 79 ARG Chi-restraints excluded: chain i residue 93 LYS Chi-restraints excluded: chain j residue 11 ILE Chi-restraints excluded: chain j residue 50 LEU Chi-restraints excluded: chain j residue 84 SER Chi-restraints excluded: chain j residue 97 LEU Chi-restraints excluded: chain j residue 136 TYR Chi-restraints excluded: chain j residue 150 PHE Chi-restraints excluded: chain j residue 164 VAL Chi-restraints excluded: chain j residue 187 GLU Chi-restraints excluded: chain j residue 199 ASP Chi-restraints excluded: chain k residue 71 VAL Chi-restraints excluded: chain k residue 74 VAL Chi-restraints excluded: chain k residue 79 LYS Chi-restraints excluded: chain k residue 117 THR Chi-restraints excluded: chain k residue 165 ILE Chi-restraints excluded: chain k residue 166 ARG Chi-restraints excluded: chain k residue 180 SER Chi-restraints excluded: chain k residue 185 ASP Chi-restraints excluded: chain k residue 198 ASP Chi-restraints excluded: chain k residue 216 LEU Chi-restraints excluded: chain k residue 226 TYR Chi-restraints excluded: chain k residue 228 LEU Chi-restraints excluded: chain k residue 230 VAL Chi-restraints excluded: chain k residue 231 LEU Chi-restraints excluded: chain k residue 254 ILE Chi-restraints excluded: chain k residue 288 THR Chi-restraints excluded: chain k residue 292 GLU Chi-restraints excluded: chain m residue 13 LEU Chi-restraints excluded: chain m residue 15 ASN Chi-restraints excluded: chain m residue 33 VAL Chi-restraints excluded: chain m residue 39 GLU Chi-restraints excluded: chain m residue 46 ILE Chi-restraints excluded: chain m residue 58 GLN Chi-restraints excluded: chain m residue 59 ASN Chi-restraints excluded: chain m residue 63 ASP Chi-restraints excluded: chain m residue 99 LEU Chi-restraints excluded: chain m residue 117 VAL Chi-restraints excluded: chain n residue 145 LYS Chi-restraints excluded: chain n residue 147 VAL Chi-restraints excluded: chain n residue 194 ILE Chi-restraints excluded: chain o residue 57 VAL Chi-restraints excluded: chain o residue 64 THR Chi-restraints excluded: chain o residue 77 THR Chi-restraints excluded: chain o residue 96 ILE Chi-restraints excluded: chain o residue 134 GLU Chi-restraints excluded: chain p residue 63 GLU Chi-restraints excluded: chain p residue 73 VAL Chi-restraints excluded: chain p residue 80 ASN Chi-restraints excluded: chain p residue 96 ARG Chi-restraints excluded: chain p residue 103 ASN Chi-restraints excluded: chain p residue 108 CYS Chi-restraints excluded: chain p residue 113 LEU Chi-restraints excluded: chain p residue 119 ASN Chi-restraints excluded: chain p residue 120 VAL Chi-restraints excluded: chain p residue 140 THR Chi-restraints excluded: chain p residue 177 PHE Chi-restraints excluded: chain p residue 197 ASP Chi-restraints excluded: chain p residue 235 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 596 random chunks: chunk 555 optimal weight: 7.9990 chunk 64 optimal weight: 10.0000 chunk 328 optimal weight: 20.0000 chunk 421 optimal weight: 20.0000 chunk 326 optimal weight: 0.8980 chunk 485 optimal weight: 7.9990 chunk 322 optimal weight: 7.9990 chunk 574 optimal weight: 2.9990 chunk 359 optimal weight: 9.9990 chunk 350 optimal weight: 10.0000 chunk 265 optimal weight: 8.9990 overall best weight: 5.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 215 ASN B 273 GLN E 130 GLN ** E 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 92 ASN G 72 GLN ** G 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 77 GLN J 130 HIS ** J 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 57 GLN ** L 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 119 GLN Q 56 GLN ** a 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 276 ASN ** c 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 139 HIS ** i 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 112 ASN ** k 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8432 moved from start: 0.4668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.063 69632 Z= 0.366 Angle : 1.404 15.094 98901 Z= 0.886 Chirality : 0.040 0.388 11258 Planarity : 0.015 0.126 8814 Dihedral : 22.842 179.961 22917 Min Nonbonded Distance : 1.756 Molprobity Statistics. All-atom Clashscore : 16.85 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.20 % Favored : 94.78 % Rotamer: Outliers : 7.47 % Allowed : 22.20 % Favored : 70.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.24 (0.12), residues: 4599 helix: 0.74 (0.12), residues: 1948 sheet: -0.56 (0.23), residues: 493 loop : -0.84 (0.13), residues: 2158 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.060 0.002 TRP p 202 HIS 0.011 0.001 HIS I 176 PHE 0.017 0.002 PHE C 91 TYR 0.021 0.002 TYR G 64 ARG 0.010 0.001 ARG d 61 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9198 Ramachandran restraints generated. 4599 Oldfield, 0 Emsley, 4599 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9198 Ramachandran restraints generated. 4599 Oldfield, 0 Emsley, 4599 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1114 residues out of total 4072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 304 poor density : 810 time to evaluate : 4.228 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 58 ARG cc_start: 0.8136 (mmt90) cc_final: 0.7718 (mmt90) REVERT: B 70 ASP cc_start: 0.7796 (t0) cc_final: 0.7404 (t0) REVERT: B 87 ARG cc_start: 0.8548 (OUTLIER) cc_final: 0.8228 (mtt180) REVERT: B 115 ILE cc_start: 0.8966 (OUTLIER) cc_final: 0.8527 (mm) REVERT: B 246 ARG cc_start: 0.9027 (OUTLIER) cc_final: 0.8196 (mtp85) REVERT: B 261 GLU cc_start: 0.8331 (tp30) cc_final: 0.8110 (tp30) REVERT: C 54 GLU cc_start: 0.8078 (tp30) cc_final: 0.7842 (tm-30) REVERT: C 89 ASP cc_start: 0.8715 (t0) cc_final: 0.8408 (t0) REVERT: C 140 GLU cc_start: 0.9415 (tm-30) cc_final: 0.9100 (tm-30) REVERT: C 157 THR cc_start: 0.8572 (m) cc_final: 0.8080 (p) REVERT: E 184 LYS cc_start: 0.7894 (mmtt) cc_final: 0.7511 (pttm) REVERT: E 417 MET cc_start: 0.7917 (mmm) cc_final: 0.7210 (tpp) REVERT: F 92 ASN cc_start: 0.8629 (OUTLIER) cc_final: 0.7831 (m110) REVERT: G 113 GLN cc_start: 0.8621 (mt0) cc_final: 0.8340 (mt0) REVERT: G 162 LEU cc_start: 0.9114 (tp) cc_final: 0.8622 (tt) REVERT: G 163 LYS cc_start: 0.8027 (tptt) cc_final: 0.7824 (mmmt) REVERT: G 201 MET cc_start: 0.8844 (tpt) cc_final: 0.8242 (tpt) REVERT: G 205 LEU cc_start: 0.9505 (OUTLIER) cc_final: 0.9242 (tt) REVERT: G 220 ILE cc_start: 0.9312 (OUTLIER) cc_final: 0.9033 (mm) REVERT: I 79 GLU cc_start: 0.8930 (OUTLIER) cc_final: 0.8680 (mp0) REVERT: I 162 MET cc_start: 0.8836 (mmm) cc_final: 0.8538 (mmm) REVERT: I 207 GLU cc_start: 0.8492 (tm-30) cc_final: 0.7990 (tm-30) REVERT: I 209 MET cc_start: 0.8236 (ttp) cc_final: 0.7876 (mtp) REVERT: I 308 THR cc_start: 0.8436 (OUTLIER) cc_final: 0.8064 (t) REVERT: J 189 TRP cc_start: 0.4125 (t-100) cc_final: 0.3762 (t-100) REVERT: K 73 ASN cc_start: 0.8154 (t0) cc_final: 0.7552 (p0) REVERT: K 76 ARG cc_start: 0.9027 (mmt-90) cc_final: 0.8399 (mpt180) REVERT: K 165 LYS cc_start: 0.8542 (tttt) cc_final: 0.8053 (ttmm) REVERT: K 189 ARG cc_start: 0.8649 (OUTLIER) cc_final: 0.8390 (ttt180) REVERT: L 77 ASN cc_start: 0.7644 (OUTLIER) cc_final: 0.7302 (p0) REVERT: N 54 ILE cc_start: 0.8821 (OUTLIER) cc_final: 0.8551 (mp) REVERT: N 57 LEU cc_start: 0.8801 (OUTLIER) cc_final: 0.8363 (mt) REVERT: N 65 LYS cc_start: 0.8855 (mttt) cc_final: 0.8602 (tttm) REVERT: O 72 MET cc_start: 0.8876 (OUTLIER) cc_final: 0.8178 (tpp) REVERT: O 78 GLN cc_start: 0.8142 (tp40) cc_final: 0.7720 (mt0) REVERT: O 88 ASP cc_start: 0.8157 (m-30) cc_final: 0.7747 (p0) REVERT: O 112 LEU cc_start: 0.8967 (tp) cc_final: 0.8702 (mt) REVERT: O 162 ASP cc_start: 0.7535 (t0) cc_final: 0.7123 (t0) REVERT: P 74 ARG cc_start: 0.8440 (ptt90) cc_final: 0.8103 (ptt90) REVERT: Q 29 ARG cc_start: 0.7999 (ttm-80) cc_final: 0.7524 (ttm-80) REVERT: Q 59 THR cc_start: 0.8495 (OUTLIER) cc_final: 0.7916 (p) REVERT: R 49 GLU cc_start: 0.8549 (mm-30) cc_final: 0.8239 (mp0) REVERT: U 8 ILE cc_start: 0.9237 (OUTLIER) cc_final: 0.8956 (mt) REVERT: U 43 ARG cc_start: 0.8912 (ttt180) cc_final: 0.8661 (ttt90) REVERT: a 152 THR cc_start: 0.8056 (p) cc_final: 0.7667 (p) REVERT: b 6 LEU cc_start: 0.8829 (OUTLIER) cc_final: 0.8421 (mt) REVERT: b 99 PHE cc_start: 0.8659 (t80) cc_final: 0.8060 (t80) REVERT: b 133 ARG cc_start: 0.6540 (mpt180) cc_final: 0.6101 (mpt180) REVERT: b 134 ARG cc_start: 0.8186 (ttt180) cc_final: 0.7413 (ptm-80) REVERT: c 3 MET cc_start: 0.7641 (mtp) cc_final: 0.7256 (mtp) REVERT: c 71 THR cc_start: 0.9389 (m) cc_final: 0.8986 (p) REVERT: c 118 GLN cc_start: 0.8494 (OUTLIER) cc_final: 0.7531 (mp10) REVERT: d 93 ARG cc_start: 0.7832 (mtm180) cc_final: 0.7042 (mtm110) REVERT: d 106 MET cc_start: 0.8910 (mmt) cc_final: 0.8597 (mmt) REVERT: d 192 THR cc_start: 0.8868 (m) cc_final: 0.8489 (p) REVERT: f 85 LEU cc_start: 0.9260 (OUTLIER) cc_final: 0.8727 (tt) REVERT: f 131 ASP cc_start: 0.6447 (p0) cc_final: 0.5626 (p0) REVERT: f 134 LYS cc_start: 0.8884 (mtpt) cc_final: 0.8476 (mtmm) REVERT: g 99 MET cc_start: 0.7416 (mmm) cc_final: 0.6261 (mmp) REVERT: g 207 TYR cc_start: 0.6251 (m-80) cc_final: 0.5650 (m-10) REVERT: g 277 ASP cc_start: 0.7812 (m-30) cc_final: 0.7366 (p0) REVERT: g 323 LEU cc_start: 0.7813 (mt) cc_final: 0.7310 (mp) REVERT: g 368 GLU cc_start: 0.8849 (tt0) cc_final: 0.8515 (mp0) REVERT: h 308 ASN cc_start: 0.8972 (OUTLIER) cc_final: 0.8673 (p0) REVERT: h 371 TYR cc_start: 0.8528 (t80) cc_final: 0.8169 (t80) REVERT: i 79 ARG cc_start: 0.8440 (OUTLIER) cc_final: 0.7624 (mtt-85) REVERT: j 52 MET cc_start: 0.7709 (ttm) cc_final: 0.7436 (tmm) REVERT: j 88 GLN cc_start: 0.8113 (tt0) cc_final: 0.7865 (tt0) REVERT: j 150 PHE cc_start: 0.7360 (OUTLIER) cc_final: 0.6102 (m-10) REVERT: j 187 GLU cc_start: 0.9088 (OUTLIER) cc_final: 0.8682 (pm20) REVERT: j 198 ILE cc_start: 0.7314 (mm) cc_final: 0.6988 (mm) REVERT: k 199 ARG cc_start: 0.8372 (mtt-85) cc_final: 0.8052 (mtt-85) REVERT: m 25 LYS cc_start: 0.9077 (mttt) cc_final: 0.8864 (mttm) REVERT: m 39 GLU cc_start: 0.7773 (OUTLIER) cc_final: 0.7070 (pp20) REVERT: m 56 TRP cc_start: 0.8550 (m-10) cc_final: 0.8224 (m-10) REVERT: m 72 ASP cc_start: 0.8334 (m-30) cc_final: 0.7857 (t0) REVERT: n 145 LYS cc_start: 0.8880 (OUTLIER) cc_final: 0.8382 (mtmm) REVERT: n 156 LYS cc_start: 0.8747 (mttt) cc_final: 0.8298 (mtpt) REVERT: o 61 LYS cc_start: 0.8883 (mmtt) cc_final: 0.8611 (mtpt) REVERT: o 111 LYS cc_start: 0.8802 (mttt) cc_final: 0.8517 (tppt) REVERT: o 122 ASN cc_start: 0.8990 (m-40) cc_final: 0.8482 (m110) REVERT: o 141 MET cc_start: 0.9275 (mmm) cc_final: 0.8936 (mmm) REVERT: p 80 ASN cc_start: 0.8035 (OUTLIER) cc_final: 0.7682 (m-40) REVERT: p 119 ASN cc_start: 0.8612 (OUTLIER) cc_final: 0.8033 (p0) REVERT: p 124 GLU cc_start: 0.8744 (tp30) cc_final: 0.8470 (pt0) REVERT: p 174 ASP cc_start: 0.8273 (m-30) cc_final: 0.7775 (m-30) REVERT: p 186 SER cc_start: 0.8422 (m) cc_final: 0.8088 (p) outliers start: 304 outliers final: 244 residues processed: 1014 average time/residue: 0.6643 time to fit residues: 1116.3801 Evaluate side-chains 1048 residues out of total 4072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 270 poor density : 778 time to evaluate : 4.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 61 ILE Chi-restraints excluded: chain B residue 79 SER Chi-restraints excluded: chain B residue 87 ARG Chi-restraints excluded: chain B residue 108 SER Chi-restraints excluded: chain B residue 115 ILE Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 147 HIS Chi-restraints excluded: chain B residue 154 ILE Chi-restraints excluded: chain B residue 161 CYS Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 197 THR Chi-restraints excluded: chain B residue 203 GLU Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain B residue 246 ARG Chi-restraints excluded: chain B residue 270 TYR Chi-restraints excluded: chain C residue 71 LEU Chi-restraints excluded: chain C residue 73 THR Chi-restraints excluded: chain C residue 77 ASP Chi-restraints excluded: chain C residue 92 LEU Chi-restraints excluded: chain C residue 115 ASN Chi-restraints excluded: chain C residue 130 HIS Chi-restraints excluded: chain C residue 135 LEU Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 94 THR Chi-restraints excluded: chain E residue 132 ILE Chi-restraints excluded: chain E residue 145 ASN Chi-restraints excluded: chain E residue 146 ILE Chi-restraints excluded: chain E residue 217 ASP Chi-restraints excluded: chain E residue 239 ARG Chi-restraints excluded: chain E residue 242 ARG Chi-restraints excluded: chain E residue 245 VAL Chi-restraints excluded: chain E residue 258 ILE Chi-restraints excluded: chain E residue 276 VAL Chi-restraints excluded: chain E residue 296 LEU Chi-restraints excluded: chain E residue 297 LYS Chi-restraints excluded: chain E residue 331 ASP Chi-restraints excluded: chain E residue 336 VAL Chi-restraints excluded: chain E residue 340 VAL Chi-restraints excluded: chain E residue 354 SER Chi-restraints excluded: chain E residue 367 SER Chi-restraints excluded: chain E residue 370 VAL Chi-restraints excluded: chain E residue 401 VAL Chi-restraints excluded: chain E residue 409 GLU Chi-restraints excluded: chain F residue 8 LEU Chi-restraints excluded: chain F residue 18 THR Chi-restraints excluded: chain F residue 25 THR Chi-restraints excluded: chain F residue 39 LEU Chi-restraints excluded: chain F residue 46 MET Chi-restraints excluded: chain F residue 67 ASP Chi-restraints excluded: chain F residue 86 ILE Chi-restraints excluded: chain F residue 88 VAL Chi-restraints excluded: chain F residue 89 ILE Chi-restraints excluded: chain F residue 92 ASN Chi-restraints excluded: chain G residue 83 SER Chi-restraints excluded: chain G residue 98 MET Chi-restraints excluded: chain G residue 99 MET Chi-restraints excluded: chain G residue 109 SER Chi-restraints excluded: chain G residue 114 THR Chi-restraints excluded: chain G residue 137 ILE Chi-restraints excluded: chain G residue 155 VAL Chi-restraints excluded: chain G residue 172 VAL Chi-restraints excluded: chain G residue 176 ASP Chi-restraints excluded: chain G residue 205 LEU Chi-restraints excluded: chain G residue 219 VAL Chi-restraints excluded: chain G residue 220 ILE Chi-restraints excluded: chain I residue 70 THR Chi-restraints excluded: chain I residue 79 GLU Chi-restraints excluded: chain I residue 90 ASN Chi-restraints excluded: chain I residue 104 ILE Chi-restraints excluded: chain I residue 175 HIS Chi-restraints excluded: chain I residue 202 ILE Chi-restraints excluded: chain I residue 206 LEU Chi-restraints excluded: chain I residue 216 ASP Chi-restraints excluded: chain I residue 226 LEU Chi-restraints excluded: chain I residue 229 LEU Chi-restraints excluded: chain I residue 277 ARG Chi-restraints excluded: chain I residue 308 THR Chi-restraints excluded: chain I residue 322 ASP Chi-restraints excluded: chain I residue 331 CYS Chi-restraints excluded: chain I residue 377 VAL Chi-restraints excluded: chain I residue 393 THR Chi-restraints excluded: chain J residue 106 ILE Chi-restraints excluded: chain J residue 115 ILE Chi-restraints excluded: chain J residue 123 SER Chi-restraints excluded: chain J residue 132 VAL Chi-restraints excluded: chain J residue 160 ILE Chi-restraints excluded: chain J residue 170 MET Chi-restraints excluded: chain J residue 171 GLU Chi-restraints excluded: chain J residue 172 VAL Chi-restraints excluded: chain K residue 65 TYR Chi-restraints excluded: chain K residue 75 LEU Chi-restraints excluded: chain K residue 98 GLN Chi-restraints excluded: chain K residue 132 THR Chi-restraints excluded: chain K residue 142 THR Chi-restraints excluded: chain K residue 146 VAL Chi-restraints excluded: chain K residue 151 VAL Chi-restraints excluded: chain K residue 152 VAL Chi-restraints excluded: chain K residue 156 LEU Chi-restraints excluded: chain K residue 161 LEU Chi-restraints excluded: chain K residue 162 SER Chi-restraints excluded: chain K residue 169 MET Chi-restraints excluded: chain K residue 178 THR Chi-restraints excluded: chain K residue 189 ARG Chi-restraints excluded: chain K residue 196 LEU Chi-restraints excluded: chain L residue 32 THR Chi-restraints excluded: chain L residue 57 GLN Chi-restraints excluded: chain L residue 59 LYS Chi-restraints excluded: chain L residue 77 ASN Chi-restraints excluded: chain N residue 30 VAL Chi-restraints excluded: chain N residue 54 ILE Chi-restraints excluded: chain N residue 56 SER Chi-restraints excluded: chain N residue 57 LEU Chi-restraints excluded: chain N residue 67 LEU Chi-restraints excluded: chain N residue 74 GLU Chi-restraints excluded: chain N residue 107 SER Chi-restraints excluded: chain N residue 109 ILE Chi-restraints excluded: chain N residue 110 VAL Chi-restraints excluded: chain N residue 121 SER Chi-restraints excluded: chain O residue 72 MET Chi-restraints excluded: chain O residue 89 VAL Chi-restraints excluded: chain O residue 113 MET Chi-restraints excluded: chain O residue 205 VAL Chi-restraints excluded: chain O residue 214 VAL Chi-restraints excluded: chain P residue 44 ASP Chi-restraints excluded: chain P residue 53 SER Chi-restraints excluded: chain P residue 83 LEU Chi-restraints excluded: chain P residue 84 SER Chi-restraints excluded: chain P residue 110 LEU Chi-restraints excluded: chain Q residue 8 VAL Chi-restraints excluded: chain Q residue 14 VAL Chi-restraints excluded: chain Q residue 30 VAL Chi-restraints excluded: chain Q residue 58 CYS Chi-restraints excluded: chain Q residue 59 THR Chi-restraints excluded: chain Q residue 103 THR Chi-restraints excluded: chain R residue 53 VAL Chi-restraints excluded: chain R residue 63 LEU Chi-restraints excluded: chain R residue 69 CYS Chi-restraints excluded: chain R residue 107 GLU Chi-restraints excluded: chain R residue 112 ILE Chi-restraints excluded: chain R residue 117 ILE Chi-restraints excluded: chain R residue 131 LEU Chi-restraints excluded: chain R residue 136 VAL Chi-restraints excluded: chain U residue 8 ILE Chi-restraints excluded: chain U residue 14 VAL Chi-restraints excluded: chain U residue 18 ASN Chi-restraints excluded: chain U residue 47 LYS Chi-restraints excluded: chain U residue 56 SER Chi-restraints excluded: chain U residue 60 CYS Chi-restraints excluded: chain U residue 62 ARG Chi-restraints excluded: chain a residue 66 LYS Chi-restraints excluded: chain a residue 105 MET Chi-restraints excluded: chain a residue 160 ILE Chi-restraints excluded: chain a residue 172 VAL Chi-restraints excluded: chain a residue 205 THR Chi-restraints excluded: chain a residue 238 SER Chi-restraints excluded: chain a residue 250 GLU Chi-restraints excluded: chain a residue 254 LYS Chi-restraints excluded: chain a residue 270 MET Chi-restraints excluded: chain b residue 6 LEU Chi-restraints excluded: chain b residue 12 ILE Chi-restraints excluded: chain b residue 70 ILE Chi-restraints excluded: chain b residue 87 LEU Chi-restraints excluded: chain b residue 94 SER Chi-restraints excluded: chain c residue 25 ASP Chi-restraints excluded: chain c residue 26 SER Chi-restraints excluded: chain c residue 27 VAL Chi-restraints excluded: chain c residue 59 ASN Chi-restraints excluded: chain c residue 106 LEU Chi-restraints excluded: chain c residue 109 ASN Chi-restraints excluded: chain c residue 114 GLU Chi-restraints excluded: chain c residue 118 GLN Chi-restraints excluded: chain c residue 123 LEU Chi-restraints excluded: chain d residue 75 MET Chi-restraints excluded: chain d residue 183 SER Chi-restraints excluded: chain d residue 191 ILE Chi-restraints excluded: chain f residue 85 LEU Chi-restraints excluded: chain f residue 113 LEU Chi-restraints excluded: chain f residue 123 CYS Chi-restraints excluded: chain f residue 139 THR Chi-restraints excluded: chain f residue 142 ARG Chi-restraints excluded: chain f residue 148 LEU Chi-restraints excluded: chain f residue 155 LEU Chi-restraints excluded: chain f residue 159 THR Chi-restraints excluded: chain f residue 160 ASP Chi-restraints excluded: chain f residue 161 THR Chi-restraints excluded: chain f residue 162 THR Chi-restraints excluded: chain g residue 142 HIS Chi-restraints excluded: chain g residue 150 LEU Chi-restraints excluded: chain g residue 178 ASP Chi-restraints excluded: chain g residue 224 VAL Chi-restraints excluded: chain g residue 246 LEU Chi-restraints excluded: chain g residue 255 PHE Chi-restraints excluded: chain g residue 265 ASN Chi-restraints excluded: chain g residue 290 HIS Chi-restraints excluded: chain g residue 296 VAL Chi-restraints excluded: chain g residue 337 ASP Chi-restraints excluded: chain g residue 356 ILE Chi-restraints excluded: chain g residue 380 LEU Chi-restraints excluded: chain h residue 298 LYS Chi-restraints excluded: chain h residue 302 LEU Chi-restraints excluded: chain h residue 308 ASN Chi-restraints excluded: chain h residue 329 TYR Chi-restraints excluded: chain h residue 346 VAL Chi-restraints excluded: chain h residue 387 ASN Chi-restraints excluded: chain i residue 48 THR Chi-restraints excluded: chain i residue 77 ASP Chi-restraints excluded: chain i residue 79 ARG Chi-restraints excluded: chain i residue 93 LYS Chi-restraints excluded: chain j residue 11 ILE Chi-restraints excluded: chain j residue 50 LEU Chi-restraints excluded: chain j residue 84 SER Chi-restraints excluded: chain j residue 97 LEU Chi-restraints excluded: chain j residue 123 LYS Chi-restraints excluded: chain j residue 124 THR Chi-restraints excluded: chain j residue 136 TYR Chi-restraints excluded: chain j residue 150 PHE Chi-restraints excluded: chain j residue 164 VAL Chi-restraints excluded: chain j residue 187 GLU Chi-restraints excluded: chain j residue 199 ASP Chi-restraints excluded: chain j residue 208 GLU Chi-restraints excluded: chain k residue 74 VAL Chi-restraints excluded: chain k residue 79 LYS Chi-restraints excluded: chain k residue 117 THR Chi-restraints excluded: chain k residue 165 ILE Chi-restraints excluded: chain k residue 166 ARG Chi-restraints excluded: chain k residue 180 SER Chi-restraints excluded: chain k residue 185 ASP Chi-restraints excluded: chain k residue 193 ILE Chi-restraints excluded: chain k residue 198 ASP Chi-restraints excluded: chain k residue 212 ASP Chi-restraints excluded: chain k residue 216 LEU Chi-restraints excluded: chain k residue 226 TYR Chi-restraints excluded: chain k residue 228 LEU Chi-restraints excluded: chain k residue 230 VAL Chi-restraints excluded: chain k residue 231 LEU Chi-restraints excluded: chain k residue 254 ILE Chi-restraints excluded: chain k residue 288 THR Chi-restraints excluded: chain k residue 292 GLU Chi-restraints excluded: chain m residue 13 LEU Chi-restraints excluded: chain m residue 15 ASN Chi-restraints excluded: chain m residue 33 VAL Chi-restraints excluded: chain m residue 39 GLU Chi-restraints excluded: chain m residue 46 ILE Chi-restraints excluded: chain m residue 63 ASP Chi-restraints excluded: chain m residue 99 LEU Chi-restraints excluded: chain m residue 117 VAL Chi-restraints excluded: chain n residue 145 LYS Chi-restraints excluded: chain n residue 147 VAL Chi-restraints excluded: chain n residue 194 ILE Chi-restraints excluded: chain o residue 57 VAL Chi-restraints excluded: chain o residue 64 THR Chi-restraints excluded: chain o residue 77 THR Chi-restraints excluded: chain o residue 78 VAL Chi-restraints excluded: chain o residue 96 ILE Chi-restraints excluded: chain o residue 98 THR Chi-restraints excluded: chain o residue 134 GLU Chi-restraints excluded: chain p residue 63 GLU Chi-restraints excluded: chain p residue 73 VAL Chi-restraints excluded: chain p residue 80 ASN Chi-restraints excluded: chain p residue 96 ARG Chi-restraints excluded: chain p residue 103 ASN Chi-restraints excluded: chain p residue 108 CYS Chi-restraints excluded: chain p residue 110 ASP Chi-restraints excluded: chain p residue 113 LEU Chi-restraints excluded: chain p residue 119 ASN Chi-restraints excluded: chain p residue 120 VAL Chi-restraints excluded: chain p residue 140 THR Chi-restraints excluded: chain p residue 163 LEU Chi-restraints excluded: chain p residue 177 PHE Chi-restraints excluded: chain p residue 197 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 596 random chunks: chunk 355 optimal weight: 1.9990 chunk 229 optimal weight: 7.9990 chunk 343 optimal weight: 7.9990 chunk 173 optimal weight: 20.0000 chunk 112 optimal weight: 0.9990 chunk 111 optimal weight: 0.9990 chunk 365 optimal weight: 30.0000 chunk 391 optimal weight: 0.6980 chunk 284 optimal weight: 7.9990 chunk 53 optimal weight: 10.0000 chunk 451 optimal weight: 1.9990 overall best weight: 1.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 273 GLN C 37 ASN C 57 HIS E 130 GLN ** E 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 57 GLN L 105 HIS N 119 GLN Q 79 HIS ** a 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 139 HIS ** i 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 112 ASN ** m 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** p 166 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8337 moved from start: 0.4931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 69632 Z= 0.188 Angle : 1.369 15.167 98901 Z= 0.875 Chirality : 0.036 0.379 11258 Planarity : 0.015 0.121 8814 Dihedral : 22.685 179.940 22909 Min Nonbonded Distance : 1.883 Molprobity Statistics. All-atom Clashscore : 14.47 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.48 % Favored : 96.48 % Rotamer: Outliers : 4.89 % Allowed : 24.88 % Favored : 70.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.39 % Cis-general : 0.00 % 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: 0.12 (0.12), residues: 4599 helix: 1.02 (0.12), residues: 1960 sheet: -0.37 (0.23), residues: 499 loop : -0.62 (0.13), residues: 2140 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.002 TRP p 202 HIS 0.011 0.001 HIS I 176 PHE 0.018 0.001 PHE C 91 TYR 0.025 0.001 TYR j 94 ARG 0.010 0.001 ARG L 84 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9198 Ramachandran restraints generated. 4599 Oldfield, 0 Emsley, 4599 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9198 Ramachandran restraints generated. 4599 Oldfield, 0 Emsley, 4599 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1075 residues out of total 4072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 199 poor density : 876 time to evaluate : 4.234 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 58 ARG cc_start: 0.8098 (mmt90) cc_final: 0.7543 (mmt90) REVERT: B 115 ILE cc_start: 0.8811 (OUTLIER) cc_final: 0.8408 (mm) REVERT: B 246 ARG cc_start: 0.8939 (OUTLIER) cc_final: 0.8115 (mtp85) REVERT: C 89 ASP cc_start: 0.8524 (t0) cc_final: 0.8272 (t0) REVERT: C 140 GLU cc_start: 0.9318 (tm-30) cc_final: 0.9068 (tm-30) REVERT: E 149 MET cc_start: 0.7325 (mmm) cc_final: 0.6832 (mmm) REVERT: E 172 MET cc_start: 0.8281 (mmp) cc_final: 0.7446 (mtt) REVERT: E 184 LYS cc_start: 0.7727 (mmtt) cc_final: 0.7193 (pttp) REVERT: E 417 MET cc_start: 0.7946 (mmm) cc_final: 0.7341 (tpp) REVERT: F 92 ASN cc_start: 0.9041 (OUTLIER) cc_final: 0.8671 (m-40) REVERT: F 121 LYS cc_start: 0.8169 (mtmm) cc_final: 0.7820 (mtmt) REVERT: G 40 GLU cc_start: 0.8359 (OUTLIER) cc_final: 0.7978 (mp0) REVERT: G 113 GLN cc_start: 0.8531 (mt0) cc_final: 0.8222 (mt0) REVERT: G 126 TYR cc_start: 0.8388 (t80) cc_final: 0.7531 (t80) REVERT: G 134 GLN cc_start: 0.8068 (mt0) cc_final: 0.7594 (mt0) REVERT: G 147 GLN cc_start: 0.7754 (tp40) cc_final: 0.7269 (tp40) REVERT: G 162 LEU cc_start: 0.9062 (tp) cc_final: 0.8529 (tt) REVERT: G 201 MET cc_start: 0.8785 (tpt) cc_final: 0.8220 (tpt) REVERT: G 205 LEU cc_start: 0.9453 (OUTLIER) cc_final: 0.9115 (tt) REVERT: G 220 ILE cc_start: 0.9249 (OUTLIER) cc_final: 0.8981 (mm) REVERT: I 79 GLU cc_start: 0.8917 (OUTLIER) cc_final: 0.8645 (mp0) REVERT: I 162 MET cc_start: 0.8697 (mmm) cc_final: 0.8445 (mmm) REVERT: I 209 MET cc_start: 0.8011 (ttp) cc_final: 0.7634 (mtp) REVERT: I 308 THR cc_start: 0.8366 (OUTLIER) cc_final: 0.7931 (t) REVERT: I 349 MET cc_start: 0.8988 (ttm) cc_final: 0.8706 (ttp) REVERT: I 365 MET cc_start: 0.8916 (mtm) cc_final: 0.8625 (mtm) REVERT: J 100 LYS cc_start: 0.8792 (mmmt) cc_final: 0.8583 (mmtm) REVERT: J 189 TRP cc_start: 0.4065 (t-100) cc_final: 0.3816 (t-100) REVERT: K 73 ASN cc_start: 0.8056 (t0) cc_final: 0.7521 (p0) REVERT: K 76 ARG cc_start: 0.8824 (mmt-90) cc_final: 0.8125 (mpt180) REVERT: K 165 LYS cc_start: 0.8442 (tttt) cc_final: 0.7922 (ttmm) REVERT: L 33 LEU cc_start: 0.9688 (mt) cc_final: 0.9222 (mt) REVERT: L 105 HIS cc_start: 0.8247 (OUTLIER) cc_final: 0.8028 (m170) REVERT: L 134 HIS cc_start: 0.7258 (m90) cc_final: 0.6929 (m-70) REVERT: N 37 ASP cc_start: 0.7671 (OUTLIER) cc_final: 0.7198 (t70) REVERT: N 43 MET cc_start: 0.8331 (tmm) cc_final: 0.8038 (tmm) REVERT: N 54 ILE cc_start: 0.8729 (OUTLIER) cc_final: 0.8510 (mp) REVERT: N 65 LYS cc_start: 0.8880 (mttt) cc_final: 0.8485 (tttm) REVERT: N 70 VAL cc_start: 0.8405 (m) cc_final: 0.8052 (p) REVERT: O 72 MET cc_start: 0.8883 (OUTLIER) cc_final: 0.8209 (tpp) REVERT: O 88 ASP cc_start: 0.8036 (m-30) cc_final: 0.7611 (p0) REVERT: O 112 LEU cc_start: 0.8903 (tp) cc_final: 0.8674 (mt) REVERT: O 162 ASP cc_start: 0.7408 (t0) cc_final: 0.7028 (t0) REVERT: P 110 LEU cc_start: 0.7242 (OUTLIER) cc_final: 0.6871 (tp) REVERT: Q 59 THR cc_start: 0.8591 (OUTLIER) cc_final: 0.8082 (p) REVERT: Q 80 GLU cc_start: 0.8808 (pp20) cc_final: 0.8414 (pp20) REVERT: R 49 GLU cc_start: 0.8548 (mm-30) cc_final: 0.8238 (mp0) REVERT: R 85 ILE cc_start: 0.9174 (tt) cc_final: 0.8822 (pt) REVERT: U 8 ILE cc_start: 0.9210 (OUTLIER) cc_final: 0.8938 (mt) REVERT: a 66 LYS cc_start: 0.6707 (OUTLIER) cc_final: 0.6463 (ptpp) REVERT: a 152 THR cc_start: 0.7928 (p) cc_final: 0.7607 (p) REVERT: b 6 LEU cc_start: 0.8690 (OUTLIER) cc_final: 0.8117 (mt) REVERT: b 83 LYS cc_start: 0.7635 (tttm) cc_final: 0.7311 (tmtt) REVERT: b 99 PHE cc_start: 0.8593 (t80) cc_final: 0.8060 (t80) REVERT: b 134 ARG cc_start: 0.8159 (ttt180) cc_final: 0.7248 (tpp-160) REVERT: c 3 MET cc_start: 0.7701 (mtp) cc_final: 0.7285 (mtp) REVERT: c 71 THR cc_start: 0.9289 (m) cc_final: 0.8811 (p) REVERT: c 106 LEU cc_start: 0.9371 (OUTLIER) cc_final: 0.9005 (pp) REVERT: c 132 ARG cc_start: 0.9378 (mmm-85) cc_final: 0.8812 (mmt-90) REVERT: c 160 THR cc_start: 0.8367 (m) cc_final: 0.7959 (t) REVERT: d 93 ARG cc_start: 0.7725 (mtm180) cc_final: 0.6963 (mtm110) REVERT: d 106 MET cc_start: 0.8638 (mmt) cc_final: 0.8407 (mmt) REVERT: d 192 THR cc_start: 0.8847 (m) cc_final: 0.8452 (p) REVERT: f 131 ASP cc_start: 0.6369 (p0) cc_final: 0.5599 (p0) REVERT: f 134 LYS cc_start: 0.8726 (mtpt) cc_final: 0.8401 (mtmm) REVERT: g 207 TYR cc_start: 0.6232 (m-80) cc_final: 0.5677 (m-10) REVERT: g 277 ASP cc_start: 0.7633 (m-30) cc_final: 0.7187 (p0) REVERT: g 319 ARG cc_start: 0.7531 (tmt170) cc_final: 0.7289 (tmt170) REVERT: h 360 GLN cc_start: 0.9053 (mt0) cc_final: 0.8643 (mp10) REVERT: h 371 TYR cc_start: 0.8397 (t80) cc_final: 0.8099 (t80) REVERT: h 378 ILE cc_start: 0.7748 (mm) cc_final: 0.7457 (mm) REVERT: i 11 MET cc_start: 0.8600 (tpp) cc_final: 0.8206 (tpp) REVERT: i 79 ARG cc_start: 0.8235 (OUTLIER) cc_final: 0.7346 (mtt-85) REVERT: j 52 MET cc_start: 0.7878 (ttm) cc_final: 0.7500 (tmm) REVERT: j 88 GLN cc_start: 0.8032 (tt0) cc_final: 0.7803 (tt0) REVERT: j 101 ARG cc_start: 0.7665 (OUTLIER) cc_final: 0.7297 (mtt180) REVERT: j 136 TYR cc_start: 0.7095 (OUTLIER) cc_final: 0.4537 (t80) REVERT: j 144 LYS cc_start: 0.8376 (mttt) cc_final: 0.7848 (mttp) REVERT: j 150 PHE cc_start: 0.7323 (OUTLIER) cc_final: 0.6050 (m-10) REVERT: j 198 ILE cc_start: 0.7251 (OUTLIER) cc_final: 0.6881 (mm) REVERT: k 199 ARG cc_start: 0.8297 (mtt-85) cc_final: 0.8004 (mtt-85) REVERT: m 22 LYS cc_start: 0.9173 (mttt) cc_final: 0.8718 (mttp) REVERT: m 56 TRP cc_start: 0.8495 (m-10) cc_final: 0.8106 (m-10) REVERT: m 60 GLU cc_start: 0.8395 (tt0) cc_final: 0.8116 (pt0) REVERT: m 62 ARG cc_start: 0.8848 (mtm110) cc_final: 0.8286 (mtm-85) REVERT: m 72 ASP cc_start: 0.8376 (m-30) cc_final: 0.7916 (t0) REVERT: n 145 LYS cc_start: 0.8922 (OUTLIER) cc_final: 0.8439 (mtmm) REVERT: n 156 LYS cc_start: 0.8862 (mttt) cc_final: 0.8449 (mtpt) REVERT: o 111 LYS cc_start: 0.8750 (mttt) cc_final: 0.8517 (tppt) REVERT: o 122 ASN cc_start: 0.8951 (m-40) cc_final: 0.8374 (m110) REVERT: o 129 GLN cc_start: 0.7912 (tp-100) cc_final: 0.7669 (tp-100) REVERT: o 141 MET cc_start: 0.9274 (mmm) cc_final: 0.8993 (mmm) REVERT: p 103 ASN cc_start: 0.8709 (OUTLIER) cc_final: 0.8442 (p0) REVERT: p 119 ASN cc_start: 0.8039 (OUTLIER) cc_final: 0.7327 (p0) REVERT: p 124 GLU cc_start: 0.8566 (tp30) cc_final: 0.8316 (pt0) REVERT: p 174 ASP cc_start: 0.8140 (m-30) cc_final: 0.7622 (m-30) REVERT: p 186 SER cc_start: 0.8376 (m) cc_final: 0.8054 (p) outliers start: 199 outliers final: 128 residues processed: 1010 average time/residue: 0.6654 time to fit residues: 1113.2803 Evaluate side-chains 968 residues out of total 4072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 154 poor density : 814 time to evaluate : 4.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 61 ILE Chi-restraints excluded: chain B residue 115 ILE Chi-restraints excluded: chain B residue 161 CYS Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 246 ARG Chi-restraints excluded: chain B residue 270 TYR Chi-restraints excluded: chain C residue 71 LEU Chi-restraints excluded: chain C residue 73 THR Chi-restraints excluded: chain C residue 77 ASP Chi-restraints excluded: chain C residue 115 ASN Chi-restraints excluded: chain C residue 130 HIS Chi-restraints excluded: chain C residue 138 TYR Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 132 ILE Chi-restraints excluded: chain E residue 145 ASN Chi-restraints excluded: chain E residue 146 ILE Chi-restraints excluded: chain E residue 217 ASP Chi-restraints excluded: chain E residue 227 ASN Chi-restraints excluded: chain E residue 239 ARG Chi-restraints excluded: chain E residue 242 ARG Chi-restraints excluded: chain E residue 245 VAL Chi-restraints excluded: chain E residue 276 VAL Chi-restraints excluded: chain E residue 297 LYS Chi-restraints excluded: chain E residue 336 VAL Chi-restraints excluded: chain E residue 340 VAL Chi-restraints excluded: chain E residue 370 VAL Chi-restraints excluded: chain F residue 46 MET Chi-restraints excluded: chain F residue 67 ASP Chi-restraints excluded: chain F residue 86 ILE Chi-restraints excluded: chain F residue 88 VAL Chi-restraints excluded: chain F residue 89 ILE Chi-restraints excluded: chain F residue 92 ASN Chi-restraints excluded: chain G residue 40 GLU Chi-restraints excluded: chain G residue 84 SER Chi-restraints excluded: chain G residue 98 MET Chi-restraints excluded: chain G residue 109 SER Chi-restraints excluded: chain G residue 153 GLU Chi-restraints excluded: chain G residue 155 VAL Chi-restraints excluded: chain G residue 205 LEU Chi-restraints excluded: chain G residue 219 VAL Chi-restraints excluded: chain G residue 220 ILE Chi-restraints excluded: chain I residue 70 THR Chi-restraints excluded: chain I residue 79 GLU Chi-restraints excluded: chain I residue 104 ILE Chi-restraints excluded: chain I residue 175 HIS Chi-restraints excluded: chain I residue 201 LEU Chi-restraints excluded: chain I residue 216 ASP Chi-restraints excluded: chain I residue 308 THR Chi-restraints excluded: chain I residue 331 CYS Chi-restraints excluded: chain I residue 377 VAL Chi-restraints excluded: chain J residue 81 LYS Chi-restraints excluded: chain J residue 106 ILE Chi-restraints excluded: chain J residue 115 ILE Chi-restraints excluded: chain J residue 123 SER Chi-restraints excluded: chain J residue 160 ILE Chi-restraints excluded: chain J residue 170 MET Chi-restraints excluded: chain J residue 172 VAL Chi-restraints excluded: chain K residue 65 TYR Chi-restraints excluded: chain K residue 81 LYS Chi-restraints excluded: chain K residue 98 GLN Chi-restraints excluded: chain K residue 142 THR Chi-restraints excluded: chain K residue 146 VAL Chi-restraints excluded: chain K residue 152 VAL Chi-restraints excluded: chain K residue 161 LEU Chi-restraints excluded: chain K residue 169 MET Chi-restraints excluded: chain K residue 178 THR Chi-restraints excluded: chain K residue 196 LEU Chi-restraints excluded: chain L residue 32 THR Chi-restraints excluded: chain L residue 59 LYS Chi-restraints excluded: chain L residue 105 HIS Chi-restraints excluded: chain N residue 37 ASP Chi-restraints excluded: chain N residue 54 ILE Chi-restraints excluded: chain N residue 56 SER Chi-restraints excluded: chain N residue 74 GLU Chi-restraints excluded: chain N residue 121 SER Chi-restraints excluded: chain O residue 72 MET Chi-restraints excluded: chain O residue 171 LEU Chi-restraints excluded: chain O residue 205 VAL Chi-restraints excluded: chain P residue 83 LEU Chi-restraints excluded: chain P residue 110 LEU Chi-restraints excluded: chain Q residue 59 THR Chi-restraints excluded: chain R residue 69 CYS Chi-restraints excluded: chain R residue 117 ILE Chi-restraints excluded: chain U residue 8 ILE Chi-restraints excluded: chain U residue 60 CYS Chi-restraints excluded: chain a residue 66 LYS Chi-restraints excluded: chain a residue 89 ILE Chi-restraints excluded: chain a residue 160 ILE Chi-restraints excluded: chain a residue 172 VAL Chi-restraints excluded: chain a residue 250 GLU Chi-restraints excluded: chain a residue 254 LYS Chi-restraints excluded: chain b residue 6 LEU Chi-restraints excluded: chain b residue 94 SER Chi-restraints excluded: chain c residue 25 ASP Chi-restraints excluded: chain c residue 106 LEU Chi-restraints excluded: chain c residue 109 ASN Chi-restraints excluded: chain c residue 114 GLU Chi-restraints excluded: chain c residue 123 LEU Chi-restraints excluded: chain d residue 191 ILE Chi-restraints excluded: chain f residue 85 LEU Chi-restraints excluded: chain f residue 123 CYS Chi-restraints excluded: chain f residue 139 THR Chi-restraints excluded: chain f residue 142 ARG Chi-restraints excluded: chain f residue 155 LEU Chi-restraints excluded: chain f residue 160 ASP Chi-restraints excluded: chain f residue 162 THR Chi-restraints excluded: chain f residue 169 VAL Chi-restraints excluded: chain g residue 142 HIS Chi-restraints excluded: chain g residue 150 LEU Chi-restraints excluded: chain g residue 178 ASP Chi-restraints excluded: chain g residue 265 ASN Chi-restraints excluded: chain g residue 296 VAL Chi-restraints excluded: chain g residue 337 ASP Chi-restraints excluded: chain g residue 380 LEU Chi-restraints excluded: chain h residue 298 LYS Chi-restraints excluded: chain h residue 302 LEU Chi-restraints excluded: chain h residue 329 TYR Chi-restraints excluded: chain h residue 387 ASN Chi-restraints excluded: chain i residue 79 ARG Chi-restraints excluded: chain j residue 14 LEU Chi-restraints excluded: chain j residue 97 LEU Chi-restraints excluded: chain j residue 101 ARG Chi-restraints excluded: chain j residue 124 THR Chi-restraints excluded: chain j residue 136 TYR Chi-restraints excluded: chain j residue 150 PHE Chi-restraints excluded: chain j residue 164 VAL Chi-restraints excluded: chain j residue 198 ILE Chi-restraints excluded: chain j residue 199 ASP Chi-restraints excluded: chain k residue 71 VAL Chi-restraints excluded: chain k residue 79 LYS Chi-restraints excluded: chain k residue 117 THR Chi-restraints excluded: chain k residue 165 ILE Chi-restraints excluded: chain k residue 166 ARG Chi-restraints excluded: chain k residue 185 ASP Chi-restraints excluded: chain k residue 216 LEU Chi-restraints excluded: chain k residue 226 TYR Chi-restraints excluded: chain k residue 231 LEU Chi-restraints excluded: chain k residue 254 ILE Chi-restraints excluded: chain k residue 288 THR Chi-restraints excluded: chain k residue 292 GLU Chi-restraints excluded: chain m residue 33 VAL Chi-restraints excluded: chain m residue 46 ILE Chi-restraints excluded: chain m residue 99 LEU Chi-restraints excluded: chain n residue 145 LYS Chi-restraints excluded: chain o residue 64 THR Chi-restraints excluded: chain o residue 96 ILE Chi-restraints excluded: chain o residue 134 GLU Chi-restraints excluded: chain p residue 73 VAL Chi-restraints excluded: chain p residue 103 ASN Chi-restraints excluded: chain p residue 108 CYS Chi-restraints excluded: chain p residue 119 ASN Chi-restraints excluded: chain p residue 177 PHE Chi-restraints excluded: chain p residue 197 ASP Chi-restraints excluded: chain p residue 199 TRP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 596 random chunks: chunk 522 optimal weight: 3.9990 chunk 550 optimal weight: 10.0000 chunk 502 optimal weight: 3.9990 chunk 535 optimal weight: 0.0770 chunk 322 optimal weight: 3.9990 chunk 233 optimal weight: 5.9990 chunk 420 optimal weight: 40.0000 chunk 164 optimal weight: 2.9990 chunk 483 optimal weight: 20.0000 chunk 506 optimal weight: 0.7980 chunk 533 optimal weight: 1.9990 overall best weight: 1.9744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 215 ASN B 273 GLN ** E 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 72 GLN ** G 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 57 GLN N 119 GLN ** a 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 139 HIS ** i 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 112 ASN ** k 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 moved from start: 0.5059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 69632 Z= 0.209 Angle : 1.363 14.834 98901 Z= 0.872 Chirality : 0.036 0.381 11258 Planarity : 0.015 0.124 8814 Dihedral : 22.479 179.371 22895 Min Nonbonded Distance : 1.861 Molprobity Statistics. All-atom Clashscore : 14.59 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.35 % Favored : 95.61 % Rotamer: Outliers : 4.32 % Allowed : 25.76 % Favored : 69.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.39 % Cis-general : 0.00 % 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: 0.24 (0.12), residues: 4599 helix: 1.15 (0.12), residues: 1945 sheet: -0.33 (0.23), residues: 503 loop : -0.59 (0.13), residues: 2151 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRP p 202 HIS 0.025 0.001 HIS L 105 PHE 0.020 0.001 PHE N 111 TYR 0.026 0.002 TYR d 63 ARG 0.010 0.000 ARG L 89 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9198 Ramachandran restraints generated. 4599 Oldfield, 0 Emsley, 4599 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9198 Ramachandran restraints generated. 4599 Oldfield, 0 Emsley, 4599 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1003 residues out of total 4072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 176 poor density : 827 time to evaluate : 4.142 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 58 ARG cc_start: 0.8138 (mmt90) cc_final: 0.7541 (mmt90) REVERT: B 87 ARG cc_start: 0.8381 (OUTLIER) cc_final: 0.8027 (mtt180) REVERT: B 115 ILE cc_start: 0.8798 (OUTLIER) cc_final: 0.8435 (mm) REVERT: B 163 GLU cc_start: 0.7785 (mm-30) cc_final: 0.7409 (mm-30) REVERT: B 246 ARG cc_start: 0.8965 (OUTLIER) cc_final: 0.8157 (mtp85) REVERT: C 79 GLU cc_start: 0.8520 (mp0) cc_final: 0.8112 (mp0) REVERT: C 89 ASP cc_start: 0.8578 (t0) cc_final: 0.8261 (t0) REVERT: C 140 GLU cc_start: 0.9329 (tm-30) cc_final: 0.9107 (tm-30) REVERT: E 149 MET cc_start: 0.7380 (mmm) cc_final: 0.7006 (mmm) REVERT: E 172 MET cc_start: 0.8299 (mmp) cc_final: 0.7472 (mtt) REVERT: E 184 LYS cc_start: 0.7760 (mmtt) cc_final: 0.7208 (pttm) REVERT: E 417 MET cc_start: 0.8046 (mmm) cc_final: 0.7443 (tpp) REVERT: G 113 GLN cc_start: 0.8397 (mt0) cc_final: 0.8062 (mt0) REVERT: G 126 TYR cc_start: 0.8291 (t80) cc_final: 0.7383 (t80) REVERT: G 134 GLN cc_start: 0.8083 (mt0) cc_final: 0.7555 (mt0) REVERT: G 147 GLN cc_start: 0.7752 (tp40) cc_final: 0.7257 (tp40) REVERT: G 201 MET cc_start: 0.8735 (tpt) cc_final: 0.8324 (tpt) REVERT: G 205 LEU cc_start: 0.9460 (OUTLIER) cc_final: 0.9111 (tt) REVERT: G 220 ILE cc_start: 0.9272 (OUTLIER) cc_final: 0.8973 (mm) REVERT: I 162 MET cc_start: 0.8748 (mmm) cc_final: 0.8475 (mmm) REVERT: I 209 MET cc_start: 0.8086 (ttp) cc_final: 0.7611 (mtp) REVERT: I 308 THR cc_start: 0.8372 (m) cc_final: 0.7961 (t) REVERT: I 349 MET cc_start: 0.9036 (ttm) cc_final: 0.8624 (ttp) REVERT: J 100 LYS cc_start: 0.8784 (mmmt) cc_final: 0.8576 (mmtm) REVERT: K 73 ASN cc_start: 0.8061 (t0) cc_final: 0.7544 (p0) REVERT: K 76 ARG cc_start: 0.8850 (mmt-90) cc_final: 0.8158 (mpt180) REVERT: K 165 LYS cc_start: 0.8441 (tttt) cc_final: 0.7922 (ttmm) REVERT: L 134 HIS cc_start: 0.7225 (m90) cc_final: 0.6917 (m-70) REVERT: N 65 LYS cc_start: 0.8724 (mttt) cc_final: 0.8418 (tttm) REVERT: N 70 VAL cc_start: 0.8413 (m) cc_final: 0.8049 (p) REVERT: O 72 MET cc_start: 0.8830 (OUTLIER) cc_final: 0.8130 (tpp) REVERT: O 88 ASP cc_start: 0.7922 (m-30) cc_final: 0.7610 (p0) REVERT: O 112 LEU cc_start: 0.8923 (tp) cc_final: 0.8688 (mt) REVERT: O 162 ASP cc_start: 0.7499 (t0) cc_final: 0.7100 (t0) REVERT: P 74 ARG cc_start: 0.8324 (ptt90) cc_final: 0.7882 (ptt90) REVERT: Q 59 THR cc_start: 0.8636 (OUTLIER) cc_final: 0.8098 (p) REVERT: R 49 GLU cc_start: 0.8471 (mm-30) cc_final: 0.8196 (mp0) REVERT: R 60 LYS cc_start: 0.8121 (tppt) cc_final: 0.7591 (tttm) REVERT: R 85 ILE cc_start: 0.9145 (tt) cc_final: 0.8789 (pt) REVERT: U 8 ILE cc_start: 0.9218 (OUTLIER) cc_final: 0.8948 (mt) REVERT: a 152 THR cc_start: 0.7835 (p) cc_final: 0.7564 (p) REVERT: b 6 LEU cc_start: 0.8733 (OUTLIER) cc_final: 0.8306 (mt) REVERT: b 87 LEU cc_start: 0.8066 (mp) cc_final: 0.7720 (tt) REVERT: b 99 PHE cc_start: 0.8556 (t80) cc_final: 0.8051 (t80) REVERT: b 133 ARG cc_start: 0.6692 (mpt180) cc_final: 0.6261 (mpt180) REVERT: b 134 ARG cc_start: 0.8037 (ttt180) cc_final: 0.7242 (ptm-80) REVERT: c 71 THR cc_start: 0.9282 (m) cc_final: 0.8830 (p) REVERT: c 106 LEU cc_start: 0.9352 (OUTLIER) cc_final: 0.8942 (pp) REVERT: c 132 ARG cc_start: 0.9297 (mmm-85) cc_final: 0.8762 (mmt-90) REVERT: d 106 MET cc_start: 0.8661 (mmt) cc_final: 0.8445 (mmt) REVERT: d 153 LYS cc_start: 0.9029 (mmmm) cc_final: 0.8710 (mmmm) REVERT: d 192 THR cc_start: 0.8757 (m) cc_final: 0.8421 (p) REVERT: f 85 LEU cc_start: 0.9190 (OUTLIER) cc_final: 0.8726 (tt) REVERT: f 131 ASP cc_start: 0.6431 (p0) cc_final: 0.5654 (p0) REVERT: f 134 LYS cc_start: 0.8767 (mtpt) cc_final: 0.8433 (mtmm) REVERT: g 207 TYR cc_start: 0.6318 (m-80) cc_final: 0.5711 (m-10) REVERT: g 277 ASP cc_start: 0.7651 (m-30) cc_final: 0.7191 (p0) REVERT: g 319 ARG cc_start: 0.7493 (tmt170) cc_final: 0.7271 (tmt170) REVERT: h 328 LYS cc_start: 0.8991 (mttt) cc_final: 0.8719 (mttp) REVERT: h 360 GLN cc_start: 0.9059 (mt0) cc_final: 0.8687 (mp10) REVERT: h 380 LYS cc_start: 0.7559 (pttt) cc_final: 0.7314 (mttm) REVERT: i 79 ARG cc_start: 0.8277 (OUTLIER) cc_final: 0.7367 (mtt-85) REVERT: j 52 MET cc_start: 0.7865 (ttm) cc_final: 0.7459 (tmm) REVERT: j 88 GLN cc_start: 0.8159 (tt0) cc_final: 0.7840 (tt0) REVERT: j 144 LYS cc_start: 0.8362 (mttt) cc_final: 0.7834 (mttp) REVERT: j 150 PHE cc_start: 0.7315 (OUTLIER) cc_final: 0.6051 (m-10) REVERT: j 187 GLU cc_start: 0.9006 (OUTLIER) cc_final: 0.8692 (pm20) REVERT: j 198 ILE cc_start: 0.7377 (OUTLIER) cc_final: 0.7000 (mm) REVERT: k 193 ILE cc_start: 0.8928 (tt) cc_final: 0.8581 (pt) REVERT: k 199 ARG cc_start: 0.8308 (mtt-85) cc_final: 0.8025 (mtt-85) REVERT: k 223 TYR cc_start: 0.8405 (t80) cc_final: 0.8133 (t80) REVERT: m 56 TRP cc_start: 0.8494 (m-10) cc_final: 0.8199 (m-10) REVERT: m 60 GLU cc_start: 0.8318 (tt0) cc_final: 0.8094 (pt0) REVERT: m 72 ASP cc_start: 0.8343 (m-30) cc_final: 0.7948 (t0) REVERT: m 90 GLN cc_start: 0.8286 (tt0) cc_final: 0.7666 (tt0) REVERT: n 145 LYS cc_start: 0.8910 (OUTLIER) cc_final: 0.8491 (mtmm) REVERT: n 156 LYS cc_start: 0.8969 (mttt) cc_final: 0.8591 (mtpt) REVERT: o 111 LYS cc_start: 0.8749 (mttt) cc_final: 0.8519 (tppt) REVERT: o 122 ASN cc_start: 0.8973 (m-40) cc_final: 0.8396 (m110) REVERT: o 129 GLN cc_start: 0.7977 (tp-100) cc_final: 0.7732 (tp-100) REVERT: o 141 MET cc_start: 0.9264 (mmm) cc_final: 0.8949 (mmm) REVERT: p 103 ASN cc_start: 0.8718 (OUTLIER) cc_final: 0.8452 (p0) REVERT: p 119 ASN cc_start: 0.8037 (OUTLIER) cc_final: 0.7355 (p0) REVERT: p 124 GLU cc_start: 0.8585 (tp30) cc_final: 0.8363 (pt0) REVERT: p 174 ASP cc_start: 0.8135 (m-30) cc_final: 0.7562 (m-30) REVERT: p 186 SER cc_start: 0.8381 (m) cc_final: 0.8041 (p) outliers start: 176 outliers final: 132 residues processed: 941 average time/residue: 0.6610 time to fit residues: 1030.9829 Evaluate side-chains 954 residues out of total 4072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 150 poor density : 804 time to evaluate : 4.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 61 ILE Chi-restraints excluded: chain B residue 87 ARG Chi-restraints excluded: chain B residue 115 ILE Chi-restraints excluded: chain B residue 147 HIS Chi-restraints excluded: chain B residue 161 CYS Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 246 ARG Chi-restraints excluded: chain B residue 270 TYR Chi-restraints excluded: chain C residue 71 LEU Chi-restraints excluded: chain C residue 73 THR Chi-restraints excluded: chain C residue 115 ASN Chi-restraints excluded: chain C residue 130 HIS Chi-restraints excluded: chain C residue 135 LEU Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 132 ILE Chi-restraints excluded: chain E residue 145 ASN Chi-restraints excluded: chain E residue 146 ILE Chi-restraints excluded: chain E residue 217 ASP Chi-restraints excluded: chain E residue 239 ARG Chi-restraints excluded: chain E residue 242 ARG Chi-restraints excluded: chain E residue 245 VAL Chi-restraints excluded: chain E residue 276 VAL Chi-restraints excluded: chain E residue 297 LYS Chi-restraints excluded: chain E residue 331 ASP Chi-restraints excluded: chain E residue 336 VAL Chi-restraints excluded: chain E residue 340 VAL Chi-restraints excluded: chain E residue 354 SER Chi-restraints excluded: chain E residue 370 VAL Chi-restraints excluded: chain E residue 409 GLU Chi-restraints excluded: chain F residue 8 LEU Chi-restraints excluded: chain F residue 25 THR Chi-restraints excluded: chain F residue 39 LEU Chi-restraints excluded: chain F residue 46 MET Chi-restraints excluded: chain F residue 67 ASP Chi-restraints excluded: chain F residue 86 ILE Chi-restraints excluded: chain F residue 88 VAL Chi-restraints excluded: chain F residue 89 ILE Chi-restraints excluded: chain G residue 98 MET Chi-restraints excluded: chain G residue 109 SER Chi-restraints excluded: chain G residue 205 LEU Chi-restraints excluded: chain G residue 219 VAL Chi-restraints excluded: chain G residue 220 ILE Chi-restraints excluded: chain I residue 70 THR Chi-restraints excluded: chain I residue 100 THR Chi-restraints excluded: chain I residue 104 ILE Chi-restraints excluded: chain I residue 175 HIS Chi-restraints excluded: chain I residue 201 LEU Chi-restraints excluded: chain I residue 216 ASP Chi-restraints excluded: chain I residue 331 CYS Chi-restraints excluded: chain I residue 377 VAL Chi-restraints excluded: chain J residue 106 ILE Chi-restraints excluded: chain J residue 115 ILE Chi-restraints excluded: chain J residue 123 SER Chi-restraints excluded: chain J residue 132 VAL Chi-restraints excluded: chain J residue 160 ILE Chi-restraints excluded: chain J residue 170 MET Chi-restraints excluded: chain J residue 172 VAL Chi-restraints excluded: chain K residue 65 TYR Chi-restraints excluded: chain K residue 98 GLN Chi-restraints excluded: chain K residue 142 THR Chi-restraints excluded: chain K residue 146 VAL Chi-restraints excluded: chain K residue 152 VAL Chi-restraints excluded: chain K residue 161 LEU Chi-restraints excluded: chain K residue 169 MET Chi-restraints excluded: chain K residue 178 THR Chi-restraints excluded: chain K residue 196 LEU Chi-restraints excluded: chain L residue 32 THR Chi-restraints excluded: chain L residue 57 GLN Chi-restraints excluded: chain L residue 59 LYS Chi-restraints excluded: chain N residue 56 SER Chi-restraints excluded: chain N residue 74 GLU Chi-restraints excluded: chain N residue 109 ILE Chi-restraints excluded: chain N residue 121 SER Chi-restraints excluded: chain O residue 72 MET Chi-restraints excluded: chain O residue 171 LEU Chi-restraints excluded: chain P residue 83 LEU Chi-restraints excluded: chain P residue 84 SER Chi-restraints excluded: chain Q residue 59 THR Chi-restraints excluded: chain R residue 69 CYS Chi-restraints excluded: chain R residue 108 ILE Chi-restraints excluded: chain R residue 117 ILE Chi-restraints excluded: chain U residue 8 ILE Chi-restraints excluded: chain a residue 105 MET Chi-restraints excluded: chain a residue 160 ILE Chi-restraints excluded: chain a residue 172 VAL Chi-restraints excluded: chain a residue 250 GLU Chi-restraints excluded: chain a residue 254 LYS Chi-restraints excluded: chain b residue 6 LEU Chi-restraints excluded: chain c residue 25 ASP Chi-restraints excluded: chain c residue 106 LEU Chi-restraints excluded: chain c residue 109 ASN Chi-restraints excluded: chain c residue 114 GLU Chi-restraints excluded: chain c residue 123 LEU Chi-restraints excluded: chain d residue 191 ILE Chi-restraints excluded: chain f residue 85 LEU Chi-restraints excluded: chain f residue 115 ILE Chi-restraints excluded: chain f residue 139 THR Chi-restraints excluded: chain f residue 142 ARG Chi-restraints excluded: chain f residue 155 LEU Chi-restraints excluded: chain f residue 160 ASP Chi-restraints excluded: chain f residue 162 THR Chi-restraints excluded: chain f residue 169 VAL Chi-restraints excluded: chain g residue 150 LEU Chi-restraints excluded: chain g residue 178 ASP Chi-restraints excluded: chain g residue 265 ASN Chi-restraints excluded: chain g residue 296 VAL Chi-restraints excluded: chain g residue 337 ASP Chi-restraints excluded: chain g residue 356 ILE Chi-restraints excluded: chain g residue 380 LEU Chi-restraints excluded: chain h residue 298 LYS Chi-restraints excluded: chain h residue 302 LEU Chi-restraints excluded: chain h residue 329 TYR Chi-restraints excluded: chain h residue 387 ASN Chi-restraints excluded: chain i residue 79 ARG Chi-restraints excluded: chain i residue 93 LYS Chi-restraints excluded: chain j residue 97 LEU Chi-restraints excluded: chain j residue 136 TYR Chi-restraints excluded: chain j residue 150 PHE Chi-restraints excluded: chain j residue 164 VAL Chi-restraints excluded: chain j residue 187 GLU Chi-restraints excluded: chain j residue 198 ILE Chi-restraints excluded: chain j residue 199 ASP Chi-restraints excluded: chain j residue 208 GLU Chi-restraints excluded: chain k residue 71 VAL Chi-restraints excluded: chain k residue 79 LYS Chi-restraints excluded: chain k residue 117 THR Chi-restraints excluded: chain k residue 165 ILE Chi-restraints excluded: chain k residue 166 ARG Chi-restraints excluded: chain k residue 180 SER Chi-restraints excluded: chain k residue 185 ASP Chi-restraints excluded: chain k residue 216 LEU Chi-restraints excluded: chain k residue 226 TYR Chi-restraints excluded: chain k residue 230 VAL Chi-restraints excluded: chain k residue 231 LEU Chi-restraints excluded: chain k residue 254 ILE Chi-restraints excluded: chain k residue 288 THR Chi-restraints excluded: chain k residue 292 GLU Chi-restraints excluded: chain m residue 33 VAL Chi-restraints excluded: chain m residue 46 ILE Chi-restraints excluded: chain m residue 99 LEU Chi-restraints excluded: chain n residue 145 LYS Chi-restraints excluded: chain o residue 57 VAL Chi-restraints excluded: chain o residue 64 THR Chi-restraints excluded: chain o residue 134 GLU Chi-restraints excluded: chain p residue 73 VAL Chi-restraints excluded: chain p residue 103 ASN Chi-restraints excluded: chain p residue 108 CYS Chi-restraints excluded: chain p residue 119 ASN Chi-restraints excluded: chain p residue 177 PHE Chi-restraints excluded: chain p residue 199 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 596 random chunks: chunk 351 optimal weight: 7.9990 chunk 566 optimal weight: 20.0000 chunk 345 optimal weight: 7.9990 chunk 268 optimal weight: 0.9980 chunk 393 optimal weight: 0.0870 chunk 593 optimal weight: 9.9990 chunk 546 optimal weight: 7.9990 chunk 472 optimal weight: 3.9990 chunk 49 optimal weight: 10.0000 chunk 365 optimal weight: 40.0000 chunk 289 optimal weight: 9.9990 overall best weight: 4.2164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 273 GLN ** E 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 72 GLN ** G 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 180 ASN L 57 GLN L 105 HIS O 224 GLN Q 44 ASN ** a 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 139 HIS ** i 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 112 ASN ** k 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8394 moved from start: 0.5126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 69632 Z= 0.302 Angle : 1.387 14.619 98901 Z= 0.880 Chirality : 0.038 0.381 11258 Planarity : 0.015 0.126 8814 Dihedral : 22.498 178.536 22889 Min Nonbonded Distance : 1.778 Molprobity Statistics. All-atom Clashscore : 16.22 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.76 % Favored : 95.19 % Rotamer: Outliers : 4.30 % Allowed : 26.01 % Favored : 69.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.39 % Cis-general : 0.00 % 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: 0.07 (0.12), residues: 4599 helix: 1.03 (0.12), residues: 1942 sheet: -0.38 (0.23), residues: 493 loop : -0.71 (0.13), residues: 2164 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP p 202 HIS 0.012 0.001 HIS I 176 PHE 0.018 0.002 PHE C 91 TYR 0.027 0.002 TYR d 63 ARG 0.011 0.001 ARG d 93 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9198 Ramachandran restraints generated. 4599 Oldfield, 0 Emsley, 4599 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9198 Ramachandran restraints generated. 4599 Oldfield, 0 Emsley, 4599 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 986 residues out of total 4072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 175 poor density : 811 time to evaluate : 4.223 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 58 ARG cc_start: 0.8145 (mmt90) cc_final: 0.7588 (mmt90) REVERT: B 87 ARG cc_start: 0.8536 (OUTLIER) cc_final: 0.8187 (mtt180) REVERT: B 115 ILE cc_start: 0.8842 (OUTLIER) cc_final: 0.8446 (mm) REVERT: B 246 ARG cc_start: 0.9017 (OUTLIER) cc_final: 0.8207 (mtp85) REVERT: C 89 ASP cc_start: 0.8672 (t0) cc_final: 0.8341 (t0) REVERT: C 157 THR cc_start: 0.8570 (m) cc_final: 0.8084 (p) REVERT: E 149 MET cc_start: 0.7651 (mmm) cc_final: 0.7301 (mmm) REVERT: E 183 ARG cc_start: 0.6686 (ttm170) cc_final: 0.6451 (ttm170) REVERT: E 184 LYS cc_start: 0.7871 (mmtt) cc_final: 0.7437 (pttm) REVERT: E 417 MET cc_start: 0.7940 (mmm) cc_final: 0.7291 (tpp) REVERT: G 53 LYS cc_start: 0.8050 (mttt) cc_final: 0.7346 (mmmt) REVERT: G 113 GLN cc_start: 0.8450 (mt0) cc_final: 0.8111 (mt0) REVERT: G 201 MET cc_start: 0.8740 (tpt) cc_final: 0.8265 (tpt) REVERT: G 205 LEU cc_start: 0.9489 (OUTLIER) cc_final: 0.9199 (tt) REVERT: G 220 ILE cc_start: 0.9302 (OUTLIER) cc_final: 0.9014 (mm) REVERT: I 162 MET cc_start: 0.8826 (mmm) cc_final: 0.8549 (mmm) REVERT: I 209 MET cc_start: 0.8162 (ttp) cc_final: 0.7678 (ttt) REVERT: I 308 THR cc_start: 0.8366 (m) cc_final: 0.7935 (t) REVERT: I 349 MET cc_start: 0.9138 (ttm) cc_final: 0.8757 (ttp) REVERT: K 68 ILE cc_start: 0.8294 (mt) cc_final: 0.7820 (pt) REVERT: K 73 ASN cc_start: 0.8126 (t0) cc_final: 0.7566 (p0) REVERT: K 76 ARG cc_start: 0.8931 (mmt-90) cc_final: 0.8326 (mpt180) REVERT: K 165 LYS cc_start: 0.8582 (tttt) cc_final: 0.8078 (ttmm) REVERT: L 134 HIS cc_start: 0.7109 (m90) cc_final: 0.6889 (m-70) REVERT: N 37 ASP cc_start: 0.7821 (OUTLIER) cc_final: 0.7511 (t70) REVERT: O 72 MET cc_start: 0.8830 (OUTLIER) cc_final: 0.8160 (tpp) REVERT: O 112 LEU cc_start: 0.8955 (tp) cc_final: 0.8703 (mt) REVERT: O 162 ASP cc_start: 0.7533 (t0) cc_final: 0.7129 (t0) REVERT: P 74 ARG cc_start: 0.8397 (ptt90) cc_final: 0.8087 (ptt90) REVERT: Q 59 THR cc_start: 0.8587 (OUTLIER) cc_final: 0.8023 (p) REVERT: R 49 GLU cc_start: 0.8485 (mm-30) cc_final: 0.8220 (mp0) REVERT: R 60 LYS cc_start: 0.8162 (tppt) cc_final: 0.7639 (tttm) REVERT: R 85 ILE cc_start: 0.9208 (tt) cc_final: 0.8874 (pt) REVERT: U 8 ILE cc_start: 0.9234 (OUTLIER) cc_final: 0.8961 (mt) REVERT: U 68 MET cc_start: 0.8727 (tpt) cc_final: 0.8117 (tpt) REVERT: U 85 GLN cc_start: 0.8793 (tm-30) cc_final: 0.8418 (tm-30) REVERT: a 152 THR cc_start: 0.7934 (p) cc_final: 0.7662 (p) REVERT: b 83 LYS cc_start: 0.7677 (tttm) cc_final: 0.7418 (tmtt) REVERT: b 134 ARG cc_start: 0.8091 (ttt180) cc_final: 0.7290 (ptm-80) REVERT: c 71 THR cc_start: 0.9347 (m) cc_final: 0.8888 (p) REVERT: c 106 LEU cc_start: 0.9337 (OUTLIER) cc_final: 0.8861 (pp) REVERT: c 132 ARG cc_start: 0.9336 (mmm-85) cc_final: 0.8766 (mmt-90) REVERT: d 106 MET cc_start: 0.8882 (mmt) cc_final: 0.8631 (mmt) REVERT: d 153 LYS cc_start: 0.8994 (mmmm) cc_final: 0.8744 (mmmm) REVERT: d 192 THR cc_start: 0.8817 (m) cc_final: 0.8433 (p) REVERT: f 85 LEU cc_start: 0.9219 (OUTLIER) cc_final: 0.8682 (tt) REVERT: g 207 TYR cc_start: 0.6139 (m-80) cc_final: 0.5534 (m-10) REVERT: g 277 ASP cc_start: 0.7723 (m-30) cc_final: 0.7252 (p0) REVERT: g 297 LYS cc_start: 0.7993 (mmmt) cc_final: 0.7749 (mmmt) REVERT: g 319 ARG cc_start: 0.7636 (tmt170) cc_final: 0.7353 (tmt170) REVERT: g 323 LEU cc_start: 0.7903 (mt) cc_final: 0.7496 (mp) REVERT: h 371 TYR cc_start: 0.8351 (t80) cc_final: 0.8035 (t80) REVERT: h 380 LYS cc_start: 0.7658 (pttt) cc_final: 0.7342 (mttm) REVERT: i 79 ARG cc_start: 0.8309 (OUTLIER) cc_final: 0.7370 (mtt-85) REVERT: j 52 MET cc_start: 0.7831 (ttm) cc_final: 0.7432 (tmm) REVERT: j 88 GLN cc_start: 0.8164 (tt0) cc_final: 0.7824 (tt0) REVERT: j 144 LYS cc_start: 0.8377 (mttt) cc_final: 0.7194 (mmmm) REVERT: j 150 PHE cc_start: 0.7132 (OUTLIER) cc_final: 0.6247 (m-10) REVERT: j 187 GLU cc_start: 0.9086 (OUTLIER) cc_final: 0.8766 (pm20) REVERT: j 198 ILE cc_start: 0.7439 (OUTLIER) cc_final: 0.7063 (mm) REVERT: k 199 ARG cc_start: 0.8259 (mtt-85) cc_final: 0.7939 (mtt-85) REVERT: m 52 MET cc_start: 0.8703 (ttm) cc_final: 0.8441 (ttp) REVERT: m 56 TRP cc_start: 0.8619 (m-10) cc_final: 0.8367 (m-10) REVERT: m 72 ASP cc_start: 0.8343 (m-30) cc_final: 0.7942 (t0) REVERT: m 90 GLN cc_start: 0.8340 (tt0) cc_final: 0.7708 (tt0) REVERT: n 145 LYS cc_start: 0.8877 (OUTLIER) cc_final: 0.8436 (mtmm) REVERT: n 156 LYS cc_start: 0.9006 (mttt) cc_final: 0.8628 (mtpt) REVERT: o 111 LYS cc_start: 0.8785 (mttt) cc_final: 0.8505 (tppt) REVERT: o 122 ASN cc_start: 0.8996 (m-40) cc_final: 0.8443 (m110) REVERT: o 129 GLN cc_start: 0.7916 (tp-100) cc_final: 0.7651 (tp-100) REVERT: o 141 MET cc_start: 0.9262 (mmm) cc_final: 0.8941 (mmm) REVERT: p 119 ASN cc_start: 0.8501 (OUTLIER) cc_final: 0.7829 (p0) REVERT: p 124 GLU cc_start: 0.8650 (tp30) cc_final: 0.8414 (pt0) REVERT: p 174 ASP cc_start: 0.8130 (m-30) cc_final: 0.7558 (m-30) REVERT: p 186 SER cc_start: 0.8447 (m) cc_final: 0.8129 (p) outliers start: 175 outliers final: 143 residues processed: 925 average time/residue: 0.6704 time to fit residues: 1027.2369 Evaluate side-chains 956 residues out of total 4072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 160 poor density : 796 time to evaluate : 4.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 61 ILE Chi-restraints excluded: chain B residue 87 ARG Chi-restraints excluded: chain B residue 108 SER Chi-restraints excluded: chain B residue 115 ILE Chi-restraints excluded: chain B residue 147 HIS Chi-restraints excluded: chain B residue 161 CYS Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 246 ARG Chi-restraints excluded: chain B residue 270 TYR Chi-restraints excluded: chain C residue 71 LEU Chi-restraints excluded: chain C residue 73 THR Chi-restraints excluded: chain C residue 115 ASN Chi-restraints excluded: chain C residue 130 HIS Chi-restraints excluded: chain C residue 135 LEU Chi-restraints excluded: chain C residue 138 TYR Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 132 ILE Chi-restraints excluded: chain E residue 145 ASN Chi-restraints excluded: chain E residue 146 ILE Chi-restraints excluded: chain E residue 217 ASP Chi-restraints excluded: chain E residue 239 ARG Chi-restraints excluded: chain E residue 242 ARG Chi-restraints excluded: chain E residue 245 VAL Chi-restraints excluded: chain E residue 276 VAL Chi-restraints excluded: chain E residue 297 LYS Chi-restraints excluded: chain E residue 331 ASP Chi-restraints excluded: chain E residue 336 VAL Chi-restraints excluded: chain E residue 340 VAL Chi-restraints excluded: chain E residue 354 SER Chi-restraints excluded: chain E residue 370 VAL Chi-restraints excluded: chain E residue 409 GLU Chi-restraints excluded: chain F residue 8 LEU Chi-restraints excluded: chain F residue 25 THR Chi-restraints excluded: chain F residue 39 LEU Chi-restraints excluded: chain F residue 46 MET Chi-restraints excluded: chain F residue 67 ASP Chi-restraints excluded: chain F residue 86 ILE Chi-restraints excluded: chain F residue 88 VAL Chi-restraints excluded: chain F residue 89 ILE Chi-restraints excluded: chain G residue 83 SER Chi-restraints excluded: chain G residue 84 SER Chi-restraints excluded: chain G residue 98 MET Chi-restraints excluded: chain G residue 109 SER Chi-restraints excluded: chain G residue 153 GLU Chi-restraints excluded: chain G residue 205 LEU Chi-restraints excluded: chain G residue 219 VAL Chi-restraints excluded: chain G residue 220 ILE Chi-restraints excluded: chain I residue 70 THR Chi-restraints excluded: chain I residue 100 THR Chi-restraints excluded: chain I residue 104 ILE Chi-restraints excluded: chain I residue 175 HIS Chi-restraints excluded: chain I residue 201 LEU Chi-restraints excluded: chain I residue 202 ILE Chi-restraints excluded: chain I residue 216 ASP Chi-restraints excluded: chain I residue 331 CYS Chi-restraints excluded: chain I residue 377 VAL Chi-restraints excluded: chain I residue 393 THR Chi-restraints excluded: chain J residue 115 ILE Chi-restraints excluded: chain J residue 123 SER Chi-restraints excluded: chain J residue 132 VAL Chi-restraints excluded: chain J residue 160 ILE Chi-restraints excluded: chain J residue 170 MET Chi-restraints excluded: chain J residue 172 VAL Chi-restraints excluded: chain K residue 65 TYR Chi-restraints excluded: chain K residue 98 GLN Chi-restraints excluded: chain K residue 142 THR Chi-restraints excluded: chain K residue 146 VAL Chi-restraints excluded: chain K residue 152 VAL Chi-restraints excluded: chain K residue 161 LEU Chi-restraints excluded: chain K residue 169 MET Chi-restraints excluded: chain K residue 178 THR Chi-restraints excluded: chain K residue 180 ASN Chi-restraints excluded: chain K residue 196 LEU Chi-restraints excluded: chain L residue 32 THR Chi-restraints excluded: chain L residue 57 GLN Chi-restraints excluded: chain N residue 37 ASP Chi-restraints excluded: chain N residue 56 SER Chi-restraints excluded: chain N residue 74 GLU Chi-restraints excluded: chain N residue 107 SER Chi-restraints excluded: chain N residue 109 ILE Chi-restraints excluded: chain N residue 121 SER Chi-restraints excluded: chain O residue 72 MET Chi-restraints excluded: chain P residue 44 ASP Chi-restraints excluded: chain P residue 83 LEU Chi-restraints excluded: chain P residue 84 SER Chi-restraints excluded: chain Q residue 59 THR Chi-restraints excluded: chain R residue 69 CYS Chi-restraints excluded: chain R residue 117 ILE Chi-restraints excluded: chain U residue 8 ILE Chi-restraints excluded: chain a residue 105 MET Chi-restraints excluded: chain a residue 160 ILE Chi-restraints excluded: chain a residue 172 VAL Chi-restraints excluded: chain a residue 238 SER Chi-restraints excluded: chain a residue 250 GLU Chi-restraints excluded: chain a residue 254 LYS Chi-restraints excluded: chain b residue 12 ILE Chi-restraints excluded: chain c residue 25 ASP Chi-restraints excluded: chain c residue 106 LEU Chi-restraints excluded: chain c residue 109 ASN Chi-restraints excluded: chain c residue 114 GLU Chi-restraints excluded: chain d residue 191 ILE Chi-restraints excluded: chain f residue 85 LEU Chi-restraints excluded: chain f residue 113 LEU Chi-restraints excluded: chain f residue 115 ILE Chi-restraints excluded: chain f residue 139 THR Chi-restraints excluded: chain f residue 142 ARG Chi-restraints excluded: chain f residue 155 LEU Chi-restraints excluded: chain f residue 160 ASP Chi-restraints excluded: chain f residue 162 THR Chi-restraints excluded: chain f residue 169 VAL Chi-restraints excluded: chain g residue 150 LEU Chi-restraints excluded: chain g residue 178 ASP Chi-restraints excluded: chain g residue 265 ASN Chi-restraints excluded: chain g residue 296 VAL Chi-restraints excluded: chain g residue 337 ASP Chi-restraints excluded: chain g residue 356 ILE Chi-restraints excluded: chain g residue 380 LEU Chi-restraints excluded: chain h residue 298 LYS Chi-restraints excluded: chain h residue 302 LEU Chi-restraints excluded: chain h residue 329 TYR Chi-restraints excluded: chain h residue 387 ASN Chi-restraints excluded: chain i residue 79 ARG Chi-restraints excluded: chain i residue 93 LYS Chi-restraints excluded: chain j residue 16 ARG Chi-restraints excluded: chain j residue 97 LEU Chi-restraints excluded: chain j residue 136 TYR Chi-restraints excluded: chain j residue 150 PHE Chi-restraints excluded: chain j residue 164 VAL Chi-restraints excluded: chain j residue 187 GLU Chi-restraints excluded: chain j residue 198 ILE Chi-restraints excluded: chain j residue 199 ASP Chi-restraints excluded: chain k residue 71 VAL Chi-restraints excluded: chain k residue 79 LYS Chi-restraints excluded: chain k residue 117 THR Chi-restraints excluded: chain k residue 165 ILE Chi-restraints excluded: chain k residue 166 ARG Chi-restraints excluded: chain k residue 180 SER Chi-restraints excluded: chain k residue 185 ASP Chi-restraints excluded: chain k residue 198 ASP Chi-restraints excluded: chain k residue 216 LEU Chi-restraints excluded: chain k residue 226 TYR Chi-restraints excluded: chain k residue 230 VAL Chi-restraints excluded: chain k residue 231 LEU Chi-restraints excluded: chain k residue 254 ILE Chi-restraints excluded: chain k residue 288 THR Chi-restraints excluded: chain k residue 292 GLU Chi-restraints excluded: chain m residue 33 VAL Chi-restraints excluded: chain m residue 46 ILE Chi-restraints excluded: chain m residue 99 LEU Chi-restraints excluded: chain n residue 145 LYS Chi-restraints excluded: chain o residue 64 THR Chi-restraints excluded: chain o residue 78 VAL Chi-restraints excluded: chain o residue 107 LEU Chi-restraints excluded: chain o residue 134 GLU Chi-restraints excluded: chain p residue 73 VAL Chi-restraints excluded: chain p residue 103 ASN Chi-restraints excluded: chain p residue 108 CYS Chi-restraints excluded: chain p residue 110 ASP Chi-restraints excluded: chain p residue 119 ASN Chi-restraints excluded: chain p residue 177 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 596 random chunks: chunk 375 optimal weight: 4.9990 chunk 503 optimal weight: 8.9990 chunk 144 optimal weight: 0.9990 chunk 435 optimal weight: 30.0000 chunk 69 optimal weight: 10.0000 chunk 131 optimal weight: 8.9990 chunk 473 optimal weight: 9.9990 chunk 198 optimal weight: 3.9990 chunk 486 optimal weight: 8.9990 chunk 59 optimal weight: 20.0000 chunk 87 optimal weight: 50.0000 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 273 GLN ** E 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 313 GLN ** J 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 180 ASN L 57 GLN N 119 GLN ** a 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 112 ASN ** k 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** p 65 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.116687 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.093399 restraints weight = 150388.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.092933 restraints weight = 145910.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.093677 restraints weight = 114345.452| |-----------------------------------------------------------------------------| r_work (final): 0.3310 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.5199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 69632 Z= 0.369 Angle : 1.406 14.535 98901 Z= 0.887 Chirality : 0.040 0.376 11258 Planarity : 0.015 0.128 8814 Dihedral : 22.552 177.792 22889 Min Nonbonded Distance : 1.749 Molprobity Statistics. All-atom Clashscore : 16.85 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.20 % Favored : 94.78 % Rotamer: Outliers : 4.57 % Allowed : 25.91 % Favored : 69.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.15 (0.12), residues: 4599 helix: 0.85 (0.12), residues: 1943 sheet: -0.55 (0.23), residues: 493 loop : -0.82 (0.13), residues: 2163 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP p 202 HIS 0.010 0.001 HIS I 176 PHE 0.032 0.002 PHE P 96 TYR 0.025 0.002 TYR a 241 ARG 0.011 0.001 ARG U 41 =============================================================================== Job complete usr+sys time: 17116.50 seconds wall clock time: 300 minutes 36.43 seconds (18036.43 seconds total)