Starting phenix.real_space_refine on Sun Sep 29 23:31:42 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zuo_11440/09_2024/6zuo_11440.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zuo_11440/09_2024/6zuo_11440.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zuo_11440/09_2024/6zuo_11440.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zuo_11440/09_2024/6zuo_11440.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zuo_11440/09_2024/6zuo_11440.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zuo_11440/09_2024/6zuo_11440.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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: 6 Type Number sf(0) Gaussians Zn 3 6.06 5 P 1665 5.49 5 S 185 5.16 5 C 42149 2.51 5 N 14159 2.21 5 O 18937 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 35 residue(s): 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 77098 Number of models: 1 Model: "" Number of chains: 38 Chain: "2" Number of atoms: 35550 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1665, 35550 Classifications: {'RNA': 1665} Modifications used: {'rna2p_pur': 129, 'rna2p_pyr': 110, 'rna3p_pur': 754, 'rna3p_pyr': 672} Link IDs: {'rna2p': 239, 'rna3p': 1425} Chain breaks: 11 Chain: "A" Number of atoms: 1705 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1705 Classifications: {'peptide': 216} Link IDs: {'PTRANS': 12, 'TRANS': 203} Chain: "B" Number of atoms: 1729 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1729 Classifications: {'peptide': 213} Link IDs: {'PTRANS': 5, 'TRANS': 207} Chain: "C" Number of atoms: 1690 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1690 Classifications: {'peptide': 218} Link IDs: {'PTRANS': 12, 'TRANS': 205} Chain: "D" Number of atoms: 1752 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1752 Classifications: {'peptide': 225} Link IDs: {'PTRANS': 11, 'TRANS': 213} Chain: "E" Number of atoms: 2076 Number of conformers: 1 Conformer: "" Number of residues, atoms: 262, 2076 Classifications: {'peptide': 262} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 247} Chain: "F" Number of atoms: 1495 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 1495 Classifications: {'peptide': 189} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 183} Chain: "G" Number of atoms: 1862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1862 Classifications: {'peptide': 230} Link IDs: {'PTRANS': 10, 'TRANS': 219} Chain: "H" Number of atoms: 1501 Number of conformers: 1 Conformer: "" Number of residues, atoms: 186, 1501 Classifications: {'peptide': 186} Link IDs: {'PTRANS': 9, 'TRANS': 176} Chain: "I" Number of atoms: 1682 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1682 Classifications: {'peptide': 205} Link IDs: {'PTRANS': 7, 'TRANS': 197} Chain: "J" Number of atoms: 1499 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 1499 Classifications: {'peptide': 180} Link IDs: {'PTRANS': 6, 'TRANS': 173} Chain: "K" Number of atoms: 800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 800 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 7, 'TRANS': 87} Chain: "L" Number of atoms: 1229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1229 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 6, 'TRANS': 144} Chain: "M" Number of atoms: 953 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 953 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 2, 'TRANS': 120} Chain: "N" Number of atoms: 1202 Number of conformers: 1 Conformer: "" Number of residues, atoms: 149, 1202 Classifications: {'peptide': 149} Link IDs: {'PTRANS': 8, 'TRANS': 140} Chain: "O" Number of atoms: 1009 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1009 Classifications: {'peptide': 135} Link IDs: {'PTRANS': 6, 'TRANS': 128} Chain: "P" Number of atoms: 984 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 984 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 7, 'TRANS': 112} Chain: "Q" Number of atoms: 1109 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1109 Classifications: {'peptide': 139} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 133} Chain: "R" Number of atoms: 990 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 990 Classifications: {'peptide': 122} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 116} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "S" Number of atoms: 1184 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1184 Classifications: {'peptide': 143} Link IDs: {'PTRANS': 3, 'TRANS': 139} Chain: "T" Number of atoms: 1122 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1122 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 4, 'TRANS': 139} Chain: "U" Number of atoms: 803 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 803 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 5, 'TRANS': 95} Chain: "V" Number of atoms: 625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 625 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 1, 'TRANS': 80} Chain: "W" Number of atoms: 1034 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1034 Classifications: {'peptide': 129} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 1, 'TRANS': 125} Chain: "X" Number of atoms: 1098 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1098 Classifications: {'peptide': 141} Link IDs: {'PTRANS': 5, 'TRANS': 135} Chain: "Y" Number of atoms: 1014 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 1014 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 4, 'TRANS': 119} Chain: "Z" Number of atoms: 574 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 574 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 2, 'TRANS': 69} Chain: "b" Number of atoms: 640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 640 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 5, 'TRANS': 76} Chain: "c" Number of atoms: 479 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 479 Classifications: {'peptide': 61} Link IDs: {'PTRANS': 1, 'TRANS': 59} Chain: "d" Number of atoms: 458 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 458 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 1, 'TRANS': 53} Chain: "e" Number of atoms: 442 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 442 Classifications: {'peptide': 56} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 52} Chain: "f" Number of atoms: 510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 510 Classifications: {'peptide': 63} Link IDs: {'PTRANS': 2, 'TRANS': 60} Chain: "g" Number of atoms: 2440 Number of conformers: 1 Conformer: "" Number of residues, atoms: 314, 2440 Classifications: {'peptide': 314} Link IDs: {'PTRANS': 10, 'TRANS': 303} Chain: "x" Number of atoms: 1365 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1365 Classifications: {'peptide': 175} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 7, 'TRANS': 167} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'GLU:plan': 3, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 18 Chain: "y" Number of atoms: 2490 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 2490 Classifications: {'peptide': 317} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 17, 'TRANS': 299} Chain breaks: 2 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'ARG:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 13 Chain: "d" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "f" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "y" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 69556 SG CYS d 21 137.619 202.313 102.454 1.00150.00 S ATOM 69580 SG CYS d 24 137.178 199.752 99.803 1.00152.35 S ATOM 69701 SG CYS d 39 134.131 201.211 100.941 1.00151.52 S ATOM 69727 SG CYS d 42 135.200 198.502 103.202 1.00153.60 S ATOM 70588 SG CYS f 121 184.359 216.013 89.462 1.00228.30 S ATOM 70742 SG CYS f 141 182.385 213.533 87.825 1.00218.86 S ATOM 70761 SG CYS f 144 180.292 216.172 90.479 1.00218.04 S ATOM 75989 SG CYS y 270 54.464 168.904 127.739 1.00207.09 S ATOM 76009 SG CYS y 273 55.110 166.541 130.389 1.00201.11 S ATOM 76128 SG CYS y 288 57.643 165.403 127.920 1.00190.07 S Time building chain proxies: 31.92, per 1000 atoms: 0.41 Number of scatterers: 77098 At special positions: 0 Unit cell: (219.44, 281.84, 187.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 3 29.99 S 185 16.00 P 1665 15.00 O 18937 8.00 N 14159 7.00 C 42149 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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: 13.23 Conformation dependent library (CDL) restraints added in 4.5 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN d 201 " pdb="ZN ZN d 201 " - pdb=" SG CYS d 39 " pdb="ZN ZN d 201 " - pdb=" SG CYS d 21 " pdb="ZN ZN d 201 " - pdb=" SG CYS d 24 " pdb="ZN ZN d 201 " - pdb=" SG CYS d 42 " pdb=" ZN f 201 " pdb="ZN ZN f 201 " - pdb=" SG CYS f 144 " pdb="ZN ZN f 201 " - pdb=" SG CYS f 141 " pdb="ZN ZN f 201 " - pdb=" SG CYS f 121 " pdb=" ZN y 500 " pdb="ZN ZN y 500 " - pdb=" SG CYS y 288 " pdb="ZN ZN y 500 " - pdb=" SG CYS y 270 " pdb="ZN ZN y 500 " - pdb=" SG CYS y 273 " Number of angles added : 6 10290 Ramachandran restraints generated. 5145 Oldfield, 0 Emsley, 5145 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9674 Finding SS restraints... Secondary structure from input PDB file: 173 helices and 64 sheets defined 34.8% alpha, 16.5% beta 520 base pairs and 916 stacking pairs defined. Time for finding SS restraints: 25.30 Creating SS restraints... Processing helix chain 'A' and resid 11 through 22 removed outlier: 3.620A pdb=" N VAL A 15 " --> pdb=" O LYS A 11 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N LEU A 16 " --> pdb=" O GLU A 12 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N LYS A 17 " --> pdb=" O GLU A 13 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N PHE A 18 " --> pdb=" O ASP A 14 " (cutoff:3.500A) Processing helix chain 'A' and resid 42 through 46 removed outlier: 3.612A pdb=" N GLY A 45 " --> pdb=" O LYS A 42 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N ILE A 46 " --> pdb=" O SER A 43 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 42 through 46' Processing helix chain 'A' and resid 50 through 65 removed outlier: 3.508A pdb=" N LEU A 59 " --> pdb=" O TRP A 55 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N LEU A 60 " --> pdb=" O GLU A 56 " (cutoff:3.500A) Processing helix chain 'A' and resid 70 through 72 No H-bonds generated for 'chain 'A' and resid 70 through 72' Processing helix chain 'A' and resid 83 through 95 removed outlier: 3.504A pdb=" N ALA A 91 " --> pdb=" O VAL A 87 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 138 Processing helix chain 'A' and resid 167 through 187 removed outlier: 3.763A pdb=" N MET A 174 " --> pdb=" O SER A 170 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ARG A 184 " --> pdb=" O ARG A 180 " (cutoff:3.500A) Processing helix chain 'A' and resid 209 through 214 Processing helix chain 'B' and resid 23 through 26 removed outlier: 3.553A pdb=" N SER B 26 " --> pdb=" O ASP B 23 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 23 through 26' Processing helix chain 'B' and resid 57 through 63 removed outlier: 3.506A pdb=" N LEU B 62 " --> pdb=" O ALA B 58 " (cutoff:3.500A) Processing helix chain 'B' and resid 106 through 114 removed outlier: 3.584A pdb=" N VAL B 114 " --> pdb=" O MET B 110 " (cutoff:3.500A) Processing helix chain 'B' and resid 157 through 179 removed outlier: 3.786A pdb=" N MET B 172 " --> pdb=" O MET B 168 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N THR B 173 " --> pdb=" O MET B 169 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N GLU B 175 " --> pdb=" O ILE B 171 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N VAL B 176 " --> pdb=" O MET B 172 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ASN B 179 " --> pdb=" O GLU B 175 " (cutoff:3.500A) Processing helix chain 'B' and resid 180 through 189 removed outlier: 3.914A pdb=" N ASN B 186 " --> pdb=" O LYS B 182 " (cutoff:3.500A) Processing helix chain 'B' and resid 191 through 201 removed outlier: 3.583A pdb=" N LYS B 199 " --> pdb=" O LYS B 195 " (cutoff:3.500A) Processing helix chain 'B' and resid 224 through 233 Processing helix chain 'C' and resid 64 through 72 removed outlier: 3.528A pdb=" N ARG C 68 " --> pdb=" O THR C 64 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LEU C 69 " --> pdb=" O LYS C 65 " (cutoff:3.500A) Processing helix chain 'C' and resid 78 through 84 removed outlier: 3.543A pdb=" N TYR C 82 " --> pdb=" O LEU C 78 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N PHE C 84 " --> pdb=" O GLU C 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 91 through 98 Processing helix chain 'C' and resid 146 through 160 removed outlier: 3.640A pdb=" N ILE C 156 " --> pdb=" O ARG C 152 " (cutoff:3.500A) Processing helix chain 'C' and resid 207 through 218 removed outlier: 3.606A pdb=" N LYS C 212 " --> pdb=" O PRO C 208 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N LEU C 213 " --> pdb=" O VAL C 209 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLY C 218 " --> pdb=" O LEU C 214 " (cutoff:3.500A) Processing helix chain 'C' and resid 232 through 246 removed outlier: 3.644A pdb=" N THR C 240 " --> pdb=" O PHE C 236 " (cutoff:3.500A) Processing helix chain 'C' and resid 252 through 257 removed outlier: 3.923A pdb=" N TRP C 256 " --> pdb=" O PRO C 253 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N LYS C 257 " --> pdb=" O ASP C 254 " (cutoff:3.500A) Processing helix chain 'C' and resid 264 through 269 Processing helix chain 'C' and resid 269 through 276 removed outlier: 3.533A pdb=" N LEU C 273 " --> pdb=" O PHE C 269 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LYS C 275 " --> pdb=" O ASP C 271 " (cutoff:3.500A) Processing helix chain 'D' and resid 6 through 30 removed outlier: 3.735A pdb=" N PHE D 11 " --> pdb=" O LYS D 7 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N VAL D 12 " --> pdb=" O LYS D 8 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ALA D 30 " --> pdb=" O THR D 26 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 60 removed outlier: 3.778A pdb=" N GLY D 60 " --> pdb=" O GLN D 56 " (cutoff:3.500A) Processing helix chain 'D' and resid 63 through 78 removed outlier: 3.637A pdb=" N ARG D 67 " --> pdb=" O GLY D 63 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N GLN D 74 " --> pdb=" O THR D 70 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LYS D 75 " --> pdb=" O ALA D 71 " (cutoff:3.500A) Processing helix chain 'D' and resid 97 through 111 Processing helix chain 'D' and resid 114 through 129 removed outlier: 3.541A pdb=" N MET D 127 " --> pdb=" O LEU D 123 " (cutoff:3.500A) Processing helix chain 'E' and resid 15 through 19 Processing helix chain 'E' and resid 43 through 49 Processing helix chain 'E' and resid 61 through 66 Processing helix chain 'E' and resid 117 through 119 No H-bonds generated for 'chain 'E' and resid 117 through 119' Processing helix chain 'E' and resid 247 through 262 removed outlier: 3.706A pdb=" N GLN E 260 " --> pdb=" O LEU E 256 " (cutoff:3.500A) Processing helix chain 'F' and resid 18 through 22 Processing helix chain 'F' and resid 32 through 37 removed outlier: 4.427A pdb=" N ASP F 37 " --> pdb=" O ILE F 33 " (cutoff:3.500A) Processing helix chain 'F' and resid 67 through 75 Processing helix chain 'F' and resid 85 through 105 removed outlier: 3.563A pdb=" N THR F 89 " --> pdb=" O LYS F 85 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N GLU F 98 " --> pdb=" O LYS F 94 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ILE F 99 " --> pdb=" O HIS F 95 " (cutoff:3.500A) Processing helix chain 'F' and resid 107 through 118 removed outlier: 3.648A pdb=" N ASN F 118 " --> pdb=" O ASN F 114 " (cutoff:3.500A) Processing helix chain 'F' and resid 142 through 161 removed outlier: 3.513A pdb=" N TRP F 152 " --> pdb=" O ASN F 148 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLY F 157 " --> pdb=" O LEU F 153 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ALA F 158 " --> pdb=" O LEU F 154 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ARG F 159 " --> pdb=" O CYS F 155 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ALA F 161 " --> pdb=" O GLY F 157 " (cutoff:3.500A) Processing helix chain 'F' and resid 168 through 180 removed outlier: 4.199A pdb=" N ALA F 174 " --> pdb=" O ALA F 170 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ILE F 178 " --> pdb=" O ALA F 174 " (cutoff:3.500A) Processing helix chain 'F' and resid 187 through 192 removed outlier: 3.636A pdb=" N LYS F 191 " --> pdb=" O SER F 187 " (cutoff:3.500A) Processing helix chain 'F' and resid 192 through 201 removed outlier: 4.192A pdb=" N ARG F 198 " --> pdb=" O ASP F 194 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N LYS F 201 " --> pdb=" O GLU F 197 " (cutoff:3.500A) Processing helix chain 'G' and resid 21 through 25 removed outlier: 3.722A pdb=" N ARG G 25 " --> pdb=" O ARG G 22 " (cutoff:3.500A) Processing helix chain 'G' and resid 137 through 146 removed outlier: 3.618A pdb=" N ARG G 142 " --> pdb=" O ALA G 138 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LYS G 143 " --> pdb=" O SER G 139 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LEU G 144 " --> pdb=" O ARG G 140 " (cutoff:3.500A) Processing helix chain 'G' and resid 153 through 157 removed outlier: 3.947A pdb=" N VAL G 157 " --> pdb=" O ARG G 154 " (cutoff:3.500A) Processing helix chain 'G' and resid 183 through 219 removed outlier: 3.621A pdb=" N ARG G 191 " --> pdb=" O HIS G 187 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ILE G 192 " --> pdb=" O LYS G 188 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ALA G 193 " --> pdb=" O ARG G 189 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N GLN G 197 " --> pdb=" O ALA G 193 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LYS G 200 " --> pdb=" O LYS G 196 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ALA G 206 " --> pdb=" O ASN G 202 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N GLU G 219 " --> pdb=" O LYS G 215 " (cutoff:3.500A) Processing helix chain 'G' and resid 219 through 228 removed outlier: 3.545A pdb=" N LYS G 223 " --> pdb=" O GLU G 219 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ARG G 224 " --> pdb=" O ALA G 220 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N GLU G 226 " --> pdb=" O GLU G 222 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ILE G 228 " --> pdb=" O ARG G 224 " (cutoff:3.500A) Processing helix chain 'H' and resid 17 through 25 removed outlier: 3.627A pdb=" N SER H 21 " --> pdb=" O ASP H 17 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N GLY H 22 " --> pdb=" O GLU H 18 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N ILE H 23 " --> pdb=" O PHE H 19 " (cutoff:3.500A) Processing helix chain 'H' and resid 26 through 27 No H-bonds generated for 'chain 'H' and resid 26 through 27' Processing helix chain 'H' and resid 28 through 32 Processing helix chain 'H' and resid 70 through 74 removed outlier: 3.558A pdb=" N LYS H 74 " --> pdb=" O SER H 71 " (cutoff:3.500A) Processing helix chain 'H' and resid 75 through 85 removed outlier: 3.661A pdb=" N LEU H 79 " --> pdb=" O ILE H 75 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N LYS H 85 " --> pdb=" O ARG H 81 " (cutoff:3.500A) Processing helix chain 'H' and resid 121 through 132 removed outlier: 3.795A pdb=" N HIS H 126 " --> pdb=" O LEU H 122 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N LEU H 130 " --> pdb=" O HIS H 126 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ASP H 132 " --> pdb=" O ALA H 128 " (cutoff:3.500A) Processing helix chain 'H' and resid 169 through 181 removed outlier: 4.133A pdb=" N PHE H 173 " --> pdb=" O LYS H 169 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N SER H 174 " --> pdb=" O VAL H 170 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N GLY H 175 " --> pdb=" O GLU H 171 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N LYS H 178 " --> pdb=" O SER H 174 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LYS H 179 " --> pdb=" O GLY H 175 " (cutoff:3.500A) Processing helix chain 'I' and resid 25 through 29 removed outlier: 3.546A pdb=" N LEU I 29 " --> pdb=" O LYS I 26 " (cutoff:3.500A) Processing helix chain 'I' and resid 49 through 51 No H-bonds generated for 'chain 'I' and resid 49 through 51' Processing helix chain 'I' and resid 88 through 93 removed outlier: 3.760A pdb=" N ARG I 92 " --> pdb=" O ASN I 88 " (cutoff:3.500A) Processing helix chain 'I' and resid 106 through 117 removed outlier: 3.549A pdb=" N SER I 115 " --> pdb=" O GLN I 111 " (cutoff:3.500A) Processing helix chain 'I' and resid 130 through 138 removed outlier: 3.597A pdb=" N ILE I 136 " --> pdb=" O GLU I 132 " (cutoff:3.500A) Processing helix chain 'I' and resid 142 through 156 removed outlier: 3.605A pdb=" N LYS I 147 " --> pdb=" O LYS I 143 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ARG I 152 " --> pdb=" O LYS I 148 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N LYS I 154 " --> pdb=" O ASP I 150 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N ASN I 155 " --> pdb=" O GLU I 151 " (cutoff:3.500A) Processing helix chain 'I' and resid 159 through 167 removed outlier: 3.505A pdb=" N GLN I 165 " --> pdb=" O LEU I 161 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N PHE I 166 " --> pdb=" O LEU I 162 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N GLN I 167 " --> pdb=" O GLU I 163 " (cutoff:3.500A) Processing helix chain 'I' and resid 178 through 183 Processing helix chain 'I' and resid 191 through 206 removed outlier: 3.761A pdb=" N ARG I 200 " --> pdb=" O GLU I 196 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ARG I 205 " --> pdb=" O LYS I 201 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N LYS I 206 " --> pdb=" O ILE I 202 " (cutoff:3.500A) Processing helix chain 'J' and resid 21 through 36 removed outlier: 3.741A pdb=" N GLN J 27 " --> pdb=" O SER J 23 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N LEU J 31 " --> pdb=" O GLN J 27 " (cutoff:3.500A) Processing helix chain 'J' and resid 40 through 63 removed outlier: 4.024A pdb=" N VAL J 46 " --> pdb=" O GLU J 42 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N PHE J 48 " --> pdb=" O TRP J 44 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLU J 59 " --> pdb=" O LYS J 55 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LEU J 63 " --> pdb=" O GLU J 59 " (cutoff:3.500A) Processing helix chain 'J' and resid 67 through 84 removed outlier: 3.598A pdb=" N ASN J 75 " --> pdb=" O LEU J 71 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N VAL J 82 " --> pdb=" O LEU J 78 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ILE J 84 " --> pdb=" O ARG J 80 " (cutoff:3.500A) Processing helix chain 'J' and resid 93 through 100 removed outlier: 3.610A pdb=" N ILE J 97 " --> pdb=" O LEU J 94 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LEU J 98 " --> pdb=" O ASP J 95 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LEU J 100 " --> pdb=" O ILE J 97 " (cutoff:3.500A) Processing helix chain 'J' and resid 101 through 106 removed outlier: 3.973A pdb=" N PHE J 105 " --> pdb=" O LYS J 101 " (cutoff:3.500A) Processing helix chain 'J' and resid 109 through 117 removed outlier: 3.918A pdb=" N PHE J 115 " --> pdb=" O GLN J 111 " (cutoff:3.500A) Processing helix chain 'J' and resid 122 through 132 removed outlier: 3.964A pdb=" N ARG J 127 " --> pdb=" O ILE J 123 " (cutoff:3.500A) Processing helix chain 'J' and resid 171 through 179 removed outlier: 3.550A pdb=" N ARG J 175 " --> pdb=" O GLY J 171 " (cutoff:3.500A) Processing helix chain 'K' and resid 4 through 19 removed outlier: 3.999A pdb=" N ARG K 8 " --> pdb=" O PRO K 4 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ALA K 10 " --> pdb=" O LYS K 6 " (cutoff:3.500A) Processing helix chain 'K' and resid 41 through 54 removed outlier: 3.504A pdb=" N ALA K 48 " --> pdb=" O HIS K 44 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N MET K 49 " --> pdb=" O VAL K 45 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N LEU K 52 " --> pdb=" O ALA K 48 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N LYS K 53 " --> pdb=" O MET K 49 " (cutoff:3.500A) Processing helix chain 'K' and resid 72 through 84 removed outlier: 3.666A pdb=" N GLN K 77 " --> pdb=" O ASN K 73 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N LEU K 79 " --> pdb=" O GLY K 75 " (cutoff:3.500A) Processing helix chain 'L' and resid 23 through 30 Processing helix chain 'L' and resid 47 through 53 removed outlier: 3.543A pdb=" N ILE L 51 " --> pdb=" O PRO L 47 " (cutoff:3.500A) Processing helix chain 'M' and resid 13 through 25 removed outlier: 3.683A pdb=" N LEU M 18 " --> pdb=" O VAL M 14 " (cutoff:3.500A) removed outlier: 5.509A pdb=" N GLN M 19 " --> pdb=" O ASN M 15 " (cutoff:3.500A) removed outlier: 4.732A pdb=" N GLU M 20 " --> pdb=" O THR M 16 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N VAL M 21 " --> pdb=" O ALA M 17 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N ALA M 25 " --> pdb=" O VAL M 21 " (cutoff:3.500A) Processing helix chain 'M' and resid 35 through 40 removed outlier: 4.626A pdb=" N ALA M 39 " --> pdb=" O ILE M 35 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N LYS M 40 " --> pdb=" O ARG M 36 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 35 through 40' Processing helix chain 'M' and resid 41 through 45 removed outlier: 3.624A pdb=" N LYS M 44 " --> pdb=" O ALA M 41 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ARG M 45 " --> pdb=" O LEU M 42 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 41 through 45' Processing helix chain 'M' and resid 58 through 69 removed outlier: 4.257A pdb=" N VAL M 62 " --> pdb=" O GLU M 58 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N VAL M 65 " --> pdb=" O TYR M 61 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N ALA M 67 " --> pdb=" O LYS M 63 " (cutoff:3.500A) Processing helix chain 'M' and resid 84 through 88 Processing helix chain 'M' and resid 119 through 132 removed outlier: 3.613A pdb=" N VAL M 123 " --> pdb=" O GLN M 119 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N GLU M 125 " --> pdb=" O LYS M 121 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N GLU M 126 " --> pdb=" O ASP M 122 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N TYR M 127 " --> pdb=" O VAL M 123 " (cutoff:3.500A) Processing helix chain 'N' and resid 29 through 44 removed outlier: 3.887A pdb=" N LYS N 39 " --> pdb=" O GLU N 35 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N LEU N 40 " --> pdb=" O GLN N 36 " (cutoff:3.500A) Processing helix chain 'N' and resid 46 through 57 removed outlier: 3.534A pdb=" N GLY N 51 " --> pdb=" O PRO N 47 " (cutoff:3.500A) Processing helix chain 'N' and resid 62 through 67 Processing helix chain 'N' and resid 70 through 77 Processing helix chain 'N' and resid 85 through 105 removed outlier: 4.073A pdb=" N LEU N 91 " --> pdb=" O ASP N 87 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ARG N 104 " --> pdb=" O LYS N 100 " (cutoff:3.500A) Processing helix chain 'N' and resid 108 through 131 removed outlier: 3.971A pdb=" N ILE N 116 " --> pdb=" O LYS N 112 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ARG N 121 " --> pdb=" O LEU N 117 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ARG N 124 " --> pdb=" O SER N 120 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N TYR N 128 " --> pdb=" O ARG N 124 " (cutoff:3.500A) Processing helix chain 'N' and resid 146 through 150 Processing helix chain 'O' and resid 58 through 62 removed outlier: 4.392A pdb=" N VAL O 62 " --> pdb=" O GLY O 58 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 58 through 62' Processing helix chain 'O' and resid 64 through 68 Processing helix chain 'O' and resid 70 through 88 removed outlier: 3.607A pdb=" N ASP O 80 " --> pdb=" O LEU O 76 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N ARG O 84 " --> pdb=" O ASP O 80 " (cutoff:3.500A) Processing helix chain 'O' and resid 109 through 122 removed outlier: 3.893A pdb=" N ALA O 115 " --> pdb=" O GLY O 111 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ARG O 117 " --> pdb=" O GLN O 113 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ARG O 121 " --> pdb=" O ARG O 117 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N SER O 122 " --> pdb=" O ALA O 118 " (cutoff:3.500A) Processing helix chain 'P' and resid 22 through 27 Processing helix chain 'P' and resid 29 through 34 removed outlier: 3.793A pdb=" N MET P 34 " --> pdb=" O TYR P 30 " (cutoff:3.500A) Processing helix chain 'P' and resid 38 through 48 removed outlier: 3.546A pdb=" N ARG P 47 " --> pdb=" O ARG P 43 " (cutoff:3.500A) Processing helix chain 'P' and resid 50 through 66 removed outlier: 3.771A pdb=" N SER P 55 " --> pdb=" O ARG P 51 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LEU P 56 " --> pdb=" O LYS P 52 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LYS P 62 " --> pdb=" O LYS P 58 " (cutoff:3.500A) Processing helix chain 'P' and resid 86 through 90 removed outlier: 3.587A pdb=" N VAL P 90 " --> pdb=" O PRO P 87 " (cutoff:3.500A) Processing helix chain 'P' and resid 116 through 120 Processing helix chain 'Q' and resid 40 through 42 No H-bonds generated for 'chain 'Q' and resid 40 through 42' Processing helix chain 'Q' and resid 44 through 47 Processing helix chain 'Q' and resid 48 through 53 Processing helix chain 'Q' and resid 54 through 59 removed outlier: 3.750A pdb=" N LEU Q 58 " --> pdb=" O PRO Q 54 " (cutoff:3.500A) Processing helix chain 'Q' and resid 76 through 99 removed outlier: 3.559A pdb=" N SER Q 87 " --> pdb=" O ALA Q 83 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LYS Q 98 " --> pdb=" O ALA Q 94 " (cutoff:3.500A) Processing helix chain 'Q' and resid 101 through 114 removed outlier: 3.598A pdb=" N LYS Q 105 " --> pdb=" O ASP Q 101 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ILE Q 111 " --> pdb=" O GLU Q 107 " (cutoff:3.500A) Processing helix chain 'Q' and resid 116 through 120 removed outlier: 3.571A pdb=" N LEU Q 119 " --> pdb=" O ASP Q 116 " (cutoff:3.500A) Processing helix chain 'R' and resid 6 through 21 removed outlier: 3.833A pdb=" N ALA R 12 " --> pdb=" O THR R 8 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N VAL R 15 " --> pdb=" O LYS R 11 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ILE R 16 " --> pdb=" O ALA R 12 " (cutoff:3.500A) Processing helix chain 'R' and resid 27 through 38 removed outlier: 3.682A pdb=" N ASN R 31 " --> pdb=" O ASP R 27 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N ARG R 33 " --> pdb=" O HIS R 29 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLU R 36 " --> pdb=" O LYS R 32 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N GLU R 37 " --> pdb=" O ARG R 33 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ILE R 38 " --> pdb=" O VAL R 34 " (cutoff:3.500A) Processing helix chain 'R' and resid 43 through 62 removed outlier: 3.581A pdb=" N ARG R 47 " --> pdb=" O SER R 43 " (cutoff:3.500A) Processing helix chain 'R' and resid 73 through 83 Processing helix chain 'R' and resid 99 through 109 removed outlier: 4.124A pdb=" N MET R 105 " --> pdb=" O ASP R 101 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N LEU R 106 " --> pdb=" O THR R 102 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LYS R 107 " --> pdb=" O LYS R 103 " (cutoff:3.500A) Processing helix chain 'S' and resid 25 through 29 Processing helix chain 'S' and resid 37 through 49 removed outlier: 3.664A pdb=" N ALA S 41 " --> pdb=" O GLY S 37 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N VAL S 43 " --> pdb=" O ARG S 39 " (cutoff:3.500A) Processing helix chain 'S' and resid 60 through 73 removed outlier: 3.953A pdb=" N VAL S 64 " --> pdb=" O THR S 60 " (cutoff:3.500A) Processing helix chain 'S' and resid 80 through 84 removed outlier: 3.693A pdb=" N PHE S 83 " --> pdb=" O PRO S 80 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N LEU S 84 " --> pdb=" O ASP S 81 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 80 through 84' Processing helix chain 'S' and resid 99 through 118 removed outlier: 4.053A pdb=" N ARG S 108 " --> pdb=" O ASP S 104 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N GLU S 109 " --> pdb=" O ASN S 105 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N ASP S 110 " --> pdb=" O LYS S 106 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LYS S 116 " --> pdb=" O GLU S 112 " (cutoff:3.500A) Processing helix chain 'S' and resid 119 through 128 Processing helix chain 'T' and resid 10 through 26 removed outlier: 3.964A pdb=" N ARG T 16 " --> pdb=" O GLN T 12 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ALA T 20 " --> pdb=" O ARG T 16 " (cutoff:3.500A) Processing helix chain 'T' and resid 31 through 36 removed outlier: 3.655A pdb=" N VAL T 34 " --> pdb=" O PRO T 31 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N ASP T 35 " --> pdb=" O GLU T 32 " (cutoff:3.500A) Processing helix chain 'T' and resid 51 through 67 removed outlier: 3.680A pdb=" N THR T 55 " --> pdb=" O ASN T 51 " (cutoff:3.500A) Processing helix chain 'T' and resid 71 through 79 Processing helix chain 'T' and resid 96 through 110 removed outlier: 3.838A pdb=" N LEU T 104 " --> pdb=" O ALA T 100 " (cutoff:3.500A) Processing helix chain 'T' and resid 124 through 144 removed outlier: 3.746A pdb=" N ALA T 141 " --> pdb=" O GLN T 137 " (cutoff:3.500A) Processing helix chain 'U' and resid 28 through 46 removed outlier: 3.719A pdb=" N ILE U 40 " --> pdb=" O CYS U 36 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ARG U 41 " --> pdb=" O ALA U 37 " (cutoff:3.500A) Processing helix chain 'U' and resid 95 through 105 removed outlier: 3.804A pdb=" N LYS U 99 " --> pdb=" O SER U 95 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N GLN U 100 " --> pdb=" O GLU U 96 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N SER U 103 " --> pdb=" O LYS U 99 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N ILE U 104 " --> pdb=" O GLN U 100 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N SER U 105 " --> pdb=" O ILE U 101 " (cutoff:3.500A) Processing helix chain 'V' and resid 56 through 62 Processing helix chain 'V' and resid 64 through 76 Processing helix chain 'W' and resid 5 through 20 removed outlier: 3.622A pdb=" N ASP W 9 " --> pdb=" O ASN W 5 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N ILE W 14 " --> pdb=" O ALA W 10 " (cutoff:3.500A) Processing helix chain 'W' and resid 31 through 44 Processing helix chain 'W' and resid 85 through 93 Processing helix chain 'W' and resid 112 through 117 Processing helix chain 'X' and resid 9 through 21 removed outlier: 3.708A pdb=" N ASP X 19 " --> pdb=" O SER X 15 " (cutoff:3.500A) Processing helix chain 'X' and resid 24 through 33 removed outlier: 4.162A pdb=" N GLY X 33 " --> pdb=" O LYS X 29 " (cutoff:3.500A) Processing helix chain 'X' and resid 34 through 39 Processing helix chain 'X' and resid 130 through 135 Processing helix chain 'Y' and resid 36 through 48 removed outlier: 3.628A pdb=" N LYS Y 46 " --> pdb=" O GLU Y 42 " (cutoff:3.500A) Processing helix chain 'Y' and resid 78 through 83 Processing helix chain 'Y' and resid 88 through 93 removed outlier: 3.644A pdb=" N ALA Y 92 " --> pdb=" O LYS Y 88 " (cutoff:3.500A) Processing helix chain 'Y' and resid 103 through 115 removed outlier: 3.622A pdb=" N ARG Y 107 " --> pdb=" O SER Y 103 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ASN Y 112 " --> pdb=" O LYS Y 108 " (cutoff:3.500A) Processing helix chain 'Z' and resid 51 through 61 Processing helix chain 'Z' and resid 62 through 65 Processing helix chain 'Z' and resid 69 through 78 Processing helix chain 'Z' and resid 80 through 94 removed outlier: 3.843A pdb=" N GLN Z 89 " --> pdb=" O ARG Z 85 " (cutoff:3.500A) Processing helix chain 'b' and resid 11 through 18 Processing helix chain 'd' and resid 41 through 46 Processing helix chain 'd' and resid 46 through 51 Processing helix chain 'e' and resid 10 through 15 Processing helix chain 'e' and resid 29 through 43 removed outlier: 3.555A pdb=" N ARG e 34 " --> pdb=" O GLY e 30 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N VAL e 43 " --> pdb=" O ASN e 39 " (cutoff:3.500A) Processing helix chain 'f' and resid 101 through 106 removed outlier: 3.515A pdb=" N TYR f 105 " --> pdb=" O ALA f 101 " (cutoff:3.500A) Processing helix chain 'x' and resid 84 through 91 removed outlier: 3.512A pdb=" N LEU x 88 " --> pdb=" O ARG x 84 " (cutoff:3.500A) Processing helix chain 'x' and resid 95 through 103 removed outlier: 4.060A pdb=" N ILE x 99 " --> pdb=" O ILE x 95 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LEU x 103 " --> pdb=" O ILE x 99 " (cutoff:3.500A) Processing helix chain 'x' and resid 126 through 129 Processing helix chain 'x' and resid 130 through 140 removed outlier: 3.752A pdb=" N PHE x 136 " --> pdb=" O LYS x 132 " (cutoff:3.500A) Processing helix chain 'x' and resid 145 through 150 Processing helix chain 'x' and resid 150 through 155 removed outlier: 3.721A pdb=" N ARG x 154 " --> pdb=" O LEU x 150 " (cutoff:3.500A) Processing helix chain 'x' and resid 172 through 185 removed outlier: 3.971A pdb=" N SER x 177 " --> pdb=" O GLY x 173 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ALA x 179 " --> pdb=" O HIS x 175 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ILE x 180 " --> pdb=" O LEU x 176 " (cutoff:3.500A) Processing helix chain 'x' and resid 188 through 198 removed outlier: 3.587A pdb=" N ASN x 196 " --> pdb=" O PHE x 192 " (cutoff:3.500A) Processing helix chain 'x' and resid 214 through 229 removed outlier: 4.110A pdb=" N THR x 223 " --> pdb=" O LYS x 219 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N ALA x 224 " --> pdb=" O MET x 220 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU x 228 " --> pdb=" O ALA x 224 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ILE x 229 " --> pdb=" O ILE x 225 " (cutoff:3.500A) Processing helix chain 'x' and resid 233 through 246 removed outlier: 4.082A pdb=" N ARG x 242 " --> pdb=" O TYR x 238 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ALA x 243 " --> pdb=" O GLY x 239 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N VAL x 244 " --> pdb=" O ASN x 240 " (cutoff:3.500A) Processing helix chain 'y' and resid 10 through 16 removed outlier: 3.577A pdb=" N PHE y 14 " --> pdb=" O ASP y 10 " (cutoff:3.500A) Processing helix chain 'y' and resid 31 through 36 removed outlier: 3.589A pdb=" N THR y 35 " --> pdb=" O ARG y 31 " (cutoff:3.500A) Processing helix chain 'y' and resid 39 through 49 removed outlier: 3.627A pdb=" N ARG y 43 " --> pdb=" O ASP y 39 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N VAL y 48 " --> pdb=" O ARG y 44 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LEU y 49 " --> pdb=" O ARG y 45 " (cutoff:3.500A) Processing helix chain 'y' and resid 50 through 53 Processing helix chain 'y' and resid 59 through 73 removed outlier: 3.574A pdb=" N ARG y 64 " --> pdb=" O PRO y 60 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N LEU y 65 " --> pdb=" O GLU y 61 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N PHE y 69 " --> pdb=" O LEU y 65 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LYS y 71 " --> pdb=" O THR y 67 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LYS y 72 " --> pdb=" O GLU y 68 " (cutoff:3.500A) Processing helix chain 'y' and resid 80 through 98 removed outlier: 3.775A pdb=" N GLN y 85 " --> pdb=" O ALA y 81 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N VAL y 86 " --> pdb=" O THR y 82 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N LEU y 87 " --> pdb=" O ASP y 83 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLN y 92 " --> pdb=" O ALA y 88 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LEU y 93 " --> pdb=" O LEU y 89 " (cutoff:3.500A) Processing helix chain 'y' and resid 99 through 103 removed outlier: 3.626A pdb=" N HIS y 102 " --> pdb=" O GLY y 99 " (cutoff:3.500A) Processing helix chain 'y' and resid 209 through 217 removed outlier: 4.379A pdb=" N SER y 212 " --> pdb=" O ILE y 209 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ASN y 213 " --> pdb=" O THR y 210 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N ILE y 214 " --> pdb=" O PRO y 211 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N LYS y 215 " --> pdb=" O SER y 212 " (cutoff:3.500A) Processing helix chain 'y' and resid 238 through 248 removed outlier: 3.904A pdb=" N VAL y 244 " --> pdb=" O ALA y 240 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LEU y 245 " --> pdb=" O MET y 241 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LEU y 246 " --> pdb=" O GLN y 242 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLN y 247 " --> pdb=" O ASN y 243 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N MET y 248 " --> pdb=" O VAL y 244 " (cutoff:3.500A) Processing helix chain 'y' and resid 319 through 323 removed outlier: 3.798A pdb=" N LEU y 322 " --> pdb=" O PRO y 319 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N ARG y 323 " --> pdb=" O ARG y 320 " (cutoff:3.500A) No H-bonds generated for 'chain 'y' and resid 319 through 323' Processing helix chain 'y' and resid 352 through 357 removed outlier: 3.787A pdb=" N GLN y 357 " --> pdb=" O GLN y 353 " (cutoff:3.500A) Processing helix chain 'y' and resid 380 through 385 Processing helix chain 'y' and resid 393 through 399 removed outlier: 3.674A pdb=" N ARG y 397 " --> pdb=" O GLY y 393 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 38 through 40 removed outlier: 6.986A pdb=" N ILE A 48 " --> pdb=" O TYR A 39 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 97 through 100 removed outlier: 5.653A pdb=" N VAL A 74 " --> pdb=" O THR A 97 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N ILE A 99 " --> pdb=" O VAL A 74 " (cutoff:3.500A) removed outlier: 5.906A pdb=" N VAL A 76 " --> pdb=" O ILE A 99 " (cutoff:3.500A) removed outlier: 5.963A pdb=" N THR A 144 " --> pdb=" O ILE A 159 " (cutoff:3.500A) removed outlier: 7.732A pdb=" N ILE A 161 " --> pdb=" O THR A 144 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N ALA A 146 " --> pdb=" O ILE A 161 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 43 through 50 removed outlier: 4.103A pdb=" N GLY B 45 " --> pdb=" O VAL B 33 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N VAL B 49 " --> pdb=" O ASP B 29 " (cutoff:3.500A) removed outlier: 8.410A pdb=" N CYS B 96 " --> pdb=" O TRP B 30 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N ASP B 32 " --> pdb=" O CYS B 96 " (cutoff:3.500A) removed outlier: 7.526A pdb=" N THR B 98 " --> pdb=" O ASP B 32 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N LYS B 34 " --> pdb=" O THR B 98 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 69 through 70 removed outlier: 3.888A pdb=" N ASP B 104 " --> pdb=" O LYS B 83 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N LYS B 214 " --> pdb=" O PHE B 138 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ARG B 136 " --> pdb=" O LYS B 216 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N LEU B 134 " --> pdb=" O LEU B 218 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 103 through 106 removed outlier: 3.519A pdb=" N LYS C 103 " --> pdb=" O GLY C 131 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 103 through 106 removed outlier: 3.519A pdb=" N LYS C 103 " --> pdb=" O GLY C 131 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N VAL C 137 " --> pdb=" O VAL C 163 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 185 through 187 Processing sheet with id=AA8, first strand: chain 'D' and resid 34 through 41 removed outlier: 3.804A pdb=" N GLU D 85 " --> pdb=" O THR D 46 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 147 through 155 removed outlier: 3.566A pdb=" N GLU D 135 " --> pdb=" O LYS D 187 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N SER D 139 " --> pdb=" O GLY D 183 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N LYS D 141 " --> pdb=" O VAL D 181 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N VAL D 181 " --> pdb=" O LYS D 141 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 147 through 155 removed outlier: 3.566A pdb=" N GLU D 135 " --> pdb=" O LYS D 187 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N SER D 139 " --> pdb=" O GLY D 183 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N LYS D 141 " --> pdb=" O VAL D 181 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N VAL D 181 " --> pdb=" O LYS D 141 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 209 through 210 Processing sheet with id=AB3, first strand: chain 'E' and resid 9 through 10 removed outlier: 4.265A pdb=" N LEU E 9 " --> pdb=" O ALA E 28 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 75 through 76 Processing sheet with id=AB5, first strand: chain 'E' and resid 136 through 141 removed outlier: 3.527A pdb=" N ILE E 136 " --> pdb=" O GLY E 132 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N LYS E 128 " --> pdb=" O VAL E 140 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N ASP E 171 " --> pdb=" O GLN E 161 " (cutoff:3.500A) removed outlier: 5.719A pdb=" N ASP E 163 " --> pdb=" O ILE E 169 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N ILE E 169 " --> pdb=" O ASP E 163 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 217 through 219 removed outlier: 6.491A pdb=" N VAL E 207 " --> pdb=" O ARG E 198 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N ARG E 198 " --> pdb=" O VAL E 207 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N HIS E 209 " --> pdb=" O THR E 196 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 229 through 230 removed outlier: 3.945A pdb=" N LYS E 233 " --> pdb=" O LYS E 230 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 123 through 127 removed outlier: 7.509A pdb=" N ASN c 45 " --> pdb=" O ALA F 138 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N GLN c 29 " --> pdb=" O LEU c 18 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N GLU c 33 " --> pdb=" O VAL c 14 " (cutoff:3.500A) removed outlier: 5.231A pdb=" N VAL c 14 " --> pdb=" O GLU c 33 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'G' and resid 14 through 17 removed outlier: 3.606A pdb=" N ILE G 5 " --> pdb=" O LYS G 14 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ILE G 113 " --> pdb=" O SER G 6 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N ASN G 56 " --> pdb=" O SER G 107 " (cutoff:3.500A) removed outlier: 5.445A pdb=" N LEU G 109 " --> pdb=" O GLY G 54 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N GLY G 54 " --> pdb=" O LEU G 109 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N LEU G 111 " --> pdb=" O ILE G 52 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N ILE G 52 " --> pdb=" O LEU G 111 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N ILE G 113 " --> pdb=" O VAL G 50 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N VAL G 50 " --> pdb=" O ILE G 113 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'G' and resid 72 through 77 Processing sheet with id=AC2, first strand: chain 'G' and resid 160 through 162 Processing sheet with id=AC3, first strand: chain 'H' and resid 47 through 53 removed outlier: 3.704A pdb=" N VAL H 53 " --> pdb=" O ARG H 57 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ARG H 57 " --> pdb=" O VAL H 53 " (cutoff:3.500A) removed outlier: 9.103A pdb=" N VAL H 93 " --> pdb=" O LYS H 58 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N ILE H 60 " --> pdb=" O VAL H 93 " (cutoff:3.500A) removed outlier: 7.492A pdb=" N ILE H 95 " --> pdb=" O ILE H 60 " (cutoff:3.500A) removed outlier: 6.114A pdb=" N ILE H 62 " --> pdb=" O ILE H 95 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'H' and resid 185 through 188 removed outlier: 8.312A pdb=" N ASN H 186 " --> pdb=" O ARG H 152 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N ILE H 154 " --> pdb=" O ASN H 186 " (cutoff:3.500A) removed outlier: 7.464A pdb=" N GLU H 188 " --> pdb=" O ILE H 154 " (cutoff:3.500A) removed outlier: 6.007A pdb=" N VAL H 156 " --> pdb=" O GLU H 188 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N LEU H 153 " --> pdb=" O ILE H 144 " (cutoff:3.500A) removed outlier: 5.186A pdb=" N ILE H 144 " --> pdb=" O LEU H 153 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N LYS H 155 " --> pdb=" O LYS H 142 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N LYS H 142 " --> pdb=" O LYS H 155 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N HIS H 157 " --> pdb=" O VAL H 140 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'I' and resid 37 through 38 removed outlier: 6.257A pdb=" N ARG I 42 " --> pdb=" O LEU I 58 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'I' and resid 62 through 67 removed outlier: 5.737A pdb=" N ARG I 77 " --> pdb=" O ASP I 105 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N LEU I 103 " --> pdb=" O ILE I 79 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N VAL I 81 " --> pdb=" O ILE I 101 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N ILE I 101 " --> pdb=" O VAL I 81 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ILE I 104 " --> pdb=" O LEU I 171 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'J' and resid 136 through 137 Processing sheet with id=AC8, first strand: chain 'K' and resid 21 through 23 removed outlier: 3.582A pdb=" N MET K 21 " --> pdb=" O TRP K 69 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'L' and resid 72 through 82 removed outlier: 18.528A pdb=" N ILE L 72 " --> pdb=" O LEU L 93 " (cutoff:3.500A) removed outlier: 15.441A pdb=" N LEU L 93 " --> pdb=" O ILE L 72 " (cutoff:3.500A) removed outlier: 9.188A pdb=" N SER L 74 " --> pdb=" O ASP L 91 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N ASP L 91 " --> pdb=" O SER L 74 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N VAL L 87 " --> pdb=" O THR L 78 " (cutoff:3.500A) removed outlier: 5.934A pdb=" N MET L 80 " --> pdb=" O THR L 85 " (cutoff:3.500A) removed outlier: 7.969A pdb=" N THR L 85 " --> pdb=" O MET L 80 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ARG L 101 " --> pdb=" O ILE L 96 " (cutoff:3.500A) removed outlier: 10.160A pdb=" N PHE L 140 " --> pdb=" O ASN L 108 " (cutoff:3.500A) removed outlier: 7.684A pdb=" N SER L 110 " --> pdb=" O PHE L 140 " (cutoff:3.500A) removed outlier: 8.244A pdb=" N VAL L 142 " --> pdb=" O SER L 110 " (cutoff:3.500A) removed outlier: 7.436A pdb=" N HIS L 112 " --> pdb=" O VAL L 142 " (cutoff:3.500A) removed outlier: 8.544A pdb=" N LYS L 144 " --> pdb=" O HIS L 112 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N THR L 127 " --> pdb=" O LEU L 143 " (cutoff:3.500A) removed outlier: 5.209A pdb=" N VAL L 145 " --> pdb=" O ILE L 125 " (cutoff:3.500A) removed outlier: 7.321A pdb=" N ILE L 125 " --> pdb=" O VAL L 145 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'M' and resid 31 through 32 removed outlier: 3.637A pdb=" N VAL M 110 " --> pdb=" O ALA M 32 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'M' and resid 51 through 52 Processing sheet with id=AD3, first strand: chain 'M' and resid 93 through 94 removed outlier: 6.632A pdb=" N LYS M 93 " --> pdb=" O ARG M 101 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'O' and resid 52 through 57 removed outlier: 6.916A pdb=" N VAL O 44 " --> pdb=" O ILE O 53 " (cutoff:3.500A) removed outlier: 4.795A pdb=" N ARG O 55 " --> pdb=" O VAL O 42 " (cutoff:3.500A) removed outlier: 7.165A pdb=" N VAL O 42 " --> pdb=" O ARG O 55 " (cutoff:3.500A) removed outlier: 5.649A pdb=" N THR O 57 " --> pdb=" O THR O 40 " (cutoff:3.500A) removed outlier: 7.114A pdb=" N THR O 40 " --> pdb=" O THR O 57 " (cutoff:3.500A) removed outlier: 7.630A pdb=" N LEU O 93 " --> pdb=" O ARG O 128 " (cutoff:3.500A) removed outlier: 8.313A pdb=" N GLU O 130 " --> pdb=" O LEU O 93 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N ILE O 95 " --> pdb=" O GLU O 130 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'P' and resid 16 through 17 Processing sheet with id=AD6, first strand: chain 'P' and resid 76 through 78 Processing sheet with id=AD7, first strand: chain 'Q' and resid 9 through 15 Processing sheet with id=AD8, first strand: chain 'R' and resid 96 through 98 Processing sheet with id=AD9, first strand: chain 'S' and resid 12 through 15 Processing sheet with id=AE1, first strand: chain 'T' and resid 81 through 83 Processing sheet with id=AE2, first strand: chain 'T' and resid 113 through 115 Processing sheet with id=AE3, first strand: chain 'U' and resid 54 through 55 Processing sheet with id=AE4, first strand: chain 'U' and resid 59 through 66 Processing sheet with id=AE5, first strand: chain 'V' and resid 35 through 39 removed outlier: 5.488A pdb=" N GLN V 49 " --> pdb=" O GLU V 38 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'W' and resid 71 through 74 Processing sheet with id=AE7, first strand: chain 'W' and resid 71 through 74 removed outlier: 5.823A pdb=" N ILE W 125 " --> pdb=" O THR W 105 " (cutoff:3.500A) removed outlier: 5.893A pdb=" N THR W 105 " --> pdb=" O ILE W 125 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'X' and resid 80 through 84 removed outlier: 3.642A pdb=" N GLU X 53 " --> pdb=" O ARG X 71 " (cutoff:3.500A) removed outlier: 6.088A pdb=" N GLN X 73 " --> pdb=" O VAL X 51 " (cutoff:3.500A) removed outlier: 5.535A pdb=" N VAL X 51 " --> pdb=" O GLN X 73 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N GLU X 99 " --> pdb=" O VAL X 125 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N VAL X 125 " --> pdb=" O GLU X 99 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N LEU X 101 " --> pdb=" O VAL X 123 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'Y' and resid 6 through 9 Processing sheet with id=AF1, first strand: chain 'Y' and resid 6 through 9 removed outlier: 7.311A pdb=" N LYS Y 68 " --> pdb=" O THR Y 62 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N THR Y 62 " --> pdb=" O LYS Y 68 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N THR Y 70 " --> pdb=" O PHE Y 60 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N PHE Y 60 " --> pdb=" O THR Y 70 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'Z' and resid 98 through 102 removed outlier: 5.974A pdb=" N LEU Z 99 " --> pdb=" O THR Z 110 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N THR Z 110 " --> pdb=" O LEU Z 99 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N SER Z 101 " --> pdb=" O ILE Z 108 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'b' and resid 32 through 36 Processing sheet with id=AF4, first strand: chain 'b' and resid 64 through 65 Processing sheet with id=AF5, first strand: chain 'd' and resid 30 through 31 removed outlier: 3.624A pdb=" N MET d 38 " --> pdb=" O ILE d 31 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'f' and resid 107 through 108 Processing sheet with id=AF7, first strand: chain 'f' and resid 133 through 134 Processing sheet with id=AF8, first strand: chain 'g' and resid 4 through 11 removed outlier: 5.251A pdb=" N MET g 5 " --> pdb=" O THR g 313 " (cutoff:3.500A) removed outlier: 5.799A pdb=" N THR g 313 " --> pdb=" O MET g 5 " (cutoff:3.500A) removed outlier: 6.099A pdb=" N LEU g 7 " --> pdb=" O GLN g 311 " (cutoff:3.500A) removed outlier: 7.075A pdb=" N GLN g 311 " --> pdb=" O LEU g 7 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N GLY g 9 " --> pdb=" O VAL g 309 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N VAL g 307 " --> pdb=" O LEU g 11 " (cutoff:3.500A) removed outlier: 7.495A pdb=" N THR g 297 " --> pdb=" O TRP g 291 " (cutoff:3.500A) removed outlier: 5.195A pdb=" N TRP g 291 " --> pdb=" O THR g 297 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N PHE g 299 " --> pdb=" O LEU g 289 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N LEU g 289 " --> pdb=" O PHE g 299 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N GLY g 301 " --> pdb=" O THR g 287 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'g' and resid 18 through 22 removed outlier: 5.897A pdb=" N ILE g 40 " --> pdb=" O ALA g 58 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N ALA g 58 " --> pdb=" O ILE g 40 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N MET g 42 " --> pdb=" O GLN g 56 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'g' and resid 70 through 71 Processing sheet with id=AG2, first strand: chain 'g' and resid 108 through 110 removed outlier: 4.168A pdb=" N SER g 110 " --> pdb=" O GLY g 123 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N GLY g 123 " --> pdb=" O SER g 110 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'g' and resid 154 through 156 removed outlier: 3.897A pdb=" N ILE g 165 " --> pdb=" O TRP g 177 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N TRP g 177 " --> pdb=" O ILE g 165 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LYS g 175 " --> pdb=" O SER g 167 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N VAL g 174 " --> pdb=" O ASN g 187 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N ASN g 187 " --> pdb=" O VAL g 174 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N VAL g 176 " --> pdb=" O LYS g 185 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'g' and resid 195 through 200 removed outlier: 4.445A pdb=" N THR g 197 " --> pdb=" O GLY g 210 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N MET g 217 " --> pdb=" O SER g 209 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N ALA g 216 " --> pdb=" O THR g 229 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N THR g 229 " --> pdb=" O ALA g 216 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N LEU g 218 " --> pdb=" O LEU g 227 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'g' and resid 239 through 240 Processing sheet with id=AG6, first strand: chain 'x' and resid 75 through 79 removed outlier: 8.014A pdb=" N HIS y 129 " --> pdb=" O ILE x 107 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N PHE x 109 " --> pdb=" O HIS y 129 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'x' and resid 159 through 164 Processing sheet with id=AG8, first strand: chain 'y' and resid 8 through 9 removed outlier: 6.839A pdb=" N VAL y 8 " --> pdb=" O LEU y 235 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG8 Processing sheet with id=AG9, first strand: chain 'y' and resid 28 through 29 Processing sheet with id=AH1, first strand: chain 'y' and resid 276 through 277 removed outlier: 3.970A pdb=" N SER y 265 " --> pdb=" O VAL y 298 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N SER y 297 " --> pdb=" O HIS y 309 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N HIS y 307 " --> pdb=" O THR y 299 " (cutoff:3.500A) 1360 hydrogen bonds defined for protein. 3801 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 1289 hydrogen bonds 2028 hydrogen bond angles 0 basepair planarities 520 basepair parallelities 916 stacking parallelities Total time for adding SS restraints: 66.05 Time building geometry restraints manager: 16.51 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 10150 1.32 - 1.44: 30551 1.44 - 1.57: 37706 1.57 - 1.69: 3319 1.69 - 1.81: 282 Bond restraints: 82008 Sorted by residual: bond pdb=" C HIS N 5 " pdb=" N ALA N 6 " ideal model delta sigma weight residual 1.329 1.249 0.080 1.35e-02 5.49e+03 3.50e+01 bond pdb=" CA THR X 82 " pdb=" CB THR X 82 " ideal model delta sigma weight residual 1.525 1.471 0.054 1.29e-02 6.01e+03 1.77e+01 bond pdb=" CA GLU G 35 " pdb=" CB GLU G 35 " ideal model delta sigma weight residual 1.531 1.471 0.060 1.52e-02 4.33e+03 1.55e+01 bond pdb=" CA LEU g 87 " pdb=" CB LEU g 87 " ideal model delta sigma weight residual 1.529 1.480 0.049 1.34e-02 5.57e+03 1.33e+01 bond pdb=" CA LEU g 32 " pdb=" CB LEU g 32 " ideal model delta sigma weight residual 1.533 1.465 0.068 2.29e-02 1.91e+03 8.85e+00 ... (remaining 82003 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.22: 116344 3.22 - 6.43: 2095 6.43 - 9.65: 219 9.65 - 12.86: 24 12.86 - 16.08: 4 Bond angle restraints: 118686 Sorted by residual: angle pdb=" N ILE y 116 " pdb=" CA ILE y 116 " pdb=" C ILE y 116 " ideal model delta sigma weight residual 111.91 105.68 6.23 8.90e-01 1.26e+00 4.90e+01 angle pdb=" C ASP c 36 " pdb=" N ASP c 37 " pdb=" CA ASP c 37 " ideal model delta sigma weight residual 121.54 133.94 -12.40 1.91e+00 2.74e-01 4.21e+01 angle pdb=" C TYR W 46 " pdb=" N ILE W 47 " pdb=" CA ILE W 47 " ideal model delta sigma weight residual 122.77 116.46 6.31 1.05e+00 9.07e-01 3.62e+01 angle pdb=" N GLN X 61 " pdb=" CA GLN X 61 " pdb=" C GLN X 61 " ideal model delta sigma weight residual 113.25 120.54 -7.29 1.30e+00 5.92e-01 3.15e+01 angle pdb=" N VAL A 140 " pdb=" CA VAL A 140 " pdb=" C VAL A 140 " ideal model delta sigma weight residual 112.43 107.39 5.04 9.20e-01 1.18e+00 3.00e+01 ... (remaining 118681 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.81: 47346 35.81 - 71.62: 4195 71.62 - 107.43: 504 107.43 - 143.24: 24 143.24 - 179.06: 39 Dihedral angle restraints: 52108 sinusoidal: 37112 harmonic: 14996 Sorted by residual: dihedral pdb=" CA ALA F 40 " pdb=" C ALA F 40 " pdb=" N VAL F 41 " pdb=" CA VAL F 41 " ideal model delta harmonic sigma weight residual -180.00 -125.81 -54.19 0 5.00e+00 4.00e-02 1.17e+02 dihedral pdb=" O4' C 21139 " pdb=" C1' C 21139 " pdb=" N1 C 21139 " pdb=" C2 C 21139 " ideal model delta sinusoidal sigma weight residual -160.00 14.96 -174.96 1 1.50e+01 4.44e-03 8.52e+01 dihedral pdb=" O4' U 2 427 " pdb=" C1' U 2 427 " pdb=" N1 U 2 427 " pdb=" C2 U 2 427 " ideal model delta sinusoidal sigma weight residual -160.00 13.41 -173.41 1 1.50e+01 4.44e-03 8.51e+01 ... (remaining 52105 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.091: 13221 0.091 - 0.181: 1283 0.181 - 0.272: 100 0.272 - 0.363: 33 0.363 - 0.453: 9 Chirality restraints: 14646 Sorted by residual: chirality pdb=" C1' G 2 534 " pdb=" O4' G 2 534 " pdb=" C2' G 2 534 " pdb=" N9 G 2 534 " both_signs ideal model delta sigma weight residual False 2.46 2.00 0.45 2.00e-01 2.50e+01 5.13e+00 chirality pdb=" C3' G 21648 " pdb=" C4' G 21648 " pdb=" O3' G 21648 " pdb=" C2' G 21648 " both_signs ideal model delta sigma weight residual False -2.74 -2.34 -0.41 2.00e-01 2.50e+01 4.20e+00 chirality pdb=" C3' A 2 60 " pdb=" C4' A 2 60 " pdb=" O3' A 2 60 " pdb=" C2' A 2 60 " both_signs ideal model delta sigma weight residual False -2.74 -2.35 -0.39 2.00e-01 2.50e+01 3.86e+00 ... (remaining 14643 not shown) Planarity restraints: 8879 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' C 21811 " 0.022 2.00e-02 2.50e+03 2.91e-02 1.90e+01 pdb=" N1 C 21811 " -0.026 2.00e-02 2.50e+03 pdb=" C2 C 21811 " 0.061 2.00e-02 2.50e+03 pdb=" O2 C 21811 " -0.043 2.00e-02 2.50e+03 pdb=" N3 C 21811 " -0.007 2.00e-02 2.50e+03 pdb=" C4 C 21811 " 0.022 2.00e-02 2.50e+03 pdb=" N4 C 21811 " -0.005 2.00e-02 2.50e+03 pdb=" C5 C 21811 " -0.007 2.00e-02 2.50e+03 pdb=" C6 C 21811 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G 2 309 " 0.052 2.00e-02 2.50e+03 2.20e-02 1.45e+01 pdb=" N9 G 2 309 " -0.050 2.00e-02 2.50e+03 pdb=" C8 G 2 309 " 0.000 2.00e-02 2.50e+03 pdb=" N7 G 2 309 " -0.001 2.00e-02 2.50e+03 pdb=" C5 G 2 309 " 0.001 2.00e-02 2.50e+03 pdb=" C6 G 2 309 " 0.002 2.00e-02 2.50e+03 pdb=" O6 G 2 309 " 0.017 2.00e-02 2.50e+03 pdb=" N1 G 2 309 " 0.002 2.00e-02 2.50e+03 pdb=" C2 G 2 309 " 0.001 2.00e-02 2.50e+03 pdb=" N2 G 2 309 " 0.003 2.00e-02 2.50e+03 pdb=" N3 G 2 309 " -0.015 2.00e-02 2.50e+03 pdb=" C4 G 2 309 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' U 2 495 " 0.048 2.00e-02 2.50e+03 2.40e-02 1.29e+01 pdb=" N1 U 2 495 " -0.048 2.00e-02 2.50e+03 pdb=" C2 U 2 495 " -0.008 2.00e-02 2.50e+03 pdb=" O2 U 2 495 " -0.005 2.00e-02 2.50e+03 pdb=" N3 U 2 495 " 0.001 2.00e-02 2.50e+03 pdb=" C4 U 2 495 " 0.006 2.00e-02 2.50e+03 pdb=" O4 U 2 495 " 0.018 2.00e-02 2.50e+03 pdb=" C5 U 2 495 " -0.005 2.00e-02 2.50e+03 pdb=" C6 U 2 495 " -0.009 2.00e-02 2.50e+03 ... (remaining 8876 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 10904 2.74 - 3.28: 67141 3.28 - 3.82: 152810 3.82 - 4.36: 180642 4.36 - 4.90: 259703 Nonbonded interactions: 671200 Sorted by model distance: nonbonded pdb=" O2' C 2 30 " pdb=" OP1 U 2 596 " model vdw 2.204 3.040 nonbonded pdb=" O2' C 21380 " pdb=" OE1 GLN A 113 " model vdw 2.206 3.040 nonbonded pdb=" OP1 A 2 398 " pdb=" O2' C 2 399 " model vdw 2.209 3.040 nonbonded pdb=" O MET B 169 " pdb=" OG1 THR B 173 " model vdw 2.210 3.040 nonbonded pdb=" OP2 C 2 989 " pdb=" OH TYR B 155 " model vdw 2.217 3.040 ... (remaining 671195 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.100 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.110 Extract box with map and model: 2.350 Check model and map are aligned: 0.440 Set scattering table: 0.570 Process input model: 193.960 Find NCS groups from input model: 1.170 Set up NCS constraints: 0.290 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: 0.030 Load rotamer database and sin/cos tables:2.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 203.650 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 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 : 0.008 0.115 82008 Z= 0.518 Angle : 1.110 16.079 118686 Z= 0.590 Chirality : 0.057 0.453 14646 Planarity : 0.007 0.079 8879 Dihedral : 21.890 179.055 42434 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.73 % Favored : 94.19 % Rotamer: Outliers : 0.40 % Allowed : 3.14 % Favored : 96.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.95 % Cis-general : 0.00 % Twisted Proline : 0.48 % Twisted General : 0.22 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.11 (0.09), residues: 5145 helix: -3.44 (0.08), residues: 1541 sheet: -2.25 (0.16), residues: 886 loop : -2.42 (0.10), residues: 2718 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.055 0.005 TRP K 64 HIS 0.020 0.003 HIS X 31 PHE 0.053 0.004 PHE L 140 TYR 0.041 0.004 TYR W 46 ARG 0.016 0.001 ARG I 5 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10290 Ramachandran restraints generated. 5145 Oldfield, 0 Emsley, 5145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10290 Ramachandran restraints generated. 5145 Oldfield, 0 Emsley, 5145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2312 residues out of total 4500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 2294 time to evaluate : 4.608 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 ASP cc_start: 0.8484 (m-30) cc_final: 0.8239 (m-30) REVERT: A 17 LYS cc_start: 0.9123 (mttp) cc_final: 0.8744 (mttt) REVERT: A 35 GLU cc_start: 0.8669 (tt0) cc_final: 0.8349 (mt-10) REVERT: A 46 ILE cc_start: 0.9296 (mt) cc_final: 0.9082 (mp) REVERT: A 75 SER cc_start: 0.9335 (t) cc_final: 0.9014 (t) REVERT: A 98 PRO cc_start: 0.9300 (Cg_endo) cc_final: 0.9069 (Cg_exo) REVERT: A 110 ASN cc_start: 0.8126 (t0) cc_final: 0.7856 (t0) REVERT: A 126 ASP cc_start: 0.8704 (t0) cc_final: 0.8449 (t0) REVERT: A 173 LEU cc_start: 0.9093 (tm) cc_final: 0.8743 (pp) REVERT: A 181 GLU cc_start: 0.8174 (tp30) cc_final: 0.7767 (tp30) REVERT: A 184 ARG cc_start: 0.7790 (mtm180) cc_final: 0.7027 (ptp90) REVERT: A 198 MET cc_start: 0.8653 (ttp) cc_final: 0.8345 (ttm) REVERT: B 27 LYS cc_start: 0.9195 (mttt) cc_final: 0.8599 (mmmt) REVERT: B 31 TYR cc_start: 0.8274 (m-10) cc_final: 0.7667 (m-80) REVERT: B 94 LYS cc_start: 0.9480 (mttt) cc_final: 0.9182 (mmmm) REVERT: B 103 MET cc_start: 0.7384 (tmm) cc_final: 0.7141 (tmm) REVERT: B 145 LYS cc_start: 0.9324 (tttt) cc_final: 0.8759 (tttp) REVERT: B 149 GLN cc_start: 0.8376 (tt0) cc_final: 0.8169 (tt0) REVERT: B 152 LYS cc_start: 0.9351 (ttpt) cc_final: 0.8907 (ttpp) REVERT: B 168 MET cc_start: 0.8788 (mtt) cc_final: 0.8546 (mtp) REVERT: B 169 MET cc_start: 0.8915 (mtp) cc_final: 0.8713 (mtp) REVERT: B 172 MET cc_start: 0.8424 (ptp) cc_final: 0.8124 (ptp) REVERT: B 180 ASP cc_start: 0.8360 (p0) cc_final: 0.6572 (p0) REVERT: B 182 LYS cc_start: 0.8829 (tmtm) cc_final: 0.8589 (tmtt) REVERT: B 187 LYS cc_start: 0.9017 (mttm) cc_final: 0.8724 (mmtm) REVERT: B 199 LYS cc_start: 0.9076 (ttmt) cc_final: 0.8603 (tptp) REVERT: B 202 GLN cc_start: 0.7974 (mm110) cc_final: 0.7553 (mt0) REVERT: B 208 HIS cc_start: 0.8078 (t-90) cc_final: 0.7285 (t-90) REVERT: C 71 LYS cc_start: 0.9371 (tttt) cc_final: 0.9120 (tttt) REVERT: C 78 LEU cc_start: 0.9453 (tp) cc_final: 0.9240 (tp) REVERT: C 80 GLU cc_start: 0.9234 (mp0) cc_final: 0.8930 (mp0) REVERT: C 84 PHE cc_start: 0.8931 (m-80) cc_final: 0.8575 (m-80) REVERT: C 96 PHE cc_start: 0.8847 (t80) cc_final: 0.8609 (t80) REVERT: C 144 SER cc_start: 0.8279 (t) cc_final: 0.7800 (p) REVERT: C 149 THR cc_start: 0.9302 (m) cc_final: 0.9027 (p) REVERT: C 183 LYS cc_start: 0.8904 (ptpt) cc_final: 0.8387 (ptpt) REVERT: C 212 LYS cc_start: 0.9372 (mmtp) cc_final: 0.9114 (mmmt) REVERT: C 220 ASP cc_start: 0.9131 (m-30) cc_final: 0.8754 (m-30) REVERT: C 223 TYR cc_start: 0.8959 (m-10) cc_final: 0.8182 (m-80) REVERT: C 246 LYS cc_start: 0.9049 (mtpt) cc_final: 0.8723 (mtmt) REVERT: D 20 GLU cc_start: 0.8283 (tt0) cc_final: 0.7975 (tt0) REVERT: D 47 GLU cc_start: 0.6840 (mt-10) cc_final: 0.6513 (pm20) REVERT: D 48 ILE cc_start: 0.8477 (mt) cc_final: 0.8276 (mm) REVERT: D 54 ARG cc_start: 0.8390 (mpp-170) cc_final: 0.8050 (mmm160) REVERT: D 58 VAL cc_start: 0.9262 (m) cc_final: 0.8657 (m) REVERT: D 62 LYS cc_start: 0.8501 (mttt) cc_final: 0.7933 (mmtt) REVERT: D 68 GLU cc_start: 0.8987 (mt-10) cc_final: 0.8744 (mt-10) REVERT: D 81 GLU cc_start: 0.8814 (mp0) cc_final: 0.8542 (mp0) REVERT: D 125 PHE cc_start: 0.8993 (t80) cc_final: 0.8762 (t80) REVERT: D 135 GLU cc_start: 0.8334 (pt0) cc_final: 0.7816 (pt0) REVERT: D 159 HIS cc_start: 0.8055 (m90) cc_final: 0.7780 (m90) REVERT: D 173 ARG cc_start: 0.8193 (mmt-90) cc_final: 0.7759 (mmm160) REVERT: D 188 ILE cc_start: 0.7991 (mm) cc_final: 0.7768 (mm) REVERT: D 189 MET cc_start: 0.8421 (ttp) cc_final: 0.8011 (ttp) REVERT: E 16 LYS cc_start: 0.9096 (tptp) cc_final: 0.8659 (tptt) REVERT: E 57 THR cc_start: 0.9121 (p) cc_final: 0.8719 (t) REVERT: E 62 LYS cc_start: 0.9010 (tppp) cc_final: 0.8767 (ttpt) REVERT: E 104 ASP cc_start: 0.8831 (t70) cc_final: 0.8403 (p0) REVERT: E 127 ARG cc_start: 0.8685 (ttm-80) cc_final: 0.8305 (ttm110) REVERT: E 136 ILE cc_start: 0.9072 (mt) cc_final: 0.8792 (mm) REVERT: E 149 TYR cc_start: 0.9370 (m-80) cc_final: 0.9095 (m-80) REVERT: E 163 ASP cc_start: 0.9061 (t0) cc_final: 0.8148 (t70) REVERT: E 196 THR cc_start: 0.9173 (m) cc_final: 0.8948 (p) REVERT: E 237 SER cc_start: 0.8669 (t) cc_final: 0.8169 (p) REVERT: F 32 ASP cc_start: 0.8098 (m-30) cc_final: 0.7662 (m-30) REVERT: F 43 GLU cc_start: 0.7491 (tp30) cc_final: 0.7228 (tp30) REVERT: F 124 ASP cc_start: 0.8087 (t0) cc_final: 0.7868 (t0) REVERT: F 153 LEU cc_start: 0.9578 (mt) cc_final: 0.9239 (mm) REVERT: F 167 LYS cc_start: 0.8581 (mtpp) cc_final: 0.8290 (tttp) REVERT: F 182 LYS cc_start: 0.9274 (mttt) cc_final: 0.9036 (mtmm) REVERT: F 191 LYS cc_start: 0.8951 (mttt) cc_final: 0.8641 (mttp) REVERT: G 84 TYR cc_start: 0.8874 (t80) cc_final: 0.8627 (t80) REVERT: G 89 THR cc_start: 0.9373 (m) cc_final: 0.8975 (p) REVERT: G 91 GLU cc_start: 0.8135 (pp20) cc_final: 0.7747 (pp20) REVERT: G 100 CYS cc_start: 0.8195 (p) cc_final: 0.7680 (p) REVERT: G 196 LYS cc_start: 0.9255 (mttt) cc_final: 0.8987 (mttm) REVERT: G 208 GLU cc_start: 0.9155 (tp30) cc_final: 0.8801 (tp30) REVERT: H 49 LYS cc_start: 0.7815 (mttt) cc_final: 0.7542 (tptt) REVERT: H 115 LYS cc_start: 0.5853 (pttt) cc_final: 0.5259 (ptpp) REVERT: H 133 LEU cc_start: 0.7068 (tp) cc_final: 0.6801 (tp) REVERT: H 134 VAL cc_start: 0.7872 (t) cc_final: 0.7542 (m) REVERT: H 142 LYS cc_start: 0.9024 (tttt) cc_final: 0.8781 (tptp) REVERT: H 155 LYS cc_start: 0.8603 (mttp) cc_final: 0.8256 (tmtt) REVERT: H 167 GLU cc_start: 0.8964 (tt0) cc_final: 0.8239 (pt0) REVERT: H 178 LYS cc_start: 0.4841 (tptp) cc_final: 0.4639 (ptpt) REVERT: I 27 TYR cc_start: 0.9077 (p90) cc_final: 0.8561 (p90) REVERT: I 54 LYS cc_start: 0.8728 (ttmt) cc_final: 0.8169 (ttpt) REVERT: I 75 LYS cc_start: 0.9215 (ttpt) cc_final: 0.8840 (ttmt) REVERT: I 94 LYS cc_start: 0.8671 (mttt) cc_final: 0.8339 (mmtm) REVERT: I 130 THR cc_start: 0.9226 (p) cc_final: 0.8683 (t) REVERT: I 153 LYS cc_start: 0.9216 (mttt) cc_final: 0.8893 (mtmm) REVERT: I 163 GLU cc_start: 0.8421 (tm-30) cc_final: 0.7770 (tm-30) REVERT: I 167 GLN cc_start: 0.8820 (mm-40) cc_final: 0.8604 (mm110) REVERT: I 178 ARG cc_start: 0.8617 (mtm110) cc_final: 0.8266 (mtp180) REVERT: I 191 GLU cc_start: 0.8352 (mt-10) cc_final: 0.8050 (mt-10) REVERT: J 30 LYS cc_start: 0.9061 (mttt) cc_final: 0.8685 (mttm) REVERT: J 48 PHE cc_start: 0.8903 (t80) cc_final: 0.8694 (t80) REVERT: J 65 GLU cc_start: 0.8733 (tm-30) cc_final: 0.8507 (tm-30) REVERT: J 67 ASP cc_start: 0.9195 (t0) cc_final: 0.8887 (t0) REVERT: J 88 ASP cc_start: 0.8660 (m-30) cc_final: 0.8230 (p0) REVERT: J 101 LYS cc_start: 0.9019 (mtpp) cc_final: 0.8677 (mtmm) REVERT: J 104 ASP cc_start: 0.8738 (m-30) cc_final: 0.8428 (m-30) REVERT: J 107 GLU cc_start: 0.8574 (mm-30) cc_final: 0.8240 (mm-30) REVERT: J 157 ILE cc_start: 0.9110 (mt) cc_final: 0.8906 (tt) REVERT: J 158 ASP cc_start: 0.8028 (m-30) cc_final: 0.7704 (m-30) REVERT: K 9 ILE cc_start: 0.9480 (mt) cc_final: 0.9250 (pt) REVERT: K 12 TYR cc_start: 0.9192 (m-10) cc_final: 0.8945 (m-10) REVERT: K 22 VAL cc_start: 0.7978 (m) cc_final: 0.7660 (t) REVERT: K 38 LYS cc_start: 0.8277 (mttt) cc_final: 0.7830 (mptt) REVERT: K 65 ARG cc_start: 0.7945 (mmm-85) cc_final: 0.7691 (mmm-85) REVERT: K 72 THR cc_start: 0.8764 (m) cc_final: 0.8070 (p) REVERT: K 85 LEU cc_start: 0.9600 (mt) cc_final: 0.9363 (mt) REVERT: L 11 GLN cc_start: 0.8802 (mm-40) cc_final: 0.8567 (mm-40) REVERT: L 103 GLU cc_start: 0.8044 (pt0) cc_final: 0.7487 (pt0) REVERT: L 104 LYS cc_start: 0.8702 (mtpm) cc_final: 0.8256 (mtpm) REVERT: L 139 ARG cc_start: 0.9007 (mpt90) cc_final: 0.8652 (mpt180) REVERT: N 32 ASP cc_start: 0.8810 (t0) cc_final: 0.8582 (t0) REVERT: N 34 LYS cc_start: 0.9454 (mttt) cc_final: 0.9055 (mttt) REVERT: N 38 TYR cc_start: 0.8960 (m-10) cc_final: 0.8501 (m-80) REVERT: N 103 GLU cc_start: 0.8706 (pt0) cc_final: 0.8503 (pt0) REVERT: O 50 LYS cc_start: 0.8400 (tttt) cc_final: 0.8175 (tttp) REVERT: O 51 GLU cc_start: 0.6420 (mp0) cc_final: 0.6161 (mp0) REVERT: O 70 SER cc_start: 0.9093 (m) cc_final: 0.8723 (p) REVERT: O 91 THR cc_start: 0.8833 (p) cc_final: 0.8613 (p) REVERT: O 124 MET cc_start: 0.8841 (mmm) cc_final: 0.8617 (mmm) REVERT: P 25 LEU cc_start: 0.8995 (mt) cc_final: 0.8672 (mt) REVERT: P 31 GLU cc_start: 0.8661 (tt0) cc_final: 0.8076 (mp0) REVERT: P 32 GLN cc_start: 0.9153 (mt0) cc_final: 0.8618 (mt0) REVERT: P 50 ARG cc_start: 0.8668 (mmt180) cc_final: 0.8388 (mmm-85) REVERT: P 77 LYS cc_start: 0.8953 (mtmt) cc_final: 0.8695 (mtmt) REVERT: P 83 MET cc_start: 0.8515 (tpt) cc_final: 0.8206 (tpp) REVERT: P 88 GLU cc_start: 0.8385 (mp0) cc_final: 0.8050 (mp0) REVERT: P 124 LYS cc_start: 0.9183 (tttt) cc_final: 0.8786 (ttmt) REVERT: Q 102 GLU cc_start: 0.9093 (tp30) cc_final: 0.8860 (tp30) REVERT: Q 105 LYS cc_start: 0.9228 (tttt) cc_final: 0.8830 (ttmt) REVERT: Q 106 LYS cc_start: 0.9518 (tttt) cc_final: 0.9124 (ptmt) REVERT: Q 116 ASP cc_start: 0.8170 (t0) cc_final: 0.7915 (t0) REVERT: R 21 TYR cc_start: 0.8780 (t80) cc_final: 0.8397 (t80) REVERT: R 22 THR cc_start: 0.8752 (m) cc_final: 0.8387 (t) REVERT: R 37 GLU cc_start: 0.9103 (mm-30) cc_final: 0.8802 (mm-30) REVERT: S 63 GLU cc_start: 0.8403 (mt-10) cc_final: 0.8047 (mt-10) REVERT: S 105 ASN cc_start: 0.8706 (t0) cc_final: 0.8206 (t0) REVERT: T 8 ASP cc_start: 0.8039 (m-30) cc_final: 0.7792 (m-30) REVERT: T 75 MET cc_start: 0.8936 (mmp) cc_final: 0.8598 (mmt) REVERT: T 133 ARG cc_start: 0.8706 (mtt180) cc_final: 0.8465 (mtt90) REVERT: T 142 ASN cc_start: 0.9058 (t0) cc_final: 0.8841 (t0) REVERT: U 51 LYS cc_start: 0.8597 (mmtt) cc_final: 0.7849 (ttmt) REVERT: U 59 LYS cc_start: 0.8843 (mptt) cc_final: 0.8484 (mptt) REVERT: U 99 LYS cc_start: 0.9183 (tttt) cc_final: 0.8947 (tptp) REVERT: V 47 ASN cc_start: 0.8520 (t0) cc_final: 0.8246 (t0) REVERT: V 49 GLN cc_start: 0.9292 (mm-40) cc_final: 0.8497 (mm-40) REVERT: V 51 LYS cc_start: 0.9078 (mttt) cc_final: 0.8542 (ttmm) REVERT: V 59 ILE cc_start: 0.9057 (mt) cc_final: 0.8796 (mt) REVERT: V 76 ASP cc_start: 0.8669 (m-30) cc_final: 0.7818 (t0) REVERT: W 5 ASN cc_start: 0.8944 (t0) cc_final: 0.8728 (t0) REVERT: W 11 LEU cc_start: 0.9450 (mt) cc_final: 0.9157 (mt) REVERT: W 24 GLN cc_start: 0.9168 (mt0) cc_final: 0.8914 (mt0) REVERT: W 49 GLU cc_start: 0.8029 (pt0) cc_final: 0.7616 (pt0) REVERT: W 55 ASP cc_start: 0.8862 (t0) cc_final: 0.8650 (t0) REVERT: W 65 LEU cc_start: 0.8328 (mt) cc_final: 0.7760 (mp) REVERT: W 91 ASN cc_start: 0.9155 (t0) cc_final: 0.8882 (t0) REVERT: W 111 MET cc_start: 0.7813 (ptp) cc_final: 0.7581 (ptp) REVERT: W 119 LYS cc_start: 0.9107 (mttt) cc_final: 0.8485 (mmtt) REVERT: W 124 LYS cc_start: 0.9148 (mttt) cc_final: 0.8926 (mttt) REVERT: X 5 ARG cc_start: 0.7886 (ttm110) cc_final: 0.7557 (ttm170) REVERT: X 8 ARG cc_start: 0.8330 (mtt180) cc_final: 0.7905 (mtp85) REVERT: X 18 ARG cc_start: 0.8673 (ptt-90) cc_final: 0.8236 (ttp80) REVERT: X 48 LYS cc_start: 0.9211 (tttt) cc_final: 0.8872 (ttmt) REVERT: X 52 LEU cc_start: 0.8978 (mt) cc_final: 0.8769 (mt) REVERT: X 66 ILE cc_start: 0.8278 (mt) cc_final: 0.8061 (mm) REVERT: X 95 GLU cc_start: 0.8463 (tp30) cc_final: 0.7960 (tp30) REVERT: Y 13 MET cc_start: 0.8677 (ttp) cc_final: 0.8385 (ttp) REVERT: Y 15 ASN cc_start: 0.8010 (m-40) cc_final: 0.7801 (m-40) REVERT: Y 43 LYS cc_start: 0.9531 (mmtt) cc_final: 0.8614 (mmmt) REVERT: Y 46 LYS cc_start: 0.9403 (ptmt) cc_final: 0.9200 (ptmm) REVERT: Y 49 LYS cc_start: 0.9413 (mmtm) cc_final: 0.9111 (mmmt) REVERT: Y 55 ILE cc_start: 0.8586 (pt) cc_final: 0.8300 (pt) REVERT: Y 78 SER cc_start: 0.9424 (t) cc_final: 0.9177 (p) REVERT: Z 49 LEU cc_start: 0.7269 (mt) cc_final: 0.7001 (pp) REVERT: Z 51 ASP cc_start: 0.8620 (t0) cc_final: 0.8326 (t0) REVERT: Z 52 LYS cc_start: 0.9181 (mtmt) cc_final: 0.8931 (mtmm) REVERT: Z 57 LYS cc_start: 0.9099 (mmtt) cc_final: 0.8595 (mtpt) REVERT: Z 96 LEU cc_start: 0.8445 (mt) cc_final: 0.8036 (mp) REVERT: b 19 HIS cc_start: 0.8532 (t-90) cc_final: 0.8095 (t70) REVERT: b 23 ARG cc_start: 0.8599 (mpt-90) cc_final: 0.7850 (mpt-90) REVERT: b 42 LYS cc_start: 0.8930 (tptt) cc_final: 0.8683 (ptpt) REVERT: c 10 LYS cc_start: 0.8812 (mttt) cc_final: 0.8450 (mtpp) REVERT: c 24 GLN cc_start: 0.8274 (mp10) cc_final: 0.8040 (mp10) REVERT: c 26 GLN cc_start: 0.8290 (pt0) cc_final: 0.7507 (pm20) REVERT: c 52 GLU cc_start: 0.8786 (tt0) cc_final: 0.8425 (tp30) REVERT: c 54 ASP cc_start: 0.7411 (m-30) cc_final: 0.7157 (m-30) REVERT: c 55 VAL cc_start: 0.8931 (OUTLIER) cc_final: 0.8685 (t) REVERT: c 59 LEU cc_start: 0.8931 (mt) cc_final: 0.8650 (tt) REVERT: e 42 PHE cc_start: 0.8773 (m-10) cc_final: 0.8411 (m-10) REVERT: f 147 THR cc_start: 0.9000 (m) cc_final: 0.8799 (m) REVERT: g 4 GLN cc_start: 0.7732 (mm-40) cc_final: 0.7483 (mp10) REVERT: g 5 MET cc_start: 0.8873 (mmt) cc_final: 0.8489 (mmp) REVERT: g 20 GLN cc_start: 0.8527 (tp-100) cc_final: 0.8202 (tp-100) REVERT: g 77 PHE cc_start: 0.9040 (m-80) cc_final: 0.8699 (m-10) REVERT: g 83 TRP cc_start: 0.8240 (m-10) cc_final: 0.7600 (m-10) REVERT: g 88 ARG cc_start: 0.7111 (tpp80) cc_final: 0.6908 (mtt-85) REVERT: g 107 ASP cc_start: 0.8664 (m-30) cc_final: 0.7909 (m-30) REVERT: g 127 LYS cc_start: 0.8477 (mtmt) cc_final: 0.8213 (mtmm) REVERT: g 143 GLN cc_start: 0.8806 (tp40) cc_final: 0.8585 (tp40) REVERT: g 165 ILE cc_start: 0.8665 (pt) cc_final: 0.8455 (tt) REVERT: g 225 LYS cc_start: 0.9284 (tttt) cc_final: 0.9025 (mmmt) REVERT: g 257 LYS cc_start: 0.7316 (mptm) cc_final: 0.6751 (ttpt) REVERT: g 304 ASP cc_start: 0.8117 (t0) cc_final: 0.7901 (t0) REVERT: g 310 TRP cc_start: 0.8175 (m100) cc_final: 0.7947 (m100) REVERT: x 76 ARG cc_start: 0.8601 (mmt-90) cc_final: 0.7780 (mpt180) REVERT: x 94 LYS cc_start: 0.9159 (ttmp) cc_final: 0.8705 (mppt) REVERT: x 99 ILE cc_start: 0.9091 (mm) cc_final: 0.8865 (tp) REVERT: x 177 SER cc_start: 0.9221 (m) cc_final: 0.8885 (t) REVERT: x 189 LYS cc_start: 0.9090 (tmtp) cc_final: 0.8595 (tmtp) REVERT: x 208 LYS cc_start: 0.9109 (mmtp) cc_final: 0.8889 (mmtp) REVERT: x 223 THR cc_start: 0.8870 (m) cc_final: 0.8644 (m) REVERT: x 232 ASN cc_start: 0.8432 (m110) cc_final: 0.8227 (m-40) REVERT: y 105 GLN cc_start: 0.4685 (pt0) cc_final: 0.4093 (mp10) REVERT: y 114 SER cc_start: 0.8555 (p) cc_final: 0.8270 (m) REVERT: y 280 MET cc_start: 0.7973 (mmm) cc_final: 0.7752 (mmt) REVERT: y 302 ASP cc_start: 0.8115 (t70) cc_final: 0.7619 (t0) REVERT: y 308 MET cc_start: 0.8298 (mtp) cc_final: 0.7987 (mpp) REVERT: y 312 ARG cc_start: 0.7207 (ttm170) cc_final: 0.6743 (mtm110) REVERT: y 348 GLN cc_start: 0.8583 (tt0) cc_final: 0.8204 (tt0) REVERT: y 350 ARG cc_start: 0.7089 (mtp85) cc_final: 0.6886 (ttp-110) REVERT: y 381 ARG cc_start: 0.8817 (mtp85) cc_final: 0.8515 (mtp85) outliers start: 18 outliers final: 5 residues processed: 2301 average time/residue: 0.8604 time to fit residues: 3200.1404 Evaluate side-chains 1741 residues out of total 4500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 1735 time to evaluate : 4.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 88 THR Chi-restraints excluded: chain B residue 210 VAL Chi-restraints excluded: chain E residue 146 THR Chi-restraints excluded: chain U residue 54 VAL Chi-restraints excluded: chain Y residue 17 LEU Chi-restraints excluded: chain c residue 55 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 674 random chunks: chunk 569 optimal weight: 10.0000 chunk 510 optimal weight: 0.0270 chunk 283 optimal weight: 2.9990 chunk 174 optimal weight: 6.9990 chunk 344 optimal weight: 2.9990 chunk 272 optimal weight: 5.9990 chunk 528 optimal weight: 1.9990 chunk 204 optimal weight: 0.7980 chunk 321 optimal weight: 9.9990 chunk 393 optimal weight: 1.9990 chunk 612 optimal weight: 5.9990 overall best weight: 1.5644 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 24 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 113 GLN A 169 HIS B 40 ASN B 75 GLN B 157 GLN B 163 GLN B 177 GLN D 57 ASN D 101 GLN E 8 HIS E 188 ASN E 201 HIS E 209 HIS ** F 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 114 ASN H 91 HIS H 112 ASN H 163 GLN I 22 HIS I 35 ASN I 99 ASN I 116 HIS ** K 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 39 ASN L 65 ASN M 28 HIS M 72 HIS N 13 GLN O 26 ASN ** O 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 38 ASN O 113 GLN Q 24 HIS Q 48 GLN R 62 GLN U 47 ASN U 85 HIS W 64 ASN W 70 ASN W 90 GLN X 127 ASN Y 63 HIS Y 94 HIS ** Z 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** g 117 ASN g 181 ASN ** g 191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 296 GLN x 106 GLN x 210 HIS x 232 ASN y 17 HIS ** y 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** y 271 HIS Total number of N/Q/H flips: 48 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 moved from start: 0.2210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 82008 Z= 0.225 Angle : 0.724 10.821 118686 Z= 0.374 Chirality : 0.043 0.298 14646 Planarity : 0.006 0.068 8879 Dihedral : 24.216 179.449 31759 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 11.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 4.05 % Allowed : 14.67 % Favored : 81.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.95 % Cis-general : 0.00 % Twisted Proline : 0.48 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.78 (0.10), residues: 5145 helix: -1.77 (0.11), residues: 1589 sheet: -1.71 (0.16), residues: 907 loop : -1.90 (0.11), residues: 2649 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP I 67 HIS 0.012 0.001 HIS K 84 PHE 0.027 0.002 PHE T 14 TYR 0.021 0.002 TYR I 113 ARG 0.011 0.001 ARG x 154 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10290 Ramachandran restraints generated. 5145 Oldfield, 0 Emsley, 5145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10290 Ramachandran restraints generated. 5145 Oldfield, 0 Emsley, 5145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2102 residues out of total 4500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 182 poor density : 1920 time to evaluate : 6.005 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 13 GLU cc_start: 0.8453 (pm20) cc_final: 0.8209 (pm20) REVERT: A 35 GLU cc_start: 0.8709 (tt0) cc_final: 0.8357 (mt-10) REVERT: A 69 GLU cc_start: 0.8270 (tm-30) cc_final: 0.8017 (tm-30) REVERT: A 75 SER cc_start: 0.8993 (t) cc_final: 0.8717 (t) REVERT: A 169 HIS cc_start: 0.8944 (m-70) cc_final: 0.8656 (m-70) REVERT: A 173 LEU cc_start: 0.9050 (OUTLIER) cc_final: 0.8800 (pp) REVERT: A 174 MET cc_start: 0.8558 (mmm) cc_final: 0.8170 (mmm) REVERT: A 181 GLU cc_start: 0.8227 (tp30) cc_final: 0.7997 (tp30) REVERT: B 29 ASP cc_start: 0.7622 (m-30) cc_final: 0.7290 (m-30) REVERT: B 51 ARG cc_start: 0.7647 (ptp-170) cc_final: 0.7443 (ptp-170) REVERT: B 75 GLN cc_start: 0.8705 (mt0) cc_final: 0.8226 (tm-30) REVERT: B 115 LYS cc_start: 0.9185 (mttt) cc_final: 0.8975 (mptt) REVERT: B 144 LYS cc_start: 0.8814 (tmtt) cc_final: 0.8275 (ttpp) REVERT: B 145 LYS cc_start: 0.9340 (tttt) cc_final: 0.8528 (tttp) REVERT: B 163 GLN cc_start: 0.9045 (mt0) cc_final: 0.8774 (mt0) REVERT: B 168 MET cc_start: 0.8720 (mtt) cc_final: 0.8472 (mtp) REVERT: B 207 LEU cc_start: 0.9103 (mp) cc_final: 0.8787 (mm) REVERT: B 208 HIS cc_start: 0.8016 (t-90) cc_final: 0.7615 (t-90) REVERT: B 216 LYS cc_start: 0.8973 (mttt) cc_final: 0.8373 (mttm) REVERT: B 217 MET cc_start: 0.8607 (tpt) cc_final: 0.8403 (tpp) REVERT: C 80 GLU cc_start: 0.9231 (mp0) cc_final: 0.8885 (mp0) REVERT: C 144 SER cc_start: 0.8473 (t) cc_final: 0.8120 (p) REVERT: C 194 ARG cc_start: 0.8475 (ttt180) cc_final: 0.8136 (ttt-90) REVERT: C 224 THR cc_start: 0.9444 (m) cc_final: 0.8879 (p) REVERT: C 242 ASP cc_start: 0.8806 (t0) cc_final: 0.8523 (t0) REVERT: C 246 LYS cc_start: 0.9109 (mtpt) cc_final: 0.8618 (mtmt) REVERT: C 260 VAL cc_start: 0.8719 (OUTLIER) cc_final: 0.8511 (m) REVERT: D 47 GLU cc_start: 0.6509 (mt-10) cc_final: 0.5960 (pm20) REVERT: D 54 ARG cc_start: 0.8350 (mpp-170) cc_final: 0.8038 (mmm160) REVERT: D 62 LYS cc_start: 0.8904 (mttt) cc_final: 0.8449 (mmtt) REVERT: D 68 GLU cc_start: 0.8945 (mt-10) cc_final: 0.8664 (mt-10) REVERT: D 81 GLU cc_start: 0.8626 (mp0) cc_final: 0.8346 (mp0) REVERT: D 117 ARG cc_start: 0.8940 (mmm160) cc_final: 0.8520 (tpm170) REVERT: D 125 PHE cc_start: 0.8946 (t80) cc_final: 0.8713 (t80) REVERT: D 126 ILE cc_start: 0.7892 (pt) cc_final: 0.7554 (pt) REVERT: D 190 LEU cc_start: 0.8670 (mp) cc_final: 0.8372 (mp) REVERT: E 104 ASP cc_start: 0.8740 (t70) cc_final: 0.8416 (p0) REVERT: E 125 LYS cc_start: 0.9258 (tttt) cc_final: 0.8971 (tttp) REVERT: E 127 ARG cc_start: 0.8608 (ttm-80) cc_final: 0.8407 (ttm110) REVERT: E 130 PHE cc_start: 0.9205 (p90) cc_final: 0.8883 (p90) REVERT: E 201 HIS cc_start: 0.8733 (m-70) cc_final: 0.8270 (m90) REVERT: E 211 LYS cc_start: 0.8957 (tttt) cc_final: 0.8753 (ttmm) REVERT: E 237 SER cc_start: 0.8815 (t) cc_final: 0.8350 (p) REVERT: F 43 GLU cc_start: 0.7272 (tp30) cc_final: 0.6906 (mm-30) REVERT: F 59 LYS cc_start: 0.7744 (ptpp) cc_final: 0.7431 (pttm) REVERT: F 106 GLU cc_start: 0.8366 (mp0) cc_final: 0.8132 (mp0) REVERT: F 124 ASP cc_start: 0.8184 (t0) cc_final: 0.7695 (t0) REVERT: F 153 LEU cc_start: 0.9609 (mt) cc_final: 0.9282 (mm) REVERT: F 182 LYS cc_start: 0.9224 (mttt) cc_final: 0.8981 (mtmm) REVERT: G 36 VAL cc_start: 0.9362 (t) cc_final: 0.9147 (p) REVERT: G 81 HIS cc_start: 0.8480 (m-70) cc_final: 0.7962 (m-70) REVERT: G 89 THR cc_start: 0.9311 (m) cc_final: 0.8999 (p) REVERT: G 96 SER cc_start: 0.8779 (m) cc_final: 0.8574 (t) REVERT: G 100 CYS cc_start: 0.8062 (p) cc_final: 0.7579 (p) REVERT: G 140 ARG cc_start: 0.8860 (mmm-85) cc_final: 0.8484 (mmt180) REVERT: G 196 LYS cc_start: 0.9211 (mttt) cc_final: 0.8927 (mttm) REVERT: H 49 LYS cc_start: 0.7599 (mttt) cc_final: 0.7396 (tptt) REVERT: H 61 ILE cc_start: 0.7912 (mm) cc_final: 0.7540 (mp) REVERT: H 118 ARG cc_start: 0.5891 (mmt90) cc_final: 0.5549 (mtt-85) REVERT: H 160 LYS cc_start: 0.8235 (tmtp) cc_final: 0.7915 (pptt) REVERT: I 7 ASN cc_start: 0.7987 (t0) cc_final: 0.7663 (t0) REVERT: I 12 ARG cc_start: 0.7846 (mtt90) cc_final: 0.7431 (mtt90) REVERT: I 19 LYS cc_start: 0.8424 (mttm) cc_final: 0.8150 (mttm) REVERT: I 25 ARG cc_start: 0.7862 (mmt90) cc_final: 0.7579 (mpt180) REVERT: I 53 LYS cc_start: 0.9041 (mttt) cc_final: 0.8725 (mtmm) REVERT: I 61 ASP cc_start: 0.8195 (OUTLIER) cc_final: 0.7950 (m-30) REVERT: I 75 LYS cc_start: 0.9115 (ttpt) cc_final: 0.8753 (ttmm) REVERT: I 94 LYS cc_start: 0.8767 (mttt) cc_final: 0.8324 (mmtm) REVERT: I 163 GLU cc_start: 0.8548 (tm-30) cc_final: 0.7975 (tm-30) REVERT: I 167 GLN cc_start: 0.8894 (mm-40) cc_final: 0.8474 (mm110) REVERT: I 178 ARG cc_start: 0.8632 (mtm180) cc_final: 0.8376 (mtp180) REVERT: J 28 GLU cc_start: 0.8827 (mt-10) cc_final: 0.8615 (mt-10) REVERT: J 65 GLU cc_start: 0.8742 (tm-30) cc_final: 0.8477 (tm-30) REVERT: J 79 ARG cc_start: 0.8716 (tpp80) cc_final: 0.8321 (mpp80) REVERT: J 88 ASP cc_start: 0.8632 (m-30) cc_final: 0.8063 (p0) REVERT: J 91 LYS cc_start: 0.9018 (mttt) cc_final: 0.8679 (mtpp) REVERT: J 101 LYS cc_start: 0.8974 (mtpp) cc_final: 0.8603 (mtmm) REVERT: J 104 ASP cc_start: 0.8834 (m-30) cc_final: 0.8341 (m-30) REVERT: J 107 GLU cc_start: 0.8906 (mm-30) cc_final: 0.8691 (mm-30) REVERT: J 138 ARG cc_start: 0.8551 (OUTLIER) cc_final: 0.8040 (mtt90) REVERT: K 46 MET cc_start: 0.9011 (ttm) cc_final: 0.8750 (mtt) REVERT: K 52 LEU cc_start: 0.9377 (mp) cc_final: 0.9155 (mp) REVERT: K 53 LYS cc_start: 0.9062 (tttt) cc_final: 0.8722 (mttt) REVERT: K 65 ARG cc_start: 0.7844 (mmm-85) cc_final: 0.7411 (mmm-85) REVERT: K 70 TYR cc_start: 0.7923 (m-80) cc_final: 0.7445 (m-80) REVERT: L 11 GLN cc_start: 0.8609 (mm-40) cc_final: 0.8330 (mm-40) REVERT: L 104 LYS cc_start: 0.8650 (mtpm) cc_final: 0.8115 (mtpm) REVERT: L 105 ARG cc_start: 0.8180 (OUTLIER) cc_final: 0.7870 (mtp180) REVERT: N 99 ARG cc_start: 0.8905 (ttm110) cc_final: 0.8487 (ttm170) REVERT: N 121 ARG cc_start: 0.8924 (mtm-85) cc_final: 0.8637 (mtm180) REVERT: O 51 GLU cc_start: 0.6929 (mp0) cc_final: 0.6487 (mp0) REVERT: O 60 MET cc_start: 0.8290 (mtt) cc_final: 0.7595 (mtt) REVERT: O 121 ARG cc_start: 0.7942 (ptp90) cc_final: 0.7601 (ptp90) REVERT: O 124 MET cc_start: 0.8904 (mmm) cc_final: 0.8680 (mmm) REVERT: P 31 GLU cc_start: 0.8749 (tt0) cc_final: 0.8277 (mp0) REVERT: P 77 LYS cc_start: 0.8911 (mtmt) cc_final: 0.8628 (mtmt) REVERT: P 83 MET cc_start: 0.8623 (tpt) cc_final: 0.8422 (tpp) REVERT: P 88 GLU cc_start: 0.8374 (mp0) cc_final: 0.8084 (mp0) REVERT: P 108 LYS cc_start: 0.8668 (mmmt) cc_final: 0.8277 (mmtm) REVERT: P 110 GLU cc_start: 0.8374 (mp0) cc_final: 0.8118 (mp0) REVERT: P 124 LYS cc_start: 0.9046 (tttt) cc_final: 0.8608 (ttpt) REVERT: Q 53 GLU cc_start: 0.8271 (mt-10) cc_final: 0.7992 (mt-10) REVERT: Q 97 GLN cc_start: 0.8560 (tt0) cc_final: 0.8355 (tt0) REVERT: Q 102 GLU cc_start: 0.9113 (tp30) cc_final: 0.8791 (tp30) REVERT: Q 116 ASP cc_start: 0.8159 (t0) cc_final: 0.7901 (t0) REVERT: R 17 ILE cc_start: 0.8957 (mm) cc_final: 0.8732 (mt) REVERT: R 21 TYR cc_start: 0.8807 (t80) cc_final: 0.8485 (t80) REVERT: R 22 THR cc_start: 0.8743 (m) cc_final: 0.8530 (t) REVERT: R 53 TYR cc_start: 0.7477 (t80) cc_final: 0.7106 (t80) REVERT: S 24 ARG cc_start: 0.8699 (mtp180) cc_final: 0.8398 (mtp180) REVERT: S 63 GLU cc_start: 0.8226 (mt-10) cc_final: 0.7971 (mt-10) REVERT: S 78 LYS cc_start: 0.8497 (tptp) cc_final: 0.8216 (tptp) REVERT: T 29 LYS cc_start: 0.9200 (mtpp) cc_final: 0.8999 (ttpp) REVERT: T 32 GLU cc_start: 0.7164 (tm-30) cc_final: 0.6758 (tm-30) REVERT: T 35 ASP cc_start: 0.8446 (m-30) cc_final: 0.8197 (t0) REVERT: T 56 ARG cc_start: 0.9133 (tpp80) cc_final: 0.8470 (tpp80) REVERT: T 67 ARG cc_start: 0.7144 (ttt90) cc_final: 0.6890 (ttt90) REVERT: T 75 MET cc_start: 0.8698 (mmp) cc_final: 0.8389 (mmt) REVERT: T 76 THR cc_start: 0.8113 (m) cc_final: 0.7714 (p) REVERT: T 79 TYR cc_start: 0.8209 (m-80) cc_final: 0.7624 (m-80) REVERT: T 94 ARG cc_start: 0.8053 (mtp180) cc_final: 0.7813 (mtt-85) REVERT: T 108 GLU cc_start: 0.8106 (mt-10) cc_final: 0.7826 (mt-10) REVERT: T 129 ARG cc_start: 0.7893 (mtm110) cc_final: 0.7511 (ttm-80) REVERT: T 142 ASN cc_start: 0.9100 (t0) cc_final: 0.8891 (t0) REVERT: U 40 ILE cc_start: 0.9190 (tt) cc_final: 0.8983 (mp) REVERT: U 44 LYS cc_start: 0.9731 (mtpp) cc_final: 0.9442 (mtmm) REVERT: U 47 ASN cc_start: 0.9531 (t0) cc_final: 0.9071 (m110) REVERT: U 49 LYS cc_start: 0.8007 (tttt) cc_final: 0.7716 (ptmt) REVERT: U 51 LYS cc_start: 0.8318 (mmtt) cc_final: 0.7656 (ttmt) REVERT: U 59 LYS cc_start: 0.8857 (mptt) cc_final: 0.8512 (mptt) REVERT: U 100 GLN cc_start: 0.9031 (tt0) cc_final: 0.8572 (tm-30) REVERT: V 7 GLU cc_start: 0.8432 (mp0) cc_final: 0.8095 (mp0) REVERT: V 8 PHE cc_start: 0.8685 (m-80) cc_final: 0.8429 (m-80) REVERT: V 15 ARG cc_start: 0.8531 (ptt180) cc_final: 0.8237 (ptt-90) REVERT: V 49 GLN cc_start: 0.9256 (mm-40) cc_final: 0.9044 (mp10) REVERT: V 51 LYS cc_start: 0.9137 (mttt) cc_final: 0.8912 (mmmm) REVERT: W 5 ASN cc_start: 0.8748 (t0) cc_final: 0.8541 (t0) REVERT: W 41 MET cc_start: 0.8933 (mtp) cc_final: 0.8678 (mtp) REVERT: W 49 GLU cc_start: 0.8060 (pt0) cc_final: 0.7218 (pt0) REVERT: W 55 ASP cc_start: 0.8590 (t0) cc_final: 0.8385 (t0) REVERT: W 91 ASN cc_start: 0.9212 (t0) cc_final: 0.8953 (t0) REVERT: W 111 MET cc_start: 0.8127 (ptp) cc_final: 0.7847 (ptp) REVERT: W 119 LYS cc_start: 0.9177 (mttt) cc_final: 0.8657 (mmtt) REVERT: X 8 ARG cc_start: 0.8223 (mtt180) cc_final: 0.7706 (mtp85) REVERT: X 48 LYS cc_start: 0.9182 (tttt) cc_final: 0.8874 (ttmt) REVERT: X 95 GLU cc_start: 0.8129 (tp30) cc_final: 0.7816 (tp30) REVERT: X 98 ASP cc_start: 0.7823 (m-30) cc_final: 0.7569 (m-30) REVERT: Y 13 MET cc_start: 0.8444 (ttp) cc_final: 0.8244 (ttp) REVERT: Y 17 LEU cc_start: 0.9008 (OUTLIER) cc_final: 0.8695 (pp) REVERT: Y 78 SER cc_start: 0.9305 (t) cc_final: 0.8884 (p) REVERT: Y 86 GLU cc_start: 0.8803 (tp30) cc_final: 0.8518 (mm-30) REVERT: Y 90 ARG cc_start: 0.8638 (mtm-85) cc_final: 0.8102 (mtm180) REVERT: Y 106 GLN cc_start: 0.9215 (mm-40) cc_final: 0.8852 (mt0) REVERT: Z 51 ASP cc_start: 0.8708 (t0) cc_final: 0.8496 (t0) REVERT: Z 66 LYS cc_start: 0.8303 (OUTLIER) cc_final: 0.8021 (ttpt) REVERT: b 19 HIS cc_start: 0.8325 (t-90) cc_final: 0.7825 (t70) REVERT: b 23 ARG cc_start: 0.8530 (mpt-90) cc_final: 0.7490 (mpt-90) REVERT: b 42 LYS cc_start: 0.8861 (tptt) cc_final: 0.8660 (ptpt) REVERT: c 10 LYS cc_start: 0.8800 (mttt) cc_final: 0.8498 (mtpp) REVERT: c 15 THR cc_start: 0.9343 (m) cc_final: 0.8710 (p) REVERT: c 26 GLN cc_start: 0.8220 (pt0) cc_final: 0.7363 (pm20) REVERT: c 52 GLU cc_start: 0.8764 (tt0) cc_final: 0.8395 (tp30) REVERT: c 54 ASP cc_start: 0.7546 (m-30) cc_final: 0.6972 (m-30) REVERT: e 23 GLU cc_start: 0.8526 (tm-30) cc_final: 0.8222 (tm-30) REVERT: e 39 ASN cc_start: 0.8888 (m-40) cc_final: 0.8597 (m-40) REVERT: g 3 GLU cc_start: 0.8558 (OUTLIER) cc_final: 0.8158 (mm-30) REVERT: g 5 MET cc_start: 0.8809 (mmt) cc_final: 0.8504 (mmm) REVERT: g 27 PHE cc_start: 0.8705 (m-10) cc_final: 0.8428 (m-10) REVERT: g 107 ASP cc_start: 0.8735 (m-30) cc_final: 0.7759 (m-30) REVERT: g 118 ARG cc_start: 0.9197 (pmm150) cc_final: 0.8825 (mtm-85) REVERT: g 126 ASP cc_start: 0.8361 (p0) cc_final: 0.7960 (p0) REVERT: g 127 LYS cc_start: 0.8564 (mtmt) cc_final: 0.8272 (mtmm) REVERT: g 143 GLN cc_start: 0.8654 (tp40) cc_final: 0.8183 (tp40) REVERT: g 206 LEU cc_start: 0.8545 (mm) cc_final: 0.8000 (mt) REVERT: g 218 LEU cc_start: 0.8922 (tp) cc_final: 0.8597 (tp) REVERT: g 285 GLN cc_start: 0.8291 (mm-40) cc_final: 0.7698 (tp40) REVERT: g 296 GLN cc_start: 0.8484 (OUTLIER) cc_final: 0.8203 (tm-30) REVERT: g 309 VAL cc_start: 0.8648 (OUTLIER) cc_final: 0.8415 (p) REVERT: x 77 LYS cc_start: 0.7881 (OUTLIER) cc_final: 0.7291 (pmmt) REVERT: x 94 LYS cc_start: 0.9118 (OUTLIER) cc_final: 0.8707 (mppt) REVERT: x 106 GLN cc_start: 0.7202 (OUTLIER) cc_final: 0.6850 (mp10) REVERT: x 126 ASP cc_start: 0.8460 (t0) cc_final: 0.8250 (t70) REVERT: x 177 SER cc_start: 0.8821 (m) cc_final: 0.8447 (t) REVERT: x 189 LYS cc_start: 0.8771 (tmtp) cc_final: 0.8383 (tmtp) REVERT: x 217 ASN cc_start: 0.8317 (m110) cc_final: 0.8056 (t0) REVERT: x 232 ASN cc_start: 0.8771 (m-40) cc_final: 0.8506 (m-40) REVERT: x 240 ASN cc_start: 0.8846 (m-40) cc_final: 0.8558 (t0) REVERT: y 105 GLN cc_start: 0.4645 (pt0) cc_final: 0.4233 (mp10) REVERT: y 114 SER cc_start: 0.8657 (p) cc_final: 0.8265 (m) REVERT: y 302 ASP cc_start: 0.8006 (t70) cc_final: 0.7612 (t0) REVERT: y 308 MET cc_start: 0.8703 (mtp) cc_final: 0.8395 (mpp) REVERT: y 312 ARG cc_start: 0.7068 (ttm170) cc_final: 0.6621 (mtm110) outliers start: 182 outliers final: 96 residues processed: 1988 average time/residue: 0.8149 time to fit residues: 2660.2754 Evaluate side-chains 1879 residues out of total 4500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 1770 time to evaluate : 4.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 173 LEU Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain A residue 185 MET Chi-restraints excluded: chain A residue 191 ARG Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 210 VAL Chi-restraints excluded: chain C residue 134 ASN Chi-restraints excluded: chain C residue 222 CYS Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 244 ILE Chi-restraints excluded: chain C residue 260 VAL Chi-restraints excluded: chain D residue 55 THR Chi-restraints excluded: chain D residue 156 LEU Chi-restraints excluded: chain D residue 168 VAL Chi-restraints excluded: chain D residue 198 ILE Chi-restraints excluded: chain D residue 208 VAL Chi-restraints excluded: chain E residue 146 THR Chi-restraints excluded: chain F residue 66 CYS Chi-restraints excluded: chain F residue 78 MET Chi-restraints excluded: chain F residue 166 ILE Chi-restraints excluded: chain F residue 169 ILE Chi-restraints excluded: chain F residue 185 SER Chi-restraints excluded: chain G residue 153 VAL Chi-restraints excluded: chain G residue 212 LEU Chi-restraints excluded: chain H residue 100 ILE Chi-restraints excluded: chain H residue 170 VAL Chi-restraints excluded: chain H residue 176 VAL Chi-restraints excluded: chain H residue 179 LYS Chi-restraints excluded: chain I residue 22 HIS Chi-restraints excluded: chain I residue 61 ASP Chi-restraints excluded: chain I residue 69 SER Chi-restraints excluded: chain I residue 159 SER Chi-restraints excluded: chain I residue 160 SER Chi-restraints excluded: chain I residue 177 SER Chi-restraints excluded: chain I residue 193 LYS Chi-restraints excluded: chain J residue 12 THR Chi-restraints excluded: chain J residue 34 GLU Chi-restraints excluded: chain J residue 138 ARG Chi-restraints excluded: chain K residue 7 ASN Chi-restraints excluded: chain K residue 79 LEU Chi-restraints excluded: chain L residue 46 THR Chi-restraints excluded: chain L residue 66 VAL Chi-restraints excluded: chain L residue 78 THR Chi-restraints excluded: chain L residue 105 ARG Chi-restraints excluded: chain N residue 26 LEU Chi-restraints excluded: chain N residue 102 LEU Chi-restraints excluded: chain N residue 143 SER Chi-restraints excluded: chain O residue 26 ASN Chi-restraints excluded: chain O residue 48 SER Chi-restraints excluded: chain P residue 105 VAL Chi-restraints excluded: chain Q residue 10 VAL Chi-restraints excluded: chain Q residue 31 LEU Chi-restraints excluded: chain Q residue 48 GLN Chi-restraints excluded: chain R residue 9 VAL Chi-restraints excluded: chain S residue 3 LEU Chi-restraints excluded: chain S residue 18 THR Chi-restraints excluded: chain S residue 43 VAL Chi-restraints excluded: chain S residue 98 VAL Chi-restraints excluded: chain T residue 9 VAL Chi-restraints excluded: chain T residue 55 THR Chi-restraints excluded: chain T residue 117 GLN Chi-restraints excluded: chain V residue 70 LEU Chi-restraints excluded: chain W residue 25 VAL Chi-restraints excluded: chain W residue 27 ILE Chi-restraints excluded: chain W residue 85 ASP Chi-restraints excluded: chain W residue 103 VAL Chi-restraints excluded: chain W residue 106 THR Chi-restraints excluded: chain Y residue 17 LEU Chi-restraints excluded: chain Y residue 47 MET Chi-restraints excluded: chain Y residue 109 GLU Chi-restraints excluded: chain Z residue 66 LYS Chi-restraints excluded: chain Z residue 69 THR Chi-restraints excluded: chain Z residue 92 LEU Chi-restraints excluded: chain Z residue 110 THR Chi-restraints excluded: chain Z residue 113 THR Chi-restraints excluded: chain b residue 33 MET Chi-restraints excluded: chain f residue 121 CYS Chi-restraints excluded: chain f residue 123 SER Chi-restraints excluded: chain g residue 3 GLU Chi-restraints excluded: chain g residue 96 THR Chi-restraints excluded: chain g residue 166 VAL Chi-restraints excluded: chain g residue 191 HIS Chi-restraints excluded: chain g residue 266 ILE Chi-restraints excluded: chain g residue 287 THR Chi-restraints excluded: chain g residue 296 GLN Chi-restraints excluded: chain g residue 309 VAL Chi-restraints excluded: chain x residue 77 LYS Chi-restraints excluded: chain x residue 78 ILE Chi-restraints excluded: chain x residue 94 LYS Chi-restraints excluded: chain x residue 106 GLN Chi-restraints excluded: chain x residue 116 VAL Chi-restraints excluded: chain x residue 118 ILE Chi-restraints excluded: chain x residue 152 LEU Chi-restraints excluded: chain x residue 198 THR Chi-restraints excluded: chain x residue 219 LYS Chi-restraints excluded: chain x residue 226 CYS Chi-restraints excluded: chain x residue 237 VAL Chi-restraints excluded: chain y residue 48 VAL Chi-restraints excluded: chain y residue 215 LYS Chi-restraints excluded: chain y residue 268 LEU Chi-restraints excluded: chain y residue 286 SER Chi-restraints excluded: chain y residue 297 SER Chi-restraints excluded: chain y residue 307 HIS Chi-restraints excluded: chain y residue 316 VAL Chi-restraints excluded: chain y residue 328 THR Chi-restraints excluded: chain y residue 341 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 674 random chunks: chunk 340 optimal weight: 7.9990 chunk 189 optimal weight: 0.5980 chunk 509 optimal weight: 2.9990 chunk 416 optimal weight: 0.0770 chunk 168 optimal weight: 10.0000 chunk 613 optimal weight: 8.9990 chunk 662 optimal weight: 10.0000 chunk 546 optimal weight: 8.9990 chunk 608 optimal weight: 6.9990 chunk 209 optimal weight: 4.9990 chunk 491 optimal weight: 0.8980 overall best weight: 1.9142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 24 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 43 ASN B 157 GLN E 161 GLN F 203 ASN H 126 HIS H 163 GLN H 165 ASN I 22 HIS I 99 ASN ** K 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 106 HIS ** L 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 26 ASN ** O 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 11 GLN Q 24 HIS ** Q 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 26 ASN S 19 ASN ** T 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 64 ASN W 70 ASN X 127 ASN ** Z 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 28 HIS d 37 ASN ** g 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 191 HIS ** g 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** x 91 ASN ** x 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** x 175 HIS ** y 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** y 124 HIS y 213 ASN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 moved from start: 0.2706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 82008 Z= 0.232 Angle : 0.687 10.597 118686 Z= 0.354 Chirality : 0.042 0.314 14646 Planarity : 0.005 0.068 8879 Dihedral : 24.029 179.984 31756 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 11.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 4.81 % Allowed : 17.50 % Favored : 77.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.95 % Cis-general : 0.00 % Twisted Proline : 0.48 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.12 (0.11), residues: 5145 helix: -0.93 (0.12), residues: 1591 sheet: -1.42 (0.16), residues: 916 loop : -1.66 (0.11), residues: 2638 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP g 259 HIS 0.018 0.001 HIS I 22 PHE 0.028 0.002 PHE J 48 TYR 0.037 0.002 TYR N 38 ARG 0.017 0.001 ARG X 11 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10290 Ramachandran restraints generated. 5145 Oldfield, 0 Emsley, 5145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10290 Ramachandran restraints generated. 5145 Oldfield, 0 Emsley, 5145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2053 residues out of total 4500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 216 poor density : 1837 time to evaluate : 4.413 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 GLU cc_start: 0.8793 (tt0) cc_final: 0.8445 (mt-10) REVERT: A 50 ASN cc_start: 0.8944 (t0) cc_final: 0.8483 (m110) REVERT: A 55 TRP cc_start: 0.8257 (t-100) cc_final: 0.8048 (t-100) REVERT: A 57 LYS cc_start: 0.8194 (mmtp) cc_final: 0.7783 (mmtp) REVERT: A 69 GLU cc_start: 0.8292 (tm-30) cc_final: 0.7887 (tm-30) REVERT: A 75 SER cc_start: 0.8871 (t) cc_final: 0.8609 (t) REVERT: A 169 HIS cc_start: 0.8900 (m-70) cc_final: 0.8509 (m-70) REVERT: A 173 LEU cc_start: 0.9130 (OUTLIER) cc_final: 0.8881 (pp) REVERT: A 181 GLU cc_start: 0.8175 (tp30) cc_final: 0.7958 (tp30) REVERT: B 29 ASP cc_start: 0.7846 (m-30) cc_final: 0.7268 (m-30) REVERT: B 48 LEU cc_start: 0.8619 (tp) cc_final: 0.7709 (mm) REVERT: B 63 LYS cc_start: 0.8853 (ttmm) cc_final: 0.8592 (mmtt) REVERT: B 75 GLN cc_start: 0.8695 (mt0) cc_final: 0.8231 (mm-40) REVERT: B 90 ASP cc_start: 0.7611 (m-30) cc_final: 0.7251 (m-30) REVERT: B 92 GLN cc_start: 0.8660 (mm-40) cc_final: 0.8362 (mm-40) REVERT: B 124 HIS cc_start: 0.7971 (p-80) cc_final: 0.7699 (p-80) REVERT: B 144 LYS cc_start: 0.9122 (tmtt) cc_final: 0.8704 (ttmm) REVERT: B 145 LYS cc_start: 0.9369 (tttt) cc_final: 0.8853 (tttp) REVERT: B 163 GLN cc_start: 0.9058 (mt0) cc_final: 0.8840 (mt0) REVERT: B 168 MET cc_start: 0.8765 (mtt) cc_final: 0.8513 (mtp) REVERT: B 202 GLN cc_start: 0.8022 (mm110) cc_final: 0.7669 (mt0) REVERT: B 208 HIS cc_start: 0.7950 (t-90) cc_final: 0.7694 (t-90) REVERT: B 217 MET cc_start: 0.8530 (tpt) cc_final: 0.8149 (tpp) REVERT: C 84 PHE cc_start: 0.8968 (m-80) cc_final: 0.8528 (m-80) REVERT: C 92 GLU cc_start: 0.8956 (mp0) cc_final: 0.8672 (mp0) REVERT: C 144 SER cc_start: 0.8497 (t) cc_final: 0.8176 (p) REVERT: C 194 ARG cc_start: 0.8475 (ttt180) cc_final: 0.8260 (ttt-90) REVERT: C 224 THR cc_start: 0.9466 (m) cc_final: 0.8982 (p) REVERT: C 242 ASP cc_start: 0.8807 (t0) cc_final: 0.8517 (t0) REVERT: C 246 LYS cc_start: 0.9128 (mtpt) cc_final: 0.8559 (mtmt) REVERT: D 54 ARG cc_start: 0.8336 (mpp-170) cc_final: 0.7969 (mmm160) REVERT: D 62 LYS cc_start: 0.8869 (mttt) cc_final: 0.8371 (mmtt) REVERT: D 68 GLU cc_start: 0.9002 (mt-10) cc_final: 0.8739 (mt-10) REVERT: D 81 GLU cc_start: 0.8597 (mp0) cc_final: 0.8353 (mp0) REVERT: D 117 ARG cc_start: 0.8946 (mmm160) cc_final: 0.8475 (tpm170) REVERT: D 125 PHE cc_start: 0.8911 (t80) cc_final: 0.8678 (t80) REVERT: D 126 ILE cc_start: 0.7914 (pt) cc_final: 0.7610 (pt) REVERT: D 127 MET cc_start: 0.9223 (mmt) cc_final: 0.8986 (mmt) REVERT: D 166 TYR cc_start: 0.8025 (p90) cc_final: 0.7734 (p90) REVERT: D 189 MET cc_start: 0.7727 (ttt) cc_final: 0.7513 (ttt) REVERT: E 88 ASP cc_start: 0.8495 (m-30) cc_final: 0.8124 (m-30) REVERT: E 104 ASP cc_start: 0.8737 (t70) cc_final: 0.8286 (p0) REVERT: E 127 ARG cc_start: 0.8666 (ttm-80) cc_final: 0.8442 (ttm110) REVERT: E 130 PHE cc_start: 0.9221 (p90) cc_final: 0.8934 (p90) REVERT: E 211 LYS cc_start: 0.9045 (tttt) cc_final: 0.8829 (ttmm) REVERT: E 237 SER cc_start: 0.8854 (t) cc_final: 0.8390 (p) REVERT: F 43 GLU cc_start: 0.7314 (tp30) cc_final: 0.7105 (tp30) REVERT: F 79 HIS cc_start: 0.5562 (OUTLIER) cc_final: 0.4967 (t70) REVERT: F 98 GLU cc_start: 0.8789 (OUTLIER) cc_final: 0.8126 (mp0) REVERT: F 106 GLU cc_start: 0.8461 (mp0) cc_final: 0.8230 (mp0) REVERT: F 124 ASP cc_start: 0.8273 (t0) cc_final: 0.7768 (t0) REVERT: F 153 LEU cc_start: 0.9522 (mt) cc_final: 0.9173 (mm) REVERT: F 182 LYS cc_start: 0.9197 (mttt) cc_final: 0.8985 (mtmm) REVERT: F 188 TYR cc_start: 0.8646 (t80) cc_final: 0.8323 (t80) REVERT: G 65 GLN cc_start: 0.7748 (tp40) cc_final: 0.7531 (tp40) REVERT: G 81 HIS cc_start: 0.8406 (m-70) cc_final: 0.8151 (m-70) REVERT: G 89 THR cc_start: 0.9346 (m) cc_final: 0.9081 (p) REVERT: G 96 SER cc_start: 0.8823 (m) cc_final: 0.8569 (t) REVERT: G 100 CYS cc_start: 0.8233 (p) cc_final: 0.7714 (p) REVERT: G 196 LYS cc_start: 0.9179 (mttt) cc_final: 0.8840 (mttm) REVERT: H 118 ARG cc_start: 0.5788 (mmt90) cc_final: 0.5582 (mtt-85) REVERT: H 147 LYS cc_start: 0.8436 (mmtt) cc_final: 0.8061 (mmtt) REVERT: H 160 LYS cc_start: 0.8151 (tmtp) cc_final: 0.7784 (pptt) REVERT: H 171 GLU cc_start: 0.8337 (tm-30) cc_final: 0.8109 (tm-30) REVERT: I 7 ASN cc_start: 0.8084 (t0) cc_final: 0.7824 (t0) REVERT: I 12 ARG cc_start: 0.7986 (mtt90) cc_final: 0.7530 (mtt90) REVERT: I 25 ARG cc_start: 0.7881 (mmt90) cc_final: 0.7557 (mpt180) REVERT: I 53 LYS cc_start: 0.9064 (mttt) cc_final: 0.8752 (mtmm) REVERT: I 54 LYS cc_start: 0.8521 (ttmt) cc_final: 0.7496 (ttpt) REVERT: I 61 ASP cc_start: 0.8141 (OUTLIER) cc_final: 0.7933 (m-30) REVERT: I 73 THR cc_start: 0.8995 (m) cc_final: 0.8486 (p) REVERT: I 75 LYS cc_start: 0.9129 (ttpt) cc_final: 0.8698 (ttmm) REVERT: I 94 LYS cc_start: 0.8769 (mttt) cc_final: 0.8490 (mmtm) REVERT: I 153 LYS cc_start: 0.9251 (mttt) cc_final: 0.8969 (mtmm) REVERT: I 163 GLU cc_start: 0.8538 (tm-30) cc_final: 0.8267 (tm-30) REVERT: I 164 GLU cc_start: 0.8640 (mt-10) cc_final: 0.8427 (pt0) REVERT: I 194 GLU cc_start: 0.8499 (mp0) cc_final: 0.8208 (mp0) REVERT: J 22 LYS cc_start: 0.8172 (mmtt) cc_final: 0.7596 (mmtp) REVERT: J 48 PHE cc_start: 0.8595 (t80) cc_final: 0.8343 (t80) REVERT: J 65 GLU cc_start: 0.8768 (tm-30) cc_final: 0.8480 (tm-30) REVERT: J 79 ARG cc_start: 0.8716 (tpp80) cc_final: 0.8352 (mpp80) REVERT: J 88 ASP cc_start: 0.8538 (m-30) cc_final: 0.8022 (p0) REVERT: J 101 LYS cc_start: 0.8987 (mtpp) cc_final: 0.8642 (mtmm) REVERT: J 103 GLU cc_start: 0.9080 (pm20) cc_final: 0.8875 (pm20) REVERT: J 104 ASP cc_start: 0.8866 (m-30) cc_final: 0.8378 (m-30) REVERT: J 158 ASP cc_start: 0.8510 (t70) cc_final: 0.7982 (t0) REVERT: K 46 MET cc_start: 0.8903 (mtm) cc_final: 0.8556 (mtt) REVERT: L 11 GLN cc_start: 0.8689 (mm-40) cc_final: 0.8381 (mm-40) REVERT: L 104 LYS cc_start: 0.8785 (mtpm) cc_final: 0.8126 (mtpm) REVERT: L 105 ARG cc_start: 0.8335 (OUTLIER) cc_final: 0.7975 (mtp180) REVERT: N 38 TYR cc_start: 0.9026 (m-80) cc_final: 0.8727 (m-80) REVERT: N 55 ARG cc_start: 0.7937 (ttp-170) cc_final: 0.7603 (ttp-170) REVERT: N 99 ARG cc_start: 0.8936 (ttm110) cc_final: 0.8669 (ttm170) REVERT: N 108 ASP cc_start: 0.8471 (t70) cc_final: 0.8214 (t0) REVERT: N 119 GLU cc_start: 0.7953 (mm-30) cc_final: 0.7742 (mm-30) REVERT: N 121 ARG cc_start: 0.8971 (mtm-85) cc_final: 0.8661 (mtm180) REVERT: O 51 GLU cc_start: 0.6713 (mp0) cc_final: 0.6484 (mp0) REVERT: O 60 MET cc_start: 0.8331 (mtt) cc_final: 0.7590 (mtt) REVERT: O 124 MET cc_start: 0.8865 (mmm) cc_final: 0.8452 (mmm) REVERT: O 128 ARG cc_start: 0.6814 (mmm160) cc_final: 0.6191 (mmm160) REVERT: P 29 SER cc_start: 0.8899 (m) cc_final: 0.8298 (t) REVERT: P 31 GLU cc_start: 0.8757 (tt0) cc_final: 0.8170 (mp0) REVERT: P 32 GLN cc_start: 0.9066 (mt0) cc_final: 0.8590 (mt0) REVERT: P 77 LYS cc_start: 0.8911 (mtmt) cc_final: 0.8656 (mtmt) REVERT: P 83 MET cc_start: 0.8647 (tpt) cc_final: 0.8327 (tpt) REVERT: P 84 ILE cc_start: 0.8567 (mt) cc_final: 0.8366 (tp) REVERT: P 88 GLU cc_start: 0.8357 (mp0) cc_final: 0.8048 (mp0) REVERT: P 124 LYS cc_start: 0.9098 (tttt) cc_final: 0.8674 (ttpt) REVERT: Q 51 LEU cc_start: 0.9150 (OUTLIER) cc_final: 0.8931 (mp) REVERT: Q 98 LYS cc_start: 0.9076 (tppt) cc_final: 0.8560 (tppt) REVERT: Q 102 GLU cc_start: 0.9164 (tp30) cc_final: 0.8851 (tp30) REVERT: Q 106 LYS cc_start: 0.9598 (tptm) cc_final: 0.9224 (tptp) REVERT: Q 110 ASP cc_start: 0.9023 (p0) cc_final: 0.8654 (p0) REVERT: Q 116 ASP cc_start: 0.8118 (t0) cc_final: 0.7829 (t0) REVERT: R 32 LYS cc_start: 0.7101 (ttpt) cc_final: 0.6895 (ttmt) REVERT: S 7 GLU cc_start: 0.7686 (tm-30) cc_final: 0.7422 (tm-30) REVERT: S 8 LYS cc_start: 0.8940 (mmmt) cc_final: 0.8676 (mmmt) REVERT: S 34 LYS cc_start: 0.8972 (mttt) cc_final: 0.8729 (mtpp) REVERT: S 63 GLU cc_start: 0.8198 (mt-10) cc_final: 0.7909 (mt-10) REVERT: S 112 GLU cc_start: 0.8414 (mm-30) cc_final: 0.8104 (tp30) REVERT: T 56 ARG cc_start: 0.9043 (tpp80) cc_final: 0.8787 (tpt-90) REVERT: T 76 THR cc_start: 0.8090 (m) cc_final: 0.7744 (p) REVERT: T 79 TYR cc_start: 0.8272 (m-80) cc_final: 0.7529 (m-80) REVERT: T 88 MET cc_start: 0.8615 (mtp) cc_final: 0.8404 (mtp) REVERT: T 129 ARG cc_start: 0.7900 (mtm110) cc_final: 0.7504 (ttm-80) REVERT: T 133 ARG cc_start: 0.8548 (mtm-85) cc_final: 0.8233 (mtt90) REVERT: T 142 ASN cc_start: 0.9050 (t0) cc_final: 0.8807 (t0) REVERT: U 46 LYS cc_start: 0.9319 (mtpp) cc_final: 0.9067 (mtmm) REVERT: U 47 ASN cc_start: 0.9489 (t0) cc_final: 0.9088 (m110) REVERT: U 51 LYS cc_start: 0.8371 (mmtt) cc_final: 0.7658 (ttmt) REVERT: U 59 LYS cc_start: 0.8834 (mptt) cc_final: 0.8552 (mptt) REVERT: U 97 ILE cc_start: 0.8348 (mp) cc_final: 0.8092 (mp) REVERT: U 100 GLN cc_start: 0.8995 (tt0) cc_final: 0.8651 (tm-30) REVERT: V 7 GLU cc_start: 0.8458 (mp0) cc_final: 0.8006 (mp0) REVERT: V 15 ARG cc_start: 0.8506 (ptt180) cc_final: 0.8126 (ptt-90) REVERT: V 49 GLN cc_start: 0.9246 (mm-40) cc_final: 0.8781 (mp10) REVERT: V 51 LYS cc_start: 0.9086 (mttt) cc_final: 0.7566 (mttt) REVERT: V 61 ARG cc_start: 0.8501 (mtp85) cc_final: 0.8195 (mtp85) REVERT: V 76 ASP cc_start: 0.8855 (m-30) cc_final: 0.8350 (t0) REVERT: W 5 ASN cc_start: 0.8729 (t0) cc_final: 0.8491 (t0) REVERT: W 23 ARG cc_start: 0.8528 (mmm160) cc_final: 0.8274 (mmm160) REVERT: W 36 ARG cc_start: 0.9115 (OUTLIER) cc_final: 0.8856 (mmt180) REVERT: W 49 GLU cc_start: 0.7442 (pt0) cc_final: 0.6406 (pt0) REVERT: W 86 LEU cc_start: 0.9063 (tp) cc_final: 0.8816 (tt) REVERT: W 90 GLN cc_start: 0.8883 (pt0) cc_final: 0.8413 (pt0) REVERT: W 91 ASN cc_start: 0.9271 (t0) cc_final: 0.9021 (t0) REVERT: W 111 MET cc_start: 0.8074 (ptp) cc_final: 0.7832 (ptp) REVERT: X 5 ARG cc_start: 0.7922 (ttm170) cc_final: 0.7677 (ttm170) REVERT: X 8 ARG cc_start: 0.8252 (mtt180) cc_final: 0.7759 (mtp85) REVERT: X 48 LYS cc_start: 0.9072 (tttt) cc_final: 0.8797 (ttmt) REVERT: X 58 GLU cc_start: 0.8317 (mm-30) cc_final: 0.8080 (mm-30) REVERT: X 95 GLU cc_start: 0.8181 (tp30) cc_final: 0.7834 (tp30) REVERT: X 98 ASP cc_start: 0.7858 (m-30) cc_final: 0.7531 (m-30) REVERT: Y 19 GLN cc_start: 0.9102 (mp10) cc_final: 0.8880 (mp10) REVERT: Y 78 SER cc_start: 0.9291 (t) cc_final: 0.8900 (p) REVERT: Y 106 GLN cc_start: 0.9188 (mm-40) cc_final: 0.8931 (mt0) REVERT: Z 51 ASP cc_start: 0.8721 (t0) cc_final: 0.8520 (t0) REVERT: b 19 HIS cc_start: 0.8286 (t-90) cc_final: 0.8063 (t70) REVERT: b 23 ARG cc_start: 0.8609 (mpt-90) cc_final: 0.8251 (mpt-90) REVERT: b 63 LEU cc_start: 0.7650 (OUTLIER) cc_final: 0.7284 (mp) REVERT: c 10 LYS cc_start: 0.8881 (mttt) cc_final: 0.8460 (mtpp) REVERT: c 13 ARG cc_start: 0.7637 (mmm160) cc_final: 0.7418 (tpp80) REVERT: c 15 THR cc_start: 0.9363 (OUTLIER) cc_final: 0.8748 (p) REVERT: c 26 GLN cc_start: 0.8240 (pt0) cc_final: 0.7279 (pm20) REVERT: c 52 GLU cc_start: 0.8750 (tt0) cc_final: 0.8363 (tp30) REVERT: c 54 ASP cc_start: 0.7531 (m-30) cc_final: 0.7330 (m-30) REVERT: e 21 LYS cc_start: 0.8593 (OUTLIER) cc_final: 0.7967 (mtpp) REVERT: e 23 GLU cc_start: 0.8472 (tm-30) cc_final: 0.8272 (tm-30) REVERT: f 148 TYR cc_start: 0.8096 (m-80) cc_final: 0.7505 (m-80) REVERT: g 3 GLU cc_start: 0.8464 (OUTLIER) cc_final: 0.8179 (mm-30) REVERT: g 5 MET cc_start: 0.8734 (mmt) cc_final: 0.8467 (mmm) REVERT: g 51 ASN cc_start: 0.8459 (p0) cc_final: 0.8220 (p0) REVERT: g 86 THR cc_start: 0.8998 (m) cc_final: 0.8642 (t) REVERT: g 118 ARG cc_start: 0.9170 (pmm150) cc_final: 0.8896 (mtm-85) REVERT: g 143 GLN cc_start: 0.8729 (tp40) cc_final: 0.8505 (mm110) REVERT: g 206 LEU cc_start: 0.8583 (mm) cc_final: 0.8017 (tp) REVERT: g 217 MET cc_start: 0.8190 (mmp) cc_final: 0.7624 (mmp) REVERT: g 218 LEU cc_start: 0.8802 (tp) cc_final: 0.8215 (tp) REVERT: g 219 TRP cc_start: 0.8423 (m100) cc_final: 0.7860 (m100) REVERT: g 246 TYR cc_start: 0.8251 (t80) cc_final: 0.8018 (t80) REVERT: g 257 LYS cc_start: 0.7056 (mptm) cc_final: 0.6725 (mmtm) REVERT: g 271 LYS cc_start: 0.8051 (tmtt) cc_final: 0.7720 (tmtt) REVERT: g 285 GLN cc_start: 0.8388 (mm-40) cc_final: 0.7854 (tp40) REVERT: g 296 GLN cc_start: 0.8538 (OUTLIER) cc_final: 0.8065 (pp30) REVERT: g 304 ASP cc_start: 0.7870 (t0) cc_final: 0.7470 (t0) REVERT: x 77 LYS cc_start: 0.8113 (OUTLIER) cc_final: 0.7564 (pmmt) REVERT: x 94 LYS cc_start: 0.9085 (OUTLIER) cc_final: 0.8731 (mppt) REVERT: x 126 ASP cc_start: 0.8469 (t0) cc_final: 0.8248 (t70) REVERT: x 163 PHE cc_start: 0.7676 (OUTLIER) cc_final: 0.7434 (m-10) REVERT: x 189 LYS cc_start: 0.8827 (tmtp) cc_final: 0.8434 (tmtp) REVERT: x 217 ASN cc_start: 0.8332 (m110) cc_final: 0.8044 (t0) REVERT: y 105 GLN cc_start: 0.4899 (pt0) cc_final: 0.4576 (mp10) REVERT: y 114 SER cc_start: 0.8642 (p) cc_final: 0.8207 (m) REVERT: y 241 MET cc_start: 0.8444 (mmt) cc_final: 0.7949 (mmm) REVERT: y 280 MET cc_start: 0.7995 (mmm) cc_final: 0.7659 (mmp) REVERT: y 308 MET cc_start: 0.8620 (mtp) cc_final: 0.8273 (mpp) REVERT: y 312 ARG cc_start: 0.7031 (ttm170) cc_final: 0.6514 (mtm110) outliers start: 216 outliers final: 138 residues processed: 1910 average time/residue: 0.8288 time to fit residues: 2626.4070 Evaluate side-chains 1873 residues out of total 4500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 153 poor density : 1720 time to evaluate : 4.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 VAL Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 173 LEU Chi-restraints excluded: chain A residue 185 MET Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 210 VAL Chi-restraints excluded: chain C residue 65 LYS Chi-restraints excluded: chain C residue 130 ILE Chi-restraints excluded: chain C residue 134 ASN Chi-restraints excluded: chain C residue 156 ILE Chi-restraints excluded: chain C residue 165 VAL Chi-restraints excluded: chain C residue 192 LEU Chi-restraints excluded: chain C residue 221 ASP Chi-restraints excluded: chain C residue 222 CYS Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 244 ILE Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 55 THR Chi-restraints excluded: chain D residue 123 LEU Chi-restraints excluded: chain D residue 158 ILE Chi-restraints excluded: chain D residue 168 VAL Chi-restraints excluded: chain D residue 198 ILE Chi-restraints excluded: chain D residue 208 VAL Chi-restraints excluded: chain E residue 32 SER Chi-restraints excluded: chain E residue 44 LEU Chi-restraints excluded: chain E residue 91 SER Chi-restraints excluded: chain E residue 146 THR Chi-restraints excluded: chain E residue 204 SER Chi-restraints excluded: chain E residue 256 LEU Chi-restraints excluded: chain F residue 78 MET Chi-restraints excluded: chain F residue 79 HIS Chi-restraints excluded: chain F residue 98 GLU Chi-restraints excluded: chain F residue 166 ILE Chi-restraints excluded: chain F residue 169 ILE Chi-restraints excluded: chain F residue 185 SER Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 153 VAL Chi-restraints excluded: chain G residue 212 LEU Chi-restraints excluded: chain H residue 100 ILE Chi-restraints excluded: chain H residue 162 GLN Chi-restraints excluded: chain H residue 170 VAL Chi-restraints excluded: chain H residue 179 LYS Chi-restraints excluded: chain I residue 61 ASP Chi-restraints excluded: chain I residue 69 SER Chi-restraints excluded: chain I residue 76 THR Chi-restraints excluded: chain I residue 159 SER Chi-restraints excluded: chain I residue 177 SER Chi-restraints excluded: chain I residue 182 CYS Chi-restraints excluded: chain I residue 193 LYS Chi-restraints excluded: chain J residue 12 THR Chi-restraints excluded: chain J residue 29 LEU Chi-restraints excluded: chain J residue 34 GLU Chi-restraints excluded: chain J residue 43 VAL Chi-restraints excluded: chain J residue 64 ASP Chi-restraints excluded: chain J residue 122 SER Chi-restraints excluded: chain K residue 74 GLU Chi-restraints excluded: chain K residue 79 LEU Chi-restraints excluded: chain K residue 88 GLU Chi-restraints excluded: chain L residue 46 THR Chi-restraints excluded: chain L residue 66 VAL Chi-restraints excluded: chain L residue 78 THR Chi-restraints excluded: chain L residue 105 ARG Chi-restraints excluded: chain L residue 146 THR Chi-restraints excluded: chain N residue 26 LEU Chi-restraints excluded: chain N residue 143 SER Chi-restraints excluded: chain O residue 26 ASN Chi-restraints excluded: chain O residue 67 ASP Chi-restraints excluded: chain O residue 81 VAL Chi-restraints excluded: chain O residue 85 CYS Chi-restraints excluded: chain O residue 91 THR Chi-restraints excluded: chain P residue 96 VAL Chi-restraints excluded: chain Q residue 10 VAL Chi-restraints excluded: chain Q residue 25 CYS Chi-restraints excluded: chain Q residue 51 LEU Chi-restraints excluded: chain Q residue 120 LEU Chi-restraints excluded: chain R residue 9 VAL Chi-restraints excluded: chain R residue 66 VAL Chi-restraints excluded: chain R residue 106 LEU Chi-restraints excluded: chain S residue 18 THR Chi-restraints excluded: chain S residue 43 VAL Chi-restraints excluded: chain S residue 98 VAL Chi-restraints excluded: chain S residue 117 ILE Chi-restraints excluded: chain T residue 9 VAL Chi-restraints excluded: chain T residue 36 THR Chi-restraints excluded: chain T residue 45 LEU Chi-restraints excluded: chain T residue 59 SER Chi-restraints excluded: chain T residue 103 VAL Chi-restraints excluded: chain T residue 117 GLN Chi-restraints excluded: chain U residue 39 LEU Chi-restraints excluded: chain V residue 70 LEU Chi-restraints excluded: chain W residue 14 ILE Chi-restraints excluded: chain W residue 25 VAL Chi-restraints excluded: chain W residue 27 ILE Chi-restraints excluded: chain W residue 33 VAL Chi-restraints excluded: chain W residue 36 ARG Chi-restraints excluded: chain W residue 40 VAL Chi-restraints excluded: chain W residue 63 VAL Chi-restraints excluded: chain W residue 103 VAL Chi-restraints excluded: chain W residue 105 THR Chi-restraints excluded: chain W residue 106 THR Chi-restraints excluded: chain X residue 13 LEU Chi-restraints excluded: chain X residue 26 GLN Chi-restraints excluded: chain X residue 118 VAL Chi-restraints excluded: chain Y residue 25 ILE Chi-restraints excluded: chain Y residue 46 LYS Chi-restraints excluded: chain Y residue 47 MET Chi-restraints excluded: chain Y residue 74 MET Chi-restraints excluded: chain Y residue 109 GLU Chi-restraints excluded: chain Z residue 69 THR Chi-restraints excluded: chain Z residue 92 LEU Chi-restraints excluded: chain Z residue 110 THR Chi-restraints excluded: chain Z residue 113 THR Chi-restraints excluded: chain b residue 63 LEU Chi-restraints excluded: chain b residue 74 THR Chi-restraints excluded: chain b residue 77 CYS Chi-restraints excluded: chain c residue 15 THR Chi-restraints excluded: chain e residue 21 LYS Chi-restraints excluded: chain e residue 29 THR Chi-restraints excluded: chain f residue 121 CYS Chi-restraints excluded: chain f residue 123 SER Chi-restraints excluded: chain g residue 3 GLU Chi-restraints excluded: chain g residue 21 ILE Chi-restraints excluded: chain g residue 87 LEU Chi-restraints excluded: chain g residue 96 THR Chi-restraints excluded: chain g residue 111 VAL Chi-restraints excluded: chain g residue 266 ILE Chi-restraints excluded: chain g residue 282 GLU Chi-restraints excluded: chain g residue 287 THR Chi-restraints excluded: chain g residue 296 GLN Chi-restraints excluded: chain x residue 77 LYS Chi-restraints excluded: chain x residue 78 ILE Chi-restraints excluded: chain x residue 88 LEU Chi-restraints excluded: chain x residue 94 LYS Chi-restraints excluded: chain x residue 116 VAL Chi-restraints excluded: chain x residue 118 ILE Chi-restraints excluded: chain x residue 152 LEU Chi-restraints excluded: chain x residue 163 PHE Chi-restraints excluded: chain x residue 176 LEU Chi-restraints excluded: chain x residue 198 THR Chi-restraints excluded: chain x residue 225 ILE Chi-restraints excluded: chain x residue 226 CYS Chi-restraints excluded: chain x residue 244 VAL Chi-restraints excluded: chain y residue 48 VAL Chi-restraints excluded: chain y residue 215 LYS Chi-restraints excluded: chain y residue 268 LEU Chi-restraints excluded: chain y residue 283 VAL Chi-restraints excluded: chain y residue 297 SER Chi-restraints excluded: chain y residue 307 HIS Chi-restraints excluded: chain y residue 328 THR Chi-restraints excluded: chain y residue 341 THR Chi-restraints excluded: chain y residue 359 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 674 random chunks: chunk 605 optimal weight: 0.0670 chunk 461 optimal weight: 4.9990 chunk 318 optimal weight: 0.0050 chunk 67 optimal weight: 8.9990 chunk 292 optimal weight: 0.9980 chunk 411 optimal weight: 10.0000 chunk 615 optimal weight: 7.9990 chunk 651 optimal weight: 5.9990 chunk 321 optimal weight: 40.0000 chunk 583 optimal weight: 6.9990 chunk 175 optimal weight: 6.9990 overall best weight: 2.4136 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 24 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 193 HIS B 43 ASN B 149 GLN B 157 GLN E 138 HIS H 163 GLN I 99 ASN J 125 HIS J 132 GLN K 28 HIS ** K 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 18 GLN ** L 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 26 ASN P 79 HIS P 114 HIS Q 24 HIS Q 29 ASN ** Q 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 26 ASN S 19 ASN ** T 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 64 ASN W 120 HIS X 127 ASN ** Z 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 26 ASN ** g 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** x 210 HIS x 217 ASN x 232 ASN ** y 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.2991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 82008 Z= 0.262 Angle : 0.689 11.220 118686 Z= 0.354 Chirality : 0.042 0.324 14646 Planarity : 0.005 0.057 8879 Dihedral : 23.930 179.569 31754 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 12.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 5.70 % Allowed : 18.62 % Favored : 75.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.95 % Cis-general : 0.00 % Twisted Proline : 0.48 % Twisted General : 0.04 % 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: -1.75 (0.11), residues: 5145 helix: -0.53 (0.13), residues: 1593 sheet: -1.21 (0.16), residues: 921 loop : -1.50 (0.12), residues: 2631 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP B 117 HIS 0.008 0.001 HIS O 32 PHE 0.023 0.002 PHE b 47 TYR 0.035 0.002 TYR I 113 ARG 0.014 0.001 ARG D 65 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10290 Ramachandran restraints generated. 5145 Oldfield, 0 Emsley, 5145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10290 Ramachandran restraints generated. 5145 Oldfield, 0 Emsley, 5145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2031 residues out of total 4500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 256 poor density : 1775 time to evaluate : 4.414 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 PHE cc_start: 0.9340 (m-80) cc_final: 0.9024 (m-80) REVERT: A 35 GLU cc_start: 0.8896 (tt0) cc_final: 0.8560 (mt-10) REVERT: A 50 ASN cc_start: 0.8899 (t0) cc_final: 0.8470 (m110) REVERT: A 55 TRP cc_start: 0.8271 (t-100) cc_final: 0.8056 (t-100) REVERT: A 69 GLU cc_start: 0.8308 (tm-30) cc_final: 0.7913 (tm-30) REVERT: A 75 SER cc_start: 0.8764 (t) cc_final: 0.8459 (t) REVERT: A 99 ILE cc_start: 0.8918 (mt) cc_final: 0.8700 (mt) REVERT: A 169 HIS cc_start: 0.8895 (m-70) cc_final: 0.8539 (m-70) REVERT: A 173 LEU cc_start: 0.9151 (OUTLIER) cc_final: 0.8829 (pp) REVERT: A 174 MET cc_start: 0.8540 (mmm) cc_final: 0.8062 (mmm) REVERT: A 181 GLU cc_start: 0.8188 (tp30) cc_final: 0.7914 (tp30) REVERT: B 29 ASP cc_start: 0.7645 (m-30) cc_final: 0.7181 (m-30) REVERT: B 30 TRP cc_start: 0.8394 (m100) cc_final: 0.7959 (m100) REVERT: B 48 LEU cc_start: 0.8839 (tp) cc_final: 0.8110 (mm) REVERT: B 63 LYS cc_start: 0.8904 (ttmm) cc_final: 0.8652 (mmtt) REVERT: B 75 GLN cc_start: 0.8728 (mt0) cc_final: 0.8188 (tm-30) REVERT: B 92 GLN cc_start: 0.8641 (mm-40) cc_final: 0.8402 (mm-40) REVERT: B 120 MET cc_start: 0.9048 (ttp) cc_final: 0.8812 (ttp) REVERT: B 124 HIS cc_start: 0.7857 (p-80) cc_final: 0.7548 (p-80) REVERT: B 144 LYS cc_start: 0.9151 (tmtt) cc_final: 0.8563 (tmtt) REVERT: B 145 LYS cc_start: 0.9338 (tttt) cc_final: 0.8885 (tttp) REVERT: B 163 GLN cc_start: 0.9037 (mt0) cc_final: 0.8740 (mt0) REVERT: B 168 MET cc_start: 0.8767 (mtt) cc_final: 0.8524 (mtp) REVERT: B 175 GLU cc_start: 0.8847 (mp0) cc_final: 0.8387 (mp0) REVERT: B 202 GLN cc_start: 0.8049 (mm110) cc_final: 0.7664 (mt0) REVERT: B 208 HIS cc_start: 0.7999 (t-90) cc_final: 0.7316 (t-90) REVERT: B 211 PHE cc_start: 0.8608 (m-80) cc_final: 0.7975 (m-80) REVERT: B 217 MET cc_start: 0.8519 (tpt) cc_final: 0.8181 (tpp) REVERT: C 65 LYS cc_start: 0.9290 (OUTLIER) cc_final: 0.8597 (tttm) REVERT: C 84 PHE cc_start: 0.8965 (m-80) cc_final: 0.8638 (m-80) REVERT: C 92 GLU cc_start: 0.8966 (mp0) cc_final: 0.8762 (mp0) REVERT: C 144 SER cc_start: 0.8484 (t) cc_final: 0.8133 (p) REVERT: C 224 THR cc_start: 0.9463 (m) cc_final: 0.9015 (p) REVERT: C 246 LYS cc_start: 0.9103 (mtpt) cc_final: 0.8694 (mtmt) REVERT: C 249 SER cc_start: 0.8959 (m) cc_final: 0.8631 (p) REVERT: D 10 LYS cc_start: 0.8544 (ttpp) cc_final: 0.8175 (ttpp) REVERT: D 54 ARG cc_start: 0.8384 (mpp-170) cc_final: 0.7969 (mmm160) REVERT: D 62 LYS cc_start: 0.8849 (mttt) cc_final: 0.8378 (mmtt) REVERT: D 66 ILE cc_start: 0.9112 (pt) cc_final: 0.8834 (mt) REVERT: D 81 GLU cc_start: 0.8640 (mp0) cc_final: 0.8400 (mp0) REVERT: D 117 ARG cc_start: 0.8955 (mmm160) cc_final: 0.8490 (tpm170) REVERT: D 125 PHE cc_start: 0.8947 (t80) cc_final: 0.8652 (t80) REVERT: D 126 ILE cc_start: 0.7903 (pt) cc_final: 0.7649 (pt) REVERT: D 127 MET cc_start: 0.9242 (mmt) cc_final: 0.8840 (mmt) REVERT: E 127 ARG cc_start: 0.8690 (ttm-80) cc_final: 0.8459 (ttm-80) REVERT: E 130 PHE cc_start: 0.9256 (p90) cc_final: 0.9026 (p90) REVERT: E 211 LYS cc_start: 0.9042 (tttt) cc_final: 0.8819 (ttmm) REVERT: E 237 SER cc_start: 0.8814 (t) cc_final: 0.8382 (p) REVERT: F 43 GLU cc_start: 0.7249 (tp30) cc_final: 0.7034 (tp30) REVERT: F 62 ARG cc_start: 0.8346 (ttm170) cc_final: 0.7885 (ttm170) REVERT: F 79 HIS cc_start: 0.5618 (OUTLIER) cc_final: 0.5009 (t70) REVERT: F 98 GLU cc_start: 0.8931 (OUTLIER) cc_final: 0.8124 (mp0) REVERT: F 106 GLU cc_start: 0.8482 (mp0) cc_final: 0.8241 (mp0) REVERT: F 124 ASP cc_start: 0.8288 (t0) cc_final: 0.7802 (t0) REVERT: F 153 LEU cc_start: 0.9510 (mt) cc_final: 0.9165 (mm) REVERT: F 182 LYS cc_start: 0.9187 (mttt) cc_final: 0.8978 (mtmm) REVERT: G 89 THR cc_start: 0.9376 (m) cc_final: 0.9069 (p) REVERT: G 96 SER cc_start: 0.8820 (m) cc_final: 0.8553 (t) REVERT: G 100 CYS cc_start: 0.8236 (p) cc_final: 0.7868 (p) REVERT: G 154 ARG cc_start: 0.9059 (mtm-85) cc_final: 0.8240 (mtm-85) REVERT: G 196 LYS cc_start: 0.9128 (mttt) cc_final: 0.8819 (mttm) REVERT: G 197 GLN cc_start: 0.8717 (mm-40) cc_final: 0.8495 (mm-40) REVERT: H 147 LYS cc_start: 0.8329 (mmtt) cc_final: 0.7998 (mmtt) REVERT: H 155 LYS cc_start: 0.8661 (mttp) cc_final: 0.8221 (tptp) REVERT: H 160 LYS cc_start: 0.7981 (tmtp) cc_final: 0.7492 (pptt) REVERT: H 171 GLU cc_start: 0.8354 (tm-30) cc_final: 0.7871 (tm-30) REVERT: I 12 ARG cc_start: 0.7858 (mtt90) cc_final: 0.7302 (mtt90) REVERT: I 25 ARG cc_start: 0.7855 (mmt90) cc_final: 0.7505 (mpt180) REVERT: I 53 LYS cc_start: 0.9047 (mttt) cc_final: 0.8753 (mtmm) REVERT: I 61 ASP cc_start: 0.8120 (OUTLIER) cc_final: 0.7875 (m-30) REVERT: I 75 LYS cc_start: 0.9105 (ttpt) cc_final: 0.8708 (ttmt) REVERT: I 94 LYS cc_start: 0.8771 (mttt) cc_final: 0.8484 (mmtm) REVERT: I 153 LYS cc_start: 0.9266 (mttt) cc_final: 0.9048 (mttp) REVERT: I 163 GLU cc_start: 0.8525 (tm-30) cc_final: 0.8309 (tm-30) REVERT: I 194 GLU cc_start: 0.8595 (mp0) cc_final: 0.8270 (mp0) REVERT: J 7 TRP cc_start: 0.9038 (m-10) cc_final: 0.8803 (m-10) REVERT: J 28 GLU cc_start: 0.8831 (mt-10) cc_final: 0.8593 (mt-10) REVERT: J 65 GLU cc_start: 0.8795 (tm-30) cc_final: 0.8517 (tm-30) REVERT: J 79 ARG cc_start: 0.8729 (tpp80) cc_final: 0.8364 (mpp80) REVERT: J 88 ASP cc_start: 0.8577 (m-30) cc_final: 0.8099 (p0) REVERT: J 101 LYS cc_start: 0.8991 (mtpp) cc_final: 0.8609 (mtmm) REVERT: J 104 ASP cc_start: 0.8874 (m-30) cc_final: 0.8420 (m-30) REVERT: J 156 HIS cc_start: 0.8210 (OUTLIER) cc_final: 0.7987 (p-80) REVERT: J 158 ASP cc_start: 0.8524 (t0) cc_final: 0.7942 (t0) REVERT: K 46 MET cc_start: 0.8804 (mtm) cc_final: 0.8524 (mtt) REVERT: K 70 TYR cc_start: 0.7993 (m-80) cc_final: 0.7780 (m-80) REVERT: K 74 GLU cc_start: 0.9239 (OUTLIER) cc_final: 0.8953 (pm20) REVERT: L 11 GLN cc_start: 0.8680 (mm-40) cc_final: 0.8355 (mm-40) REVERT: L 104 LYS cc_start: 0.8828 (mtpm) cc_final: 0.8057 (mtpm) REVERT: L 105 ARG cc_start: 0.8370 (OUTLIER) cc_final: 0.8027 (mtp180) REVERT: M 45 ARG cc_start: 0.7887 (OUTLIER) cc_final: 0.7641 (pmt100) REVERT: N 38 TYR cc_start: 0.9056 (m-10) cc_final: 0.8775 (m-80) REVERT: N 55 ARG cc_start: 0.7867 (ttp-170) cc_final: 0.7596 (ttp-170) REVERT: N 99 ARG cc_start: 0.8935 (ttm110) cc_final: 0.8575 (ttm170) REVERT: N 121 ARG cc_start: 0.8989 (mtm-85) cc_final: 0.8693 (mtm180) REVERT: O 60 MET cc_start: 0.8360 (mtt) cc_final: 0.7674 (mtt) REVERT: O 125 LYS cc_start: 0.8451 (tptm) cc_final: 0.8200 (tptt) REVERT: O 128 ARG cc_start: 0.7042 (mmm160) cc_final: 0.6838 (mmm160) REVERT: P 29 SER cc_start: 0.8909 (m) cc_final: 0.8276 (t) REVERT: P 31 GLU cc_start: 0.8739 (tt0) cc_final: 0.8156 (mp0) REVERT: P 32 GLN cc_start: 0.9063 (mt0) cc_final: 0.8581 (mt0) REVERT: P 77 LYS cc_start: 0.8916 (mtmt) cc_final: 0.8616 (mtmt) REVERT: P 83 MET cc_start: 0.8661 (tpt) cc_final: 0.8357 (tpt) REVERT: P 88 GLU cc_start: 0.8272 (mp0) cc_final: 0.7961 (mp0) REVERT: P 108 LYS cc_start: 0.8653 (mmmt) cc_final: 0.8297 (mmmm) REVERT: P 118 GLU cc_start: 0.8472 (pt0) cc_final: 0.8192 (pt0) REVERT: P 124 LYS cc_start: 0.9156 (tttt) cc_final: 0.8716 (ttpt) REVERT: Q 97 GLN cc_start: 0.8876 (tm-30) cc_final: 0.8665 (tm-30) REVERT: Q 102 GLU cc_start: 0.9160 (tp30) cc_final: 0.8925 (tp30) REVERT: Q 116 ASP cc_start: 0.8162 (t0) cc_final: 0.7857 (t0) REVERT: R 17 ILE cc_start: 0.8990 (mm) cc_final: 0.8788 (mt) REVERT: R 21 TYR cc_start: 0.8732 (t80) cc_final: 0.8433 (t80) REVERT: R 23 ARG cc_start: 0.8208 (mtm-85) cc_final: 0.7925 (mtm-85) REVERT: S 8 LYS cc_start: 0.8954 (mmmt) cc_final: 0.8703 (mmmt) REVERT: S 34 LYS cc_start: 0.9046 (mttt) cc_final: 0.8692 (mtpp) REVERT: S 63 GLU cc_start: 0.8288 (mt-10) cc_final: 0.8020 (mt-10) REVERT: S 78 LYS cc_start: 0.8516 (OUTLIER) cc_final: 0.8151 (tptt) REVERT: S 112 GLU cc_start: 0.8407 (mm-30) cc_final: 0.8129 (tp30) REVERT: T 35 ASP cc_start: 0.8632 (t0) cc_final: 0.8389 (t0) REVERT: T 56 ARG cc_start: 0.9036 (tpp80) cc_final: 0.8835 (tpt-90) REVERT: T 67 ARG cc_start: 0.7101 (OUTLIER) cc_final: 0.6819 (ttt90) REVERT: T 76 THR cc_start: 0.8109 (m) cc_final: 0.7729 (p) REVERT: T 79 TYR cc_start: 0.8304 (m-80) cc_final: 0.7528 (m-80) REVERT: T 88 MET cc_start: 0.8637 (mtp) cc_final: 0.8373 (mtp) REVERT: T 129 ARG cc_start: 0.7950 (mtm110) cc_final: 0.7554 (ttm-80) REVERT: T 142 ASN cc_start: 0.9087 (t0) cc_final: 0.8837 (t0) REVERT: U 46 LYS cc_start: 0.9336 (mtpp) cc_final: 0.9073 (mtmm) REVERT: U 47 ASN cc_start: 0.9466 (t0) cc_final: 0.9076 (m110) REVERT: U 51 LYS cc_start: 0.8386 (mmtt) cc_final: 0.7704 (ttmt) REVERT: U 59 LYS cc_start: 0.8845 (mptt) cc_final: 0.8557 (mptt) REVERT: U 97 ILE cc_start: 0.8333 (mp) cc_final: 0.7999 (mp) REVERT: U 99 LYS cc_start: 0.9249 (ptpt) cc_final: 0.8485 (tptp) REVERT: U 100 GLN cc_start: 0.9073 (tt0) cc_final: 0.8621 (tm-30) REVERT: V 7 GLU cc_start: 0.8533 (mp0) cc_final: 0.8091 (mp0) REVERT: V 8 PHE cc_start: 0.8725 (m-80) cc_final: 0.8390 (m-80) REVERT: V 47 ASN cc_start: 0.8738 (p0) cc_final: 0.7895 (p0) REVERT: V 49 GLN cc_start: 0.9208 (mm-40) cc_final: 0.8890 (mp10) REVERT: V 61 ARG cc_start: 0.8495 (mtp85) cc_final: 0.8115 (mtp85) REVERT: W 5 ASN cc_start: 0.8762 (t0) cc_final: 0.8504 (t0) REVERT: W 23 ARG cc_start: 0.8576 (mmm160) cc_final: 0.8270 (mmm160) REVERT: W 49 GLU cc_start: 0.7415 (pt0) cc_final: 0.6407 (pt0) REVERT: W 51 GLU cc_start: 0.8105 (mm-30) cc_final: 0.7651 (mm-30) REVERT: W 86 LEU cc_start: 0.9054 (tp) cc_final: 0.8761 (tt) REVERT: W 90 GLN cc_start: 0.8865 (pt0) cc_final: 0.8346 (pt0) REVERT: W 91 ASN cc_start: 0.9258 (t0) cc_final: 0.9015 (t0) REVERT: W 111 MET cc_start: 0.7983 (ptp) cc_final: 0.7751 (ptp) REVERT: X 8 ARG cc_start: 0.8293 (mtt180) cc_final: 0.7806 (mtp85) REVERT: X 18 ARG cc_start: 0.8816 (ttp80) cc_final: 0.8594 (ttp80) REVERT: X 48 LYS cc_start: 0.9057 (tttt) cc_final: 0.8782 (ttmt) REVERT: X 58 GLU cc_start: 0.8405 (mm-30) cc_final: 0.8163 (mm-30) REVERT: X 95 GLU cc_start: 0.8176 (tp30) cc_final: 0.7793 (tp30) REVERT: X 98 ASP cc_start: 0.7867 (m-30) cc_final: 0.7489 (m-30) REVERT: Y 19 GLN cc_start: 0.9127 (mp10) cc_final: 0.8895 (mp10) REVERT: Y 78 SER cc_start: 0.9282 (t) cc_final: 0.8966 (p) REVERT: Y 86 GLU cc_start: 0.8756 (mm-30) cc_final: 0.8053 (tp30) REVERT: Y 106 GLN cc_start: 0.9143 (mm-40) cc_final: 0.8942 (mt0) REVERT: b 23 ARG cc_start: 0.8626 (mpt-90) cc_final: 0.8258 (mpt-90) REVERT: b 63 LEU cc_start: 0.7619 (OUTLIER) cc_final: 0.7246 (mp) REVERT: c 10 LYS cc_start: 0.8887 (mttt) cc_final: 0.8481 (mtpp) REVERT: c 13 ARG cc_start: 0.7672 (mmm160) cc_final: 0.7282 (tpp80) REVERT: c 15 THR cc_start: 0.9383 (OUTLIER) cc_final: 0.8800 (p) REVERT: c 26 GLN cc_start: 0.8216 (pt0) cc_final: 0.7247 (pm20) REVERT: c 31 ARG cc_start: 0.9039 (OUTLIER) cc_final: 0.8669 (tpm-80) REVERT: c 35 MET cc_start: 0.8808 (mmm) cc_final: 0.8541 (mmt) REVERT: c 52 GLU cc_start: 0.8773 (tt0) cc_final: 0.8412 (tp30) REVERT: c 54 ASP cc_start: 0.7489 (m-30) cc_final: 0.7236 (m-30) REVERT: g 3 GLU cc_start: 0.8541 (OUTLIER) cc_final: 0.8233 (mm-30) REVERT: g 4 GLN cc_start: 0.6381 (mp10) cc_final: 0.6153 (mp10) REVERT: g 5 MET cc_start: 0.8771 (mmt) cc_final: 0.8474 (mmm) REVERT: g 76 GLN cc_start: 0.8533 (tp-100) cc_final: 0.8138 (tp-100) REVERT: g 86 THR cc_start: 0.8995 (m) cc_final: 0.8605 (t) REVERT: g 100 ARG cc_start: 0.8011 (mmm-85) cc_final: 0.7730 (tpp80) REVERT: g 118 ARG cc_start: 0.9193 (pmm150) cc_final: 0.8906 (mtm-85) REVERT: g 143 GLN cc_start: 0.8750 (tp40) cc_final: 0.8320 (tp40) REVERT: g 191 HIS cc_start: 0.7700 (OUTLIER) cc_final: 0.7316 (t-90) REVERT: g 206 LEU cc_start: 0.8641 (mm) cc_final: 0.8130 (tp) REVERT: g 241 PHE cc_start: 0.8371 (OUTLIER) cc_final: 0.8043 (m-10) REVERT: g 285 GLN cc_start: 0.8415 (mm-40) cc_final: 0.7906 (tp-100) REVERT: x 77 LYS cc_start: 0.8335 (OUTLIER) cc_final: 0.8026 (mtmm) REVERT: x 90 GLU cc_start: 0.9216 (tp30) cc_final: 0.8961 (tp30) REVERT: x 94 LYS cc_start: 0.9093 (OUTLIER) cc_final: 0.8727 (mppt) REVERT: x 117 GLU cc_start: 0.7850 (OUTLIER) cc_final: 0.7004 (mm-30) REVERT: x 126 ASP cc_start: 0.8482 (t0) cc_final: 0.8205 (t70) REVERT: x 163 PHE cc_start: 0.7650 (OUTLIER) cc_final: 0.7372 (m-10) REVERT: x 189 LYS cc_start: 0.8820 (tmtp) cc_final: 0.8439 (tmtp) REVERT: x 208 LYS cc_start: 0.9080 (mmtp) cc_final: 0.8799 (mmtp) REVERT: x 217 ASN cc_start: 0.8375 (m-40) cc_final: 0.8033 (t0) REVERT: x 232 ASN cc_start: 0.8853 (m-40) cc_final: 0.8600 (m-40) REVERT: y 105 GLN cc_start: 0.4942 (pt0) cc_final: 0.4731 (mp10) REVERT: y 114 SER cc_start: 0.8666 (p) cc_final: 0.8191 (m) REVERT: y 280 MET cc_start: 0.8028 (mmm) cc_final: 0.7673 (mmp) REVERT: y 308 MET cc_start: 0.8636 (mtp) cc_final: 0.8275 (mpp) REVERT: y 312 ARG cc_start: 0.6954 (ttm170) cc_final: 0.6597 (mtm110) REVERT: y 405 ARG cc_start: 0.6180 (ppt170) cc_final: 0.5873 (ppt170) outliers start: 256 outliers final: 165 residues processed: 1867 average time/residue: 0.8073 time to fit residues: 2488.6836 Evaluate side-chains 1876 residues out of total 4500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 186 poor density : 1690 time to evaluate : 4.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 125 THR Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 173 LEU Chi-restraints excluded: chain A residue 185 MET Chi-restraints excluded: chain B residue 56 LYS Chi-restraints excluded: chain B residue 210 VAL Chi-restraints excluded: chain C residue 65 LYS Chi-restraints excluded: chain C residue 108 LYS Chi-restraints excluded: chain C residue 130 ILE Chi-restraints excluded: chain C residue 156 ILE Chi-restraints excluded: chain C residue 165 VAL Chi-restraints excluded: chain C residue 192 LEU Chi-restraints excluded: chain C residue 221 ASP Chi-restraints excluded: chain C residue 222 CYS Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain D residue 4 GLN Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 16 ILE Chi-restraints excluded: chain D residue 53 THR Chi-restraints excluded: chain D residue 55 THR Chi-restraints excluded: chain D residue 158 ILE Chi-restraints excluded: chain D residue 168 VAL Chi-restraints excluded: chain D residue 198 ILE Chi-restraints excluded: chain D residue 208 VAL Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 32 SER Chi-restraints excluded: chain E residue 44 LEU Chi-restraints excluded: chain E residue 45 ILE Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 146 THR Chi-restraints excluded: chain E residue 177 THR Chi-restraints excluded: chain E residue 204 SER Chi-restraints excluded: chain E residue 256 LEU Chi-restraints excluded: chain F residue 35 LEU Chi-restraints excluded: chain F residue 78 MET Chi-restraints excluded: chain F residue 79 HIS Chi-restraints excluded: chain F residue 90 VAL Chi-restraints excluded: chain F residue 98 GLU Chi-restraints excluded: chain F residue 166 ILE Chi-restraints excluded: chain F residue 169 ILE Chi-restraints excluded: chain F residue 185 SER Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 153 VAL Chi-restraints excluded: chain G residue 212 LEU Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 100 ILE Chi-restraints excluded: chain H residue 122 LEU Chi-restraints excluded: chain H residue 151 SER Chi-restraints excluded: chain H residue 162 GLN Chi-restraints excluded: chain H residue 179 LYS Chi-restraints excluded: chain I residue 61 ASP Chi-restraints excluded: chain I residue 69 SER Chi-restraints excluded: chain I residue 76 THR Chi-restraints excluded: chain I residue 102 VAL Chi-restraints excluded: chain I residue 148 LYS Chi-restraints excluded: chain I residue 157 LYS Chi-restraints excluded: chain I residue 159 SER Chi-restraints excluded: chain I residue 160 SER Chi-restraints excluded: chain I residue 177 SER Chi-restraints excluded: chain I residue 182 CYS Chi-restraints excluded: chain I residue 193 LYS Chi-restraints excluded: chain J residue 12 THR Chi-restraints excluded: chain J residue 29 LEU Chi-restraints excluded: chain J residue 34 GLU Chi-restraints excluded: chain J residue 43 VAL Chi-restraints excluded: chain J residue 55 LYS Chi-restraints excluded: chain J residue 64 ASP Chi-restraints excluded: chain J residue 98 LEU Chi-restraints excluded: chain J residue 122 SER Chi-restraints excluded: chain J residue 156 HIS Chi-restraints excluded: chain K residue 74 GLU Chi-restraints excluded: chain K residue 79 LEU Chi-restraints excluded: chain K residue 88 GLU Chi-restraints excluded: chain L residue 46 THR Chi-restraints excluded: chain L residue 56 ILE Chi-restraints excluded: chain L residue 66 VAL Chi-restraints excluded: chain L residue 78 THR Chi-restraints excluded: chain L residue 105 ARG Chi-restraints excluded: chain L residue 146 THR Chi-restraints excluded: chain M residue 45 ARG Chi-restraints excluded: chain N residue 26 LEU Chi-restraints excluded: chain N residue 30 SER Chi-restraints excluded: chain N residue 54 LEU Chi-restraints excluded: chain N residue 143 SER Chi-restraints excluded: chain O residue 26 ASN Chi-restraints excluded: chain O residue 67 ASP Chi-restraints excluded: chain O residue 81 VAL Chi-restraints excluded: chain O residue 91 THR Chi-restraints excluded: chain P residue 96 VAL Chi-restraints excluded: chain P residue 105 VAL Chi-restraints excluded: chain Q residue 10 VAL Chi-restraints excluded: chain Q residue 25 CYS Chi-restraints excluded: chain Q residue 31 LEU Chi-restraints excluded: chain Q residue 55 VAL Chi-restraints excluded: chain Q residue 66 VAL Chi-restraints excluded: chain R residue 6 THR Chi-restraints excluded: chain R residue 9 VAL Chi-restraints excluded: chain R residue 22 THR Chi-restraints excluded: chain R residue 40 ILE Chi-restraints excluded: chain S residue 18 THR Chi-restraints excluded: chain S residue 20 ILE Chi-restraints excluded: chain S residue 43 VAL Chi-restraints excluded: chain S residue 71 MET Chi-restraints excluded: chain S residue 78 LYS Chi-restraints excluded: chain S residue 98 VAL Chi-restraints excluded: chain S residue 117 ILE Chi-restraints excluded: chain T residue 45 LEU Chi-restraints excluded: chain T residue 55 THR Chi-restraints excluded: chain T residue 59 SER Chi-restraints excluded: chain T residue 67 ARG Chi-restraints excluded: chain U residue 39 LEU Chi-restraints excluded: chain W residue 14 ILE Chi-restraints excluded: chain W residue 25 VAL Chi-restraints excluded: chain W residue 27 ILE Chi-restraints excluded: chain W residue 32 LYS Chi-restraints excluded: chain W residue 33 VAL Chi-restraints excluded: chain W residue 36 ARG Chi-restraints excluded: chain W residue 40 VAL Chi-restraints excluded: chain W residue 63 VAL Chi-restraints excluded: chain W residue 103 VAL Chi-restraints excluded: chain W residue 105 THR Chi-restraints excluded: chain W residue 106 THR Chi-restraints excluded: chain X residue 13 LEU Chi-restraints excluded: chain X residue 77 ASN Chi-restraints excluded: chain X residue 118 VAL Chi-restraints excluded: chain X residue 128 VAL Chi-restraints excluded: chain Y residue 17 LEU Chi-restraints excluded: chain Y residue 25 ILE Chi-restraints excluded: chain Y residue 46 LYS Chi-restraints excluded: chain Y residue 55 ILE Chi-restraints excluded: chain Y residue 74 MET Chi-restraints excluded: chain Z residue 58 LEU Chi-restraints excluded: chain Z residue 69 THR Chi-restraints excluded: chain Z residue 92 LEU Chi-restraints excluded: chain Z residue 108 ILE Chi-restraints excluded: chain Z residue 110 THR Chi-restraints excluded: chain Z residue 113 THR Chi-restraints excluded: chain b residue 63 LEU Chi-restraints excluded: chain b residue 74 THR Chi-restraints excluded: chain b residue 77 CYS Chi-restraints excluded: chain c residue 15 THR Chi-restraints excluded: chain c residue 31 ARG Chi-restraints excluded: chain d residue 32 ARG Chi-restraints excluded: chain d residue 36 LEU Chi-restraints excluded: chain e residue 21 LYS Chi-restraints excluded: chain e residue 29 THR Chi-restraints excluded: chain f residue 121 CYS Chi-restraints excluded: chain f residue 123 SER Chi-restraints excluded: chain g residue 3 GLU Chi-restraints excluded: chain g residue 24 THR Chi-restraints excluded: chain g residue 96 THR Chi-restraints excluded: chain g residue 111 VAL Chi-restraints excluded: chain g residue 191 HIS Chi-restraints excluded: chain g residue 207 CYS Chi-restraints excluded: chain g residue 241 PHE Chi-restraints excluded: chain g residue 245 ARG Chi-restraints excluded: chain g residue 261 LEU Chi-restraints excluded: chain g residue 266 ILE Chi-restraints excluded: chain g residue 287 THR Chi-restraints excluded: chain x residue 77 LYS Chi-restraints excluded: chain x residue 78 ILE Chi-restraints excluded: chain x residue 88 LEU Chi-restraints excluded: chain x residue 94 LYS Chi-restraints excluded: chain x residue 116 VAL Chi-restraints excluded: chain x residue 117 GLU Chi-restraints excluded: chain x residue 118 ILE Chi-restraints excluded: chain x residue 152 LEU Chi-restraints excluded: chain x residue 163 PHE Chi-restraints excluded: chain x residue 177 SER Chi-restraints excluded: chain x residue 198 THR Chi-restraints excluded: chain x residue 225 ILE Chi-restraints excluded: chain x residue 226 CYS Chi-restraints excluded: chain y residue 48 VAL Chi-restraints excluded: chain y residue 126 SER Chi-restraints excluded: chain y residue 215 LYS Chi-restraints excluded: chain y residue 268 LEU Chi-restraints excluded: chain y residue 286 SER Chi-restraints excluded: chain y residue 297 SER Chi-restraints excluded: chain y residue 307 HIS Chi-restraints excluded: chain y residue 316 VAL Chi-restraints excluded: chain y residue 328 THR Chi-restraints excluded: chain y residue 341 THR Chi-restraints excluded: chain y residue 359 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 674 random chunks: chunk 542 optimal weight: 3.9990 chunk 369 optimal weight: 2.9990 chunk 9 optimal weight: 5.9990 chunk 485 optimal weight: 2.9990 chunk 268 optimal weight: 6.9990 chunk 555 optimal weight: 3.9990 chunk 450 optimal weight: 5.9990 chunk 0 optimal weight: 6.9990 chunk 332 optimal weight: 10.0000 chunk 584 optimal weight: 10.0000 chunk 164 optimal weight: 10.0000 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 157 GLN B 177 GLN H 163 GLN I 99 ASN J 132 GLN K 28 HIS ** K 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 11 GLN L 106 HIS ** L 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 113 GLN P 114 HIS Q 11 GLN Q 24 HIS ** Q 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 26 ASN S 19 ASN W 64 ASN X 127 ASN ** Z 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 49 HIS d 26 ASN g 133 ASN g 237 ASN ** g 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** x 210 HIS y 85 GLN ** y 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7992 moved from start: 0.3180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.064 82008 Z= 0.383 Angle : 0.749 10.201 118686 Z= 0.383 Chirality : 0.045 0.360 14646 Planarity : 0.005 0.077 8879 Dihedral : 23.895 179.980 31754 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 14.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.60 % Favored : 94.40 % Rotamer: Outliers : 6.10 % Allowed : 19.28 % Favored : 74.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.95 % Cis-general : 0.00 % Twisted Proline : 0.48 % 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: -1.70 (0.11), residues: 5145 helix: -0.47 (0.13), residues: 1611 sheet: -1.26 (0.16), residues: 925 loop : -1.44 (0.12), residues: 2609 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP I 67 HIS 0.009 0.001 HIS S 135 PHE 0.027 0.002 PHE T 14 TYR 0.033 0.002 TYR I 113 ARG 0.014 0.001 ARG F 135 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10290 Ramachandran restraints generated. 5145 Oldfield, 0 Emsley, 5145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10290 Ramachandran restraints generated. 5145 Oldfield, 0 Emsley, 5145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2005 residues out of total 4500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 274 poor density : 1731 time to evaluate : 4.387 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 13 GLU cc_start: 0.8603 (pm20) cc_final: 0.8397 (pm20) REVERT: A 18 PHE cc_start: 0.9372 (m-80) cc_final: 0.9088 (m-80) REVERT: A 33 GLN cc_start: 0.8918 (mm-40) cc_final: 0.8446 (mm-40) REVERT: A 35 GLU cc_start: 0.8881 (tt0) cc_final: 0.8487 (mt-10) REVERT: A 50 ASN cc_start: 0.8937 (t0) cc_final: 0.8508 (m110) REVERT: A 52 LYS cc_start: 0.7956 (ttmt) cc_final: 0.7485 (ttmt) REVERT: A 69 GLU cc_start: 0.8373 (tm-30) cc_final: 0.7938 (tm-30) REVERT: A 75 SER cc_start: 0.8818 (t) cc_final: 0.8542 (t) REVERT: A 99 ILE cc_start: 0.8871 (mt) cc_final: 0.8597 (mt) REVERT: A 169 HIS cc_start: 0.8988 (m-70) cc_final: 0.8618 (m-70) REVERT: A 173 LEU cc_start: 0.9193 (OUTLIER) cc_final: 0.8798 (pp) REVERT: A 174 MET cc_start: 0.8563 (mmm) cc_final: 0.8161 (mmm) REVERT: A 181 GLU cc_start: 0.8243 (tp30) cc_final: 0.7922 (tp30) REVERT: A 185 MET cc_start: 0.9460 (OUTLIER) cc_final: 0.8840 (tpp) REVERT: A 198 MET cc_start: 0.7989 (ttm) cc_final: 0.7363 (ttt) REVERT: B 29 ASP cc_start: 0.7707 (m-30) cc_final: 0.7100 (m-30) REVERT: B 48 LEU cc_start: 0.8815 (tp) cc_final: 0.8495 (mm) REVERT: B 63 LYS cc_start: 0.8913 (ttmm) cc_final: 0.8449 (tptt) REVERT: B 75 GLN cc_start: 0.8744 (OUTLIER) cc_final: 0.8136 (tm-30) REVERT: B 92 GLN cc_start: 0.8620 (mm-40) cc_final: 0.8348 (mm-40) REVERT: B 98 THR cc_start: 0.8562 (p) cc_final: 0.8313 (t) REVERT: B 120 MET cc_start: 0.9032 (ttp) cc_final: 0.8745 (ttp) REVERT: B 124 HIS cc_start: 0.7950 (p-80) cc_final: 0.7633 (p-80) REVERT: B 144 LYS cc_start: 0.9095 (tmtt) cc_final: 0.8605 (ttpp) REVERT: B 145 LYS cc_start: 0.9328 (tttt) cc_final: 0.8779 (tttp) REVERT: B 159 GLN cc_start: 0.8821 (mm-40) cc_final: 0.8456 (mm-40) REVERT: B 163 GLN cc_start: 0.9041 (mt0) cc_final: 0.8790 (mt0) REVERT: B 168 MET cc_start: 0.8786 (mtt) cc_final: 0.8557 (mtp) REVERT: B 175 GLU cc_start: 0.9147 (mp0) cc_final: 0.8756 (mp0) REVERT: B 202 GLN cc_start: 0.8093 (mm110) cc_final: 0.7722 (mt0) REVERT: B 208 HIS cc_start: 0.8000 (t-90) cc_final: 0.7519 (t-90) REVERT: B 211 PHE cc_start: 0.8594 (m-80) cc_final: 0.8271 (m-80) REVERT: B 217 MET cc_start: 0.8537 (tpt) cc_final: 0.8016 (tpp) REVERT: C 65 LYS cc_start: 0.9247 (OUTLIER) cc_final: 0.8689 (tttm) REVERT: C 84 PHE cc_start: 0.8980 (m-80) cc_final: 0.8630 (m-80) REVERT: C 92 GLU cc_start: 0.8965 (mp0) cc_final: 0.8744 (mp0) REVERT: C 144 SER cc_start: 0.8393 (t) cc_final: 0.7994 (p) REVERT: C 152 ARG cc_start: 0.8884 (ttp-110) cc_final: 0.8643 (ttp-110) REVERT: C 223 TYR cc_start: 0.8897 (m-80) cc_final: 0.8619 (m-80) REVERT: C 224 THR cc_start: 0.9495 (m) cc_final: 0.9034 (p) REVERT: C 246 LYS cc_start: 0.9141 (mtpt) cc_final: 0.8829 (mtmt) REVERT: C 249 SER cc_start: 0.9005 (m) cc_final: 0.8690 (p) REVERT: D 18 LYS cc_start: 0.8718 (mmmm) cc_final: 0.8426 (mmmm) REVERT: D 54 ARG cc_start: 0.8448 (mpp-170) cc_final: 0.7947 (mmm160) REVERT: D 62 LYS cc_start: 0.8822 (mttt) cc_final: 0.8308 (mmmt) REVERT: D 81 GLU cc_start: 0.8640 (mp0) cc_final: 0.8418 (mp0) REVERT: D 117 ARG cc_start: 0.8940 (mmm160) cc_final: 0.8424 (tpm170) REVERT: D 125 PHE cc_start: 0.8948 (t80) cc_final: 0.8556 (t80) REVERT: D 126 ILE cc_start: 0.7951 (pt) cc_final: 0.7683 (pt) REVERT: D 127 MET cc_start: 0.9317 (mmt) cc_final: 0.8872 (mmt) REVERT: D 159 HIS cc_start: 0.8241 (m170) cc_final: 0.7887 (m170) REVERT: E 88 ASP cc_start: 0.8721 (m-30) cc_final: 0.8394 (m-30) REVERT: E 127 ARG cc_start: 0.8729 (ttm-80) cc_final: 0.8509 (ttm-80) REVERT: E 130 PHE cc_start: 0.9285 (p90) cc_final: 0.9053 (p90) REVERT: E 211 LYS cc_start: 0.9023 (tttt) cc_final: 0.8818 (ttmm) REVERT: E 237 SER cc_start: 0.8925 (t) cc_final: 0.8310 (p) REVERT: F 25 THR cc_start: 0.9028 (p) cc_final: 0.8822 (p) REVERT: F 43 GLU cc_start: 0.7314 (tp30) cc_final: 0.7064 (tp30) REVERT: F 62 ARG cc_start: 0.8423 (ttm170) cc_final: 0.8006 (ttm170) REVERT: F 79 HIS cc_start: 0.5805 (OUTLIER) cc_final: 0.5136 (t70) REVERT: F 98 GLU cc_start: 0.8946 (OUTLIER) cc_final: 0.8178 (mp0) REVERT: F 106 GLU cc_start: 0.8606 (mp0) cc_final: 0.8357 (mp0) REVERT: F 124 ASP cc_start: 0.8237 (t0) cc_final: 0.7833 (t0) REVERT: F 153 LEU cc_start: 0.9511 (mt) cc_final: 0.9173 (mm) REVERT: G 89 THR cc_start: 0.9372 (m) cc_final: 0.9018 (p) REVERT: G 91 GLU cc_start: 0.8323 (pp20) cc_final: 0.7925 (pp20) REVERT: G 92 ARG cc_start: 0.8831 (mtm-85) cc_final: 0.8447 (mtm-85) REVERT: G 96 SER cc_start: 0.8896 (m) cc_final: 0.8590 (t) REVERT: G 100 CYS cc_start: 0.8327 (p) cc_final: 0.8040 (p) REVERT: G 101 ILE cc_start: 0.8992 (mt) cc_final: 0.8785 (mt) REVERT: G 154 ARG cc_start: 0.9067 (mtm-85) cc_final: 0.8232 (mtm-85) REVERT: G 196 LYS cc_start: 0.9155 (mttt) cc_final: 0.8856 (mttm) REVERT: G 197 GLN cc_start: 0.8900 (mm-40) cc_final: 0.8618 (mm-40) REVERT: H 147 LYS cc_start: 0.8410 (mmtt) cc_final: 0.8014 (mmtt) REVERT: H 155 LYS cc_start: 0.8621 (mttp) cc_final: 0.8263 (tptp) REVERT: H 160 LYS cc_start: 0.7927 (tmtp) cc_final: 0.7464 (pptt) REVERT: H 171 GLU cc_start: 0.8348 (tm-30) cc_final: 0.7841 (tm-30) REVERT: I 12 ARG cc_start: 0.7914 (mtt90) cc_final: 0.7464 (mtt90) REVERT: I 17 LYS cc_start: 0.8224 (ptmm) cc_final: 0.8013 (ptmm) REVERT: I 25 ARG cc_start: 0.7893 (mmt90) cc_final: 0.7472 (mpt180) REVERT: I 27 TYR cc_start: 0.9097 (p90) cc_final: 0.8676 (p90) REVERT: I 53 LYS cc_start: 0.9014 (mttt) cc_final: 0.8737 (mtmm) REVERT: I 61 ASP cc_start: 0.8104 (OUTLIER) cc_final: 0.7864 (m-30) REVERT: I 73 THR cc_start: 0.9149 (OUTLIER) cc_final: 0.8719 (p) REVERT: I 75 LYS cc_start: 0.9088 (ttpt) cc_final: 0.8704 (ttmt) REVERT: I 94 LYS cc_start: 0.8824 (mttt) cc_final: 0.8553 (mmtm) REVERT: I 155 ASN cc_start: 0.8896 (m-40) cc_final: 0.8652 (m-40) REVERT: I 163 GLU cc_start: 0.8515 (tm-30) cc_final: 0.8295 (tm-30) REVERT: I 194 GLU cc_start: 0.8567 (mp0) cc_final: 0.8297 (mp0) REVERT: J 7 TRP cc_start: 0.9107 (m-10) cc_final: 0.8855 (m-10) REVERT: J 11 LYS cc_start: 0.8524 (ttmt) cc_final: 0.8311 (ttmt) REVERT: J 22 LYS cc_start: 0.8155 (mmtt) cc_final: 0.7649 (mmtp) REVERT: J 48 PHE cc_start: 0.8465 (t80) cc_final: 0.8206 (t80) REVERT: J 65 GLU cc_start: 0.8823 (tm-30) cc_final: 0.8552 (tm-30) REVERT: J 79 ARG cc_start: 0.8757 (tpp80) cc_final: 0.8380 (mpp80) REVERT: J 88 ASP cc_start: 0.8550 (m-30) cc_final: 0.7973 (p0) REVERT: J 91 LYS cc_start: 0.9275 (mttt) cc_final: 0.9034 (mtpp) REVERT: J 101 LYS cc_start: 0.8987 (mtpp) cc_final: 0.8593 (mtmm) REVERT: J 104 ASP cc_start: 0.8866 (m-30) cc_final: 0.8445 (m-30) REVERT: J 156 HIS cc_start: 0.8560 (OUTLIER) cc_final: 0.8141 (p-80) REVERT: J 158 ASP cc_start: 0.8568 (t0) cc_final: 0.8088 (t0) REVERT: K 46 MET cc_start: 0.8835 (mtm) cc_final: 0.8633 (mtm) REVERT: K 55 ARG cc_start: 0.8836 (ttp-110) cc_final: 0.8621 (mtm110) REVERT: K 65 ARG cc_start: 0.7897 (mmm-85) cc_final: 0.7670 (mmt90) REVERT: K 70 TYR cc_start: 0.8061 (m-80) cc_final: 0.7727 (m-80) REVERT: K 74 GLU cc_start: 0.9220 (OUTLIER) cc_final: 0.9015 (pm20) REVERT: L 11 GLN cc_start: 0.8625 (mm110) cc_final: 0.8301 (mm-40) REVERT: L 103 GLU cc_start: 0.8423 (pt0) cc_final: 0.7921 (pt0) REVERT: L 104 LYS cc_start: 0.8912 (mtpm) cc_final: 0.8314 (mtpm) REVERT: L 135 SER cc_start: 0.8526 (t) cc_final: 0.8263 (t) REVERT: M 12 MET cc_start: 0.4300 (ptt) cc_final: 0.4100 (ptt) REVERT: M 45 ARG cc_start: 0.7963 (OUTLIER) cc_final: 0.7709 (pmt100) REVERT: M 85 LEU cc_start: 0.6657 (mt) cc_final: 0.6271 (mt) REVERT: N 35 GLU cc_start: 0.8809 (pp20) cc_final: 0.8607 (pp20) REVERT: O 50 LYS cc_start: 0.8589 (tttp) cc_final: 0.8220 (tptm) REVERT: O 51 GLU cc_start: 0.6709 (mp0) cc_final: 0.6246 (mp0) REVERT: O 60 MET cc_start: 0.8420 (mtt) cc_final: 0.7758 (mtt) REVERT: O 125 LYS cc_start: 0.8486 (tptm) cc_final: 0.8214 (tptt) REVERT: O 128 ARG cc_start: 0.7110 (mmm160) cc_final: 0.6885 (mmm160) REVERT: P 29 SER cc_start: 0.8888 (m) cc_final: 0.8260 (t) REVERT: P 31 GLU cc_start: 0.8791 (tt0) cc_final: 0.8228 (mp0) REVERT: P 32 GLN cc_start: 0.9067 (mt0) cc_final: 0.8609 (mt0) REVERT: P 83 MET cc_start: 0.8681 (tpt) cc_final: 0.8182 (tpt) REVERT: P 124 LYS cc_start: 0.9223 (tttt) cc_final: 0.8738 (ttpt) REVERT: Q 51 LEU cc_start: 0.9166 (OUTLIER) cc_final: 0.8924 (mp) REVERT: Q 97 GLN cc_start: 0.8844 (tm-30) cc_final: 0.8549 (tm-30) REVERT: Q 98 LYS cc_start: 0.9007 (tppt) cc_final: 0.8748 (tppt) REVERT: Q 105 LYS cc_start: 0.9419 (tttp) cc_final: 0.9077 (tttp) REVERT: Q 106 LYS cc_start: 0.9629 (tptm) cc_final: 0.9308 (tptp) REVERT: Q 110 ASP cc_start: 0.9077 (p0) cc_final: 0.8693 (p0) REVERT: Q 116 ASP cc_start: 0.8248 (t0) cc_final: 0.7942 (t0) REVERT: R 21 TYR cc_start: 0.8731 (t80) cc_final: 0.8371 (t80) REVERT: R 49 LYS cc_start: 0.8451 (mtpp) cc_final: 0.8166 (mtpp) REVERT: S 63 GLU cc_start: 0.8296 (mt-10) cc_final: 0.7876 (mt-10) REVERT: S 78 LYS cc_start: 0.8630 (tptp) cc_final: 0.8348 (tptp) REVERT: T 35 ASP cc_start: 0.8677 (t0) cc_final: 0.8399 (t0) REVERT: T 67 ARG cc_start: 0.6995 (OUTLIER) cc_final: 0.6729 (ttt90) REVERT: T 76 THR cc_start: 0.8146 (m) cc_final: 0.7789 (p) REVERT: T 79 TYR cc_start: 0.8379 (m-80) cc_final: 0.7585 (m-80) REVERT: T 88 MET cc_start: 0.8702 (mtp) cc_final: 0.8455 (mtp) REVERT: T 129 ARG cc_start: 0.7935 (mtm110) cc_final: 0.7670 (ttm-80) REVERT: T 142 ASN cc_start: 0.9134 (t0) cc_final: 0.8867 (t0) REVERT: U 46 LYS cc_start: 0.9304 (mtpp) cc_final: 0.9064 (mtmm) REVERT: U 47 ASN cc_start: 0.9472 (t0) cc_final: 0.9104 (m110) REVERT: U 49 LYS cc_start: 0.8135 (tttt) cc_final: 0.7900 (ptmt) REVERT: U 51 LYS cc_start: 0.8394 (mmtt) cc_final: 0.7656 (ttmt) REVERT: U 59 LYS cc_start: 0.8843 (mptt) cc_final: 0.8522 (mptt) REVERT: U 97 ILE cc_start: 0.8307 (mp) cc_final: 0.8020 (mp) REVERT: U 99 LYS cc_start: 0.9297 (ptpt) cc_final: 0.8613 (tptp) REVERT: U 100 GLN cc_start: 0.9094 (tt0) cc_final: 0.8533 (tm-30) REVERT: V 7 GLU cc_start: 0.8581 (mp0) cc_final: 0.8042 (mp0) REVERT: V 8 PHE cc_start: 0.8731 (m-80) cc_final: 0.8530 (m-80) REVERT: V 47 ASN cc_start: 0.8736 (p0) cc_final: 0.8451 (p0) REVERT: V 49 GLN cc_start: 0.9219 (mm-40) cc_final: 0.8720 (mp10) REVERT: V 51 LYS cc_start: 0.9164 (mttt) cc_final: 0.8920 (mtmt) REVERT: V 59 ILE cc_start: 0.9202 (mt) cc_final: 0.8776 (mt) REVERT: V 61 ARG cc_start: 0.8470 (mtp85) cc_final: 0.8098 (mtp85) REVERT: V 76 ASP cc_start: 0.8741 (m-30) cc_final: 0.8167 (m-30) REVERT: W 5 ASN cc_start: 0.8863 (t0) cc_final: 0.8608 (t0) REVERT: W 11 LEU cc_start: 0.9242 (mt) cc_final: 0.9000 (mt) REVERT: W 23 ARG cc_start: 0.8635 (mmm160) cc_final: 0.8290 (mmm160) REVERT: W 24 GLN cc_start: 0.9078 (mt0) cc_final: 0.8806 (mt0) REVERT: W 49 GLU cc_start: 0.7490 (pt0) cc_final: 0.6415 (pt0) REVERT: W 51 GLU cc_start: 0.8111 (mm-30) cc_final: 0.7687 (mm-30) REVERT: W 86 LEU cc_start: 0.9040 (tp) cc_final: 0.8830 (tt) REVERT: W 91 ASN cc_start: 0.9275 (t0) cc_final: 0.9017 (t0) REVERT: X 8 ARG cc_start: 0.8313 (mtt180) cc_final: 0.7862 (mtp85) REVERT: X 48 LYS cc_start: 0.9143 (tttt) cc_final: 0.8846 (ttmt) REVERT: X 58 GLU cc_start: 0.8440 (mm-30) cc_final: 0.8147 (mm-30) REVERT: X 95 GLU cc_start: 0.8239 (tp30) cc_final: 0.7801 (tp30) REVERT: X 98 ASP cc_start: 0.7875 (m-30) cc_final: 0.7471 (m-30) REVERT: Y 19 GLN cc_start: 0.9146 (mp10) cc_final: 0.8885 (mp10) REVERT: c 10 LYS cc_start: 0.8886 (mttt) cc_final: 0.8546 (mtpp) REVERT: c 15 THR cc_start: 0.9463 (OUTLIER) cc_final: 0.9008 (p) REVERT: c 26 GLN cc_start: 0.8234 (pt0) cc_final: 0.7179 (pm20) REVERT: c 52 GLU cc_start: 0.8750 (tt0) cc_final: 0.8401 (tp30) REVERT: c 54 ASP cc_start: 0.7564 (m-30) cc_final: 0.7088 (m-30) REVERT: g 3 GLU cc_start: 0.8566 (OUTLIER) cc_final: 0.8345 (mm-30) REVERT: g 4 GLN cc_start: 0.6627 (mp10) cc_final: 0.6226 (mp10) REVERT: g 5 MET cc_start: 0.8846 (mmt) cc_final: 0.8443 (mmp) REVERT: g 76 GLN cc_start: 0.8570 (tp-100) cc_final: 0.8117 (tp-100) REVERT: g 86 THR cc_start: 0.9001 (m) cc_final: 0.8561 (t) REVERT: g 100 ARG cc_start: 0.8005 (mmm-85) cc_final: 0.7713 (tpp80) REVERT: g 118 ARG cc_start: 0.9148 (pmm150) cc_final: 0.8889 (mtm-85) REVERT: g 143 GLN cc_start: 0.8761 (tp40) cc_final: 0.8318 (tp40) REVERT: g 184 LEU cc_start: 0.9188 (tp) cc_final: 0.8971 (tp) REVERT: g 191 HIS cc_start: 0.7698 (OUTLIER) cc_final: 0.7415 (t-90) REVERT: g 206 LEU cc_start: 0.8764 (mm) cc_final: 0.8251 (tp) REVERT: g 215 GLN cc_start: 0.8282 (mt0) cc_final: 0.7937 (mt0) REVERT: g 219 TRP cc_start: 0.8626 (m100) cc_final: 0.8046 (m100) REVERT: g 285 GLN cc_start: 0.8420 (mm-40) cc_final: 0.8034 (tp40) REVERT: x 77 LYS cc_start: 0.8294 (OUTLIER) cc_final: 0.7814 (mtmm) REVERT: x 117 GLU cc_start: 0.7920 (OUTLIER) cc_final: 0.7622 (mm-30) REVERT: x 123 GLU cc_start: 0.8334 (mt-10) cc_final: 0.8105 (mp0) REVERT: x 126 ASP cc_start: 0.8560 (t0) cc_final: 0.8355 (t70) REVERT: x 163 PHE cc_start: 0.7669 (OUTLIER) cc_final: 0.7299 (m-10) REVERT: x 186 LYS cc_start: 0.8681 (ttmp) cc_final: 0.8473 (mmmt) REVERT: x 189 LYS cc_start: 0.8932 (tmtp) cc_final: 0.8495 (tmtp) REVERT: x 208 LYS cc_start: 0.9148 (mmtp) cc_final: 0.8816 (mmtp) REVERT: x 217 ASN cc_start: 0.8370 (m-40) cc_final: 0.8036 (m-40) REVERT: x 232 ASN cc_start: 0.8916 (m-40) cc_final: 0.8612 (m-40) REVERT: y 105 GLN cc_start: 0.5209 (pt0) cc_final: 0.4948 (mp10) REVERT: y 114 SER cc_start: 0.8723 (p) cc_final: 0.8274 (m) REVERT: y 241 MET cc_start: 0.8361 (mmt) cc_final: 0.7860 (mmm) REVERT: y 308 MET cc_start: 0.8616 (mtp) cc_final: 0.8140 (mpp) REVERT: y 312 ARG cc_start: 0.7014 (ttm170) cc_final: 0.6636 (mtm110) REVERT: y 405 ARG cc_start: 0.6231 (ppt170) cc_final: 0.5803 (ppt170) outliers start: 274 outliers final: 202 residues processed: 1825 average time/residue: 0.8766 time to fit residues: 2669.7120 Evaluate side-chains 1889 residues out of total 4500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 221 poor density : 1668 time to evaluate : 4.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 125 THR Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 173 LEU Chi-restraints excluded: chain A residue 185 MET Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 56 LYS Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 75 GLN Chi-restraints excluded: chain B residue 207 LEU Chi-restraints excluded: chain B residue 210 VAL Chi-restraints excluded: chain C residue 65 LYS Chi-restraints excluded: chain C residue 130 ILE Chi-restraints excluded: chain C residue 156 ILE Chi-restraints excluded: chain C residue 165 VAL Chi-restraints excluded: chain C residue 174 ILE Chi-restraints excluded: chain C residue 192 LEU Chi-restraints excluded: chain C residue 221 ASP Chi-restraints excluded: chain C residue 222 CYS Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain D residue 4 GLN Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 16 ILE Chi-restraints excluded: chain D residue 55 THR Chi-restraints excluded: chain D residue 168 VAL Chi-restraints excluded: chain D residue 198 ILE Chi-restraints excluded: chain D residue 208 VAL Chi-restraints excluded: chain E residue 32 SER Chi-restraints excluded: chain E residue 44 LEU Chi-restraints excluded: chain E residue 57 THR Chi-restraints excluded: chain E residue 146 THR Chi-restraints excluded: chain E residue 177 THR Chi-restraints excluded: chain E residue 192 ILE Chi-restraints excluded: chain E residue 204 SER Chi-restraints excluded: chain E residue 223 SER Chi-restraints excluded: chain E residue 256 LEU Chi-restraints excluded: chain F residue 35 LEU Chi-restraints excluded: chain F residue 78 MET Chi-restraints excluded: chain F residue 79 HIS Chi-restraints excluded: chain F residue 90 VAL Chi-restraints excluded: chain F residue 93 VAL Chi-restraints excluded: chain F residue 98 GLU Chi-restraints excluded: chain F residue 100 ILE Chi-restraints excluded: chain F residue 147 VAL Chi-restraints excluded: chain F residue 166 ILE Chi-restraints excluded: chain F residue 169 ILE Chi-restraints excluded: chain F residue 185 SER Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 50 VAL Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain G residue 153 VAL Chi-restraints excluded: chain G residue 212 LEU Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 100 ILE Chi-restraints excluded: chain H residue 122 LEU Chi-restraints excluded: chain H residue 130 LEU Chi-restraints excluded: chain H residue 151 SER Chi-restraints excluded: chain H residue 170 VAL Chi-restraints excluded: chain I residue 61 ASP Chi-restraints excluded: chain I residue 69 SER Chi-restraints excluded: chain I residue 71 CYS Chi-restraints excluded: chain I residue 73 THR Chi-restraints excluded: chain I residue 76 THR Chi-restraints excluded: chain I residue 88 ASN Chi-restraints excluded: chain I residue 99 ASN Chi-restraints excluded: chain I residue 102 VAL Chi-restraints excluded: chain I residue 159 SER Chi-restraints excluded: chain I residue 160 SER Chi-restraints excluded: chain I residue 177 SER Chi-restraints excluded: chain I residue 182 CYS Chi-restraints excluded: chain I residue 193 LYS Chi-restraints excluded: chain J residue 12 THR Chi-restraints excluded: chain J residue 29 LEU Chi-restraints excluded: chain J residue 34 GLU Chi-restraints excluded: chain J residue 43 VAL Chi-restraints excluded: chain J residue 55 LYS Chi-restraints excluded: chain J residue 64 ASP Chi-restraints excluded: chain J residue 98 LEU Chi-restraints excluded: chain J residue 122 SER Chi-restraints excluded: chain J residue 156 HIS Chi-restraints excluded: chain K residue 74 GLU Chi-restraints excluded: chain K residue 79 LEU Chi-restraints excluded: chain L residue 46 THR Chi-restraints excluded: chain L residue 56 ILE Chi-restraints excluded: chain L residue 66 VAL Chi-restraints excluded: chain L residue 78 THR Chi-restraints excluded: chain L residue 105 ARG Chi-restraints excluded: chain L residue 146 THR Chi-restraints excluded: chain M residue 45 ARG Chi-restraints excluded: chain N residue 26 LEU Chi-restraints excluded: chain N residue 30 SER Chi-restraints excluded: chain N residue 54 LEU Chi-restraints excluded: chain N residue 102 LEU Chi-restraints excluded: chain N residue 143 SER Chi-restraints excluded: chain O residue 26 ASN Chi-restraints excluded: chain O residue 81 VAL Chi-restraints excluded: chain O residue 91 THR Chi-restraints excluded: chain O residue 105 THR Chi-restraints excluded: chain O residue 113 GLN Chi-restraints excluded: chain P residue 65 LYS Chi-restraints excluded: chain P residue 96 VAL Chi-restraints excluded: chain P residue 105 VAL Chi-restraints excluded: chain P residue 121 ILE Chi-restraints excluded: chain Q residue 10 VAL Chi-restraints excluded: chain Q residue 25 CYS Chi-restraints excluded: chain Q residue 31 LEU Chi-restraints excluded: chain Q residue 51 LEU Chi-restraints excluded: chain Q residue 55 VAL Chi-restraints excluded: chain Q residue 66 VAL Chi-restraints excluded: chain R residue 6 THR Chi-restraints excluded: chain R residue 9 VAL Chi-restraints excluded: chain R residue 22 THR Chi-restraints excluded: chain R residue 38 ILE Chi-restraints excluded: chain R residue 40 ILE Chi-restraints excluded: chain R residue 61 ILE Chi-restraints excluded: chain R residue 66 VAL Chi-restraints excluded: chain S residue 18 THR Chi-restraints excluded: chain S residue 20 ILE Chi-restraints excluded: chain S residue 33 ILE Chi-restraints excluded: chain S residue 43 VAL Chi-restraints excluded: chain S residue 71 MET Chi-restraints excluded: chain S residue 98 VAL Chi-restraints excluded: chain S residue 117 ILE Chi-restraints excluded: chain T residue 4 VAL Chi-restraints excluded: chain T residue 12 GLN Chi-restraints excluded: chain T residue 13 GLU Chi-restraints excluded: chain T residue 36 THR Chi-restraints excluded: chain T residue 37 VAL Chi-restraints excluded: chain T residue 45 LEU Chi-restraints excluded: chain T residue 55 THR Chi-restraints excluded: chain T residue 59 SER Chi-restraints excluded: chain T residue 67 ARG Chi-restraints excluded: chain T residue 103 VAL Chi-restraints excluded: chain T residue 123 LEU Chi-restraints excluded: chain U residue 34 LYS Chi-restraints excluded: chain U residue 39 LEU Chi-restraints excluded: chain V residue 69 ILE Chi-restraints excluded: chain W residue 14 ILE Chi-restraints excluded: chain W residue 25 VAL Chi-restraints excluded: chain W residue 27 ILE Chi-restraints excluded: chain W residue 32 LYS Chi-restraints excluded: chain W residue 33 VAL Chi-restraints excluded: chain W residue 36 ARG Chi-restraints excluded: chain W residue 40 VAL Chi-restraints excluded: chain W residue 42 MET Chi-restraints excluded: chain W residue 63 VAL Chi-restraints excluded: chain W residue 103 VAL Chi-restraints excluded: chain W residue 105 THR Chi-restraints excluded: chain W residue 106 THR Chi-restraints excluded: chain W residue 112 ASP Chi-restraints excluded: chain X residue 13 LEU Chi-restraints excluded: chain X residue 77 ASN Chi-restraints excluded: chain X residue 118 VAL Chi-restraints excluded: chain X residue 128 VAL Chi-restraints excluded: chain Y residue 17 LEU Chi-restraints excluded: chain Y residue 25 ILE Chi-restraints excluded: chain Y residue 46 LYS Chi-restraints excluded: chain Y residue 55 ILE Chi-restraints excluded: chain Z residue 48 VAL Chi-restraints excluded: chain Z residue 58 LEU Chi-restraints excluded: chain Z residue 68 ILE Chi-restraints excluded: chain Z residue 69 THR Chi-restraints excluded: chain Z residue 92 LEU Chi-restraints excluded: chain Z residue 108 ILE Chi-restraints excluded: chain Z residue 110 THR Chi-restraints excluded: chain Z residue 113 THR Chi-restraints excluded: chain b residue 74 THR Chi-restraints excluded: chain b residue 77 CYS Chi-restraints excluded: chain c residue 15 THR Chi-restraints excluded: chain d residue 32 ARG Chi-restraints excluded: chain d residue 36 LEU Chi-restraints excluded: chain e residue 21 LYS Chi-restraints excluded: chain e residue 29 THR Chi-restraints excluded: chain e residue 45 VAL Chi-restraints excluded: chain f residue 121 CYS Chi-restraints excluded: chain f residue 123 SER Chi-restraints excluded: chain g residue 3 GLU Chi-restraints excluded: chain g residue 21 ILE Chi-restraints excluded: chain g residue 24 THR Chi-restraints excluded: chain g residue 30 MET Chi-restraints excluded: chain g residue 42 MET Chi-restraints excluded: chain g residue 96 THR Chi-restraints excluded: chain g residue 111 VAL Chi-restraints excluded: chain g residue 128 THR Chi-restraints excluded: chain g residue 173 LEU Chi-restraints excluded: chain g residue 189 ILE Chi-restraints excluded: chain g residue 191 HIS Chi-restraints excluded: chain g residue 207 CYS Chi-restraints excluded: chain g residue 261 LEU Chi-restraints excluded: chain g residue 265 ILE Chi-restraints excluded: chain g residue 266 ILE Chi-restraints excluded: chain g residue 282 GLU Chi-restraints excluded: chain g residue 287 THR Chi-restraints excluded: chain x residue 77 LYS Chi-restraints excluded: chain x residue 78 ILE Chi-restraints excluded: chain x residue 88 LEU Chi-restraints excluded: chain x residue 116 VAL Chi-restraints excluded: chain x residue 117 GLU Chi-restraints excluded: chain x residue 118 ILE Chi-restraints excluded: chain x residue 150 LEU Chi-restraints excluded: chain x residue 152 LEU Chi-restraints excluded: chain x residue 163 PHE Chi-restraints excluded: chain x residue 165 ILE Chi-restraints excluded: chain x residue 214 SER Chi-restraints excluded: chain x residue 225 ILE Chi-restraints excluded: chain x residue 226 CYS Chi-restraints excluded: chain y residue 48 VAL Chi-restraints excluded: chain y residue 126 SER Chi-restraints excluded: chain y residue 215 LYS Chi-restraints excluded: chain y residue 268 LEU Chi-restraints excluded: chain y residue 286 SER Chi-restraints excluded: chain y residue 297 SER Chi-restraints excluded: chain y residue 307 HIS Chi-restraints excluded: chain y residue 316 VAL Chi-restraints excluded: chain y residue 328 THR Chi-restraints excluded: chain y residue 341 THR Chi-restraints excluded: chain y residue 359 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 674 random chunks: chunk 219 optimal weight: 5.9990 chunk 586 optimal weight: 1.9990 chunk 128 optimal weight: 10.0000 chunk 382 optimal weight: 0.2980 chunk 160 optimal weight: 10.0000 chunk 652 optimal weight: 7.9990 chunk 541 optimal weight: 0.7980 chunk 301 optimal weight: 0.6980 chunk 54 optimal weight: 5.9990 chunk 215 optimal weight: 3.9990 chunk 342 optimal weight: 0.1980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 157 GLN B 177 GLN ** F 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 163 ASN H 163 GLN J 132 GLN K 28 HIS ** K 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 114 HIS Q 24 HIS Q 29 ASN Q 48 GLN S 19 ASN ** Z 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 4 GLN d 26 ASN e 15 GLN e 58 ASN g 64 HIS y 85 GLN y 118 HIS Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7902 moved from start: 0.3532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.080 82008 Z= 0.170 Angle : 0.666 11.729 118686 Z= 0.338 Chirality : 0.040 0.285 14646 Planarity : 0.005 0.114 8879 Dihedral : 23.846 179.460 31754 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 11.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 4.32 % Allowed : 21.42 % Favored : 74.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.95 % Cis-general : 0.00 % Twisted Proline : 0.48 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.38 (0.11), residues: 5145 helix: -0.11 (0.13), residues: 1610 sheet: -1.13 (0.16), residues: 965 loop : -1.29 (0.12), residues: 2570 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 117 HIS 0.008 0.001 HIS f 135 PHE 0.028 0.002 PHE J 48 TYR 0.060 0.002 TYR N 38 ARG 0.017 0.001 ARG N 121 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10290 Ramachandran restraints generated. 5145 Oldfield, 0 Emsley, 5145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10290 Ramachandran restraints generated. 5145 Oldfield, 0 Emsley, 5145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2023 residues out of total 4500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 194 poor density : 1829 time to evaluate : 4.443 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 GLN cc_start: 0.8995 (mm-40) cc_final: 0.8507 (mm-40) REVERT: A 35 GLU cc_start: 0.8876 (tt0) cc_final: 0.8513 (mt-10) REVERT: A 41 ARG cc_start: 0.8769 (OUTLIER) cc_final: 0.8542 (tpt-90) REVERT: A 50 ASN cc_start: 0.8781 (t0) cc_final: 0.8334 (m110) REVERT: A 69 GLU cc_start: 0.8342 (tm-30) cc_final: 0.7965 (tm-30) REVERT: A 75 SER cc_start: 0.8782 (t) cc_final: 0.8483 (t) REVERT: A 99 ILE cc_start: 0.8826 (mt) cc_final: 0.8588 (mt) REVERT: A 156 TYR cc_start: 0.8881 (m-80) cc_final: 0.8457 (m-80) REVERT: A 169 HIS cc_start: 0.8935 (m-70) cc_final: 0.8649 (m-70) REVERT: A 173 LEU cc_start: 0.9101 (OUTLIER) cc_final: 0.8692 (pp) REVERT: A 181 GLU cc_start: 0.8250 (tp30) cc_final: 0.7912 (tp30) REVERT: A 185 MET cc_start: 0.9357 (OUTLIER) cc_final: 0.8876 (tpp) REVERT: B 29 ASP cc_start: 0.7682 (m-30) cc_final: 0.7290 (m-30) REVERT: B 51 ARG cc_start: 0.7809 (ptp-170) cc_final: 0.7451 (ptp-170) REVERT: B 63 LYS cc_start: 0.8831 (ttmm) cc_final: 0.8257 (tppt) REVERT: B 75 GLN cc_start: 0.8591 (mt0) cc_final: 0.8222 (mm-40) REVERT: B 90 ASP cc_start: 0.7529 (m-30) cc_final: 0.7226 (m-30) REVERT: B 92 GLN cc_start: 0.8576 (mm-40) cc_final: 0.8252 (mm-40) REVERT: B 124 HIS cc_start: 0.7833 (p-80) cc_final: 0.7482 (p-80) REVERT: B 144 LYS cc_start: 0.9116 (tmtt) cc_final: 0.8555 (tmtt) REVERT: B 145 LYS cc_start: 0.9303 (tttt) cc_final: 0.8906 (tttp) REVERT: B 159 GLN cc_start: 0.8790 (mm-40) cc_final: 0.8557 (mm-40) REVERT: B 163 GLN cc_start: 0.8999 (mt0) cc_final: 0.8740 (mt0) REVERT: B 168 MET cc_start: 0.8781 (mtt) cc_final: 0.8499 (mtp) REVERT: B 170 GLU cc_start: 0.8843 (pp20) cc_final: 0.8592 (pp20) REVERT: B 175 GLU cc_start: 0.9153 (mp0) cc_final: 0.8781 (mp0) REVERT: B 202 GLN cc_start: 0.8056 (mm110) cc_final: 0.7744 (mt0) REVERT: B 208 HIS cc_start: 0.7981 (t-90) cc_final: 0.7279 (t-90) REVERT: B 211 PHE cc_start: 0.8562 (m-80) cc_final: 0.8328 (m-80) REVERT: B 217 MET cc_start: 0.8481 (tpt) cc_final: 0.8233 (tpp) REVERT: C 65 LYS cc_start: 0.9228 (OUTLIER) cc_final: 0.8554 (tttm) REVERT: C 68 ARG cc_start: 0.8852 (mmm160) cc_final: 0.8624 (mmm160) REVERT: C 72 ASP cc_start: 0.8535 (m-30) cc_final: 0.7847 (m-30) REVERT: C 79 GLU cc_start: 0.8929 (mm-30) cc_final: 0.8728 (mp0) REVERT: C 84 PHE cc_start: 0.8958 (m-80) cc_final: 0.8644 (m-80) REVERT: C 144 SER cc_start: 0.8481 (t) cc_final: 0.8197 (p) REVERT: C 223 TYR cc_start: 0.8695 (m-80) cc_final: 0.8452 (m-80) REVERT: C 224 THR cc_start: 0.9368 (m) cc_final: 0.9107 (p) REVERT: C 246 LYS cc_start: 0.9162 (mtpt) cc_final: 0.8875 (mtmt) REVERT: C 249 SER cc_start: 0.8958 (m) cc_final: 0.8675 (p) REVERT: D 54 ARG cc_start: 0.8374 (mpp-170) cc_final: 0.7945 (mmm160) REVERT: D 62 LYS cc_start: 0.8776 (mttt) cc_final: 0.8178 (mmmt) REVERT: D 66 ILE cc_start: 0.9092 (pt) cc_final: 0.8824 (mt) REVERT: D 81 GLU cc_start: 0.8709 (mp0) cc_final: 0.8406 (mp0) REVERT: D 117 ARG cc_start: 0.8940 (mmm160) cc_final: 0.8390 (tpm170) REVERT: D 123 LEU cc_start: 0.8766 (mt) cc_final: 0.8545 (mp) REVERT: D 125 PHE cc_start: 0.8888 (t80) cc_final: 0.8607 (t80) REVERT: D 127 MET cc_start: 0.9249 (mmt) cc_final: 0.8786 (mmt) REVERT: D 157 MET cc_start: 0.7698 (tpp) cc_final: 0.6657 (tpp) REVERT: D 173 ARG cc_start: 0.8242 (mmm160) cc_final: 0.7631 (mmm160) REVERT: D 178 ARG cc_start: 0.8350 (tpm170) cc_final: 0.8105 (tpm170) REVERT: E 104 ASP cc_start: 0.8728 (t70) cc_final: 0.8115 (p0) REVERT: E 127 ARG cc_start: 0.8649 (ttm-80) cc_final: 0.8426 (ttm110) REVERT: E 130 PHE cc_start: 0.9256 (p90) cc_final: 0.9039 (p90) REVERT: E 180 LEU cc_start: 0.9063 (OUTLIER) cc_final: 0.8854 (tt) REVERT: E 237 SER cc_start: 0.8720 (t) cc_final: 0.8338 (p) REVERT: F 36 GLN cc_start: 0.8532 (tt0) cc_final: 0.8037 (tm-30) REVERT: F 43 GLU cc_start: 0.7290 (tp30) cc_final: 0.6968 (tp30) REVERT: F 79 HIS cc_start: 0.4794 (OUTLIER) cc_final: 0.4156 (t70) REVERT: F 98 GLU cc_start: 0.8973 (OUTLIER) cc_final: 0.8196 (mp0) REVERT: F 106 GLU cc_start: 0.8501 (mp0) cc_final: 0.8246 (mp0) REVERT: F 124 ASP cc_start: 0.8238 (t0) cc_final: 0.7802 (t0) REVERT: F 153 LEU cc_start: 0.9524 (mt) cc_final: 0.9172 (mm) REVERT: G 89 THR cc_start: 0.9274 (m) cc_final: 0.9023 (p) REVERT: G 91 GLU cc_start: 0.8212 (pp20) cc_final: 0.7884 (pp20) REVERT: G 92 ARG cc_start: 0.8642 (mtm-85) cc_final: 0.7879 (mtt180) REVERT: G 96 SER cc_start: 0.8765 (m) cc_final: 0.8510 (t) REVERT: G 100 CYS cc_start: 0.8316 (p) cc_final: 0.8084 (p) REVERT: G 196 LYS cc_start: 0.9081 (mttt) cc_final: 0.8841 (mttm) REVERT: H 147 LYS cc_start: 0.8330 (mmtt) cc_final: 0.8011 (mmtt) REVERT: H 155 LYS cc_start: 0.8550 (mttp) cc_final: 0.8160 (tptp) REVERT: H 160 LYS cc_start: 0.7764 (tmtp) cc_final: 0.7446 (pptt) REVERT: H 171 GLU cc_start: 0.8228 (tm-30) cc_final: 0.7709 (tm-30) REVERT: I 12 ARG cc_start: 0.7911 (mtt90) cc_final: 0.7408 (mtt90) REVERT: I 17 LYS cc_start: 0.8214 (ptmm) cc_final: 0.8001 (ptmm) REVERT: I 19 LYS cc_start: 0.8406 (mttm) cc_final: 0.8063 (mtpp) REVERT: I 53 LYS cc_start: 0.9064 (mttt) cc_final: 0.8772 (mtmm) REVERT: I 58 LEU cc_start: 0.9095 (mp) cc_final: 0.8879 (mp) REVERT: I 61 ASP cc_start: 0.8013 (OUTLIER) cc_final: 0.7812 (m-30) REVERT: I 75 LYS cc_start: 0.9068 (ttpt) cc_final: 0.8719 (ttmt) REVERT: I 94 LYS cc_start: 0.8789 (mttt) cc_final: 0.8486 (mmtm) REVERT: I 153 LYS cc_start: 0.9238 (mttt) cc_final: 0.8908 (mttp) REVERT: I 163 GLU cc_start: 0.8544 (tm-30) cc_final: 0.8314 (tm-30) REVERT: I 194 GLU cc_start: 0.8610 (mp0) cc_final: 0.8253 (mp0) REVERT: I 197 PHE cc_start: 0.8958 (t80) cc_final: 0.8678 (t80) REVERT: J 7 TRP cc_start: 0.8937 (m-10) cc_final: 0.8726 (m-10) REVERT: J 24 ARG cc_start: 0.9171 (OUTLIER) cc_final: 0.7239 (ttm-80) REVERT: J 65 GLU cc_start: 0.8830 (tm-30) cc_final: 0.8544 (tm-30) REVERT: J 79 ARG cc_start: 0.8693 (tpp80) cc_final: 0.8124 (tmt170) REVERT: J 88 ASP cc_start: 0.8490 (m-30) cc_final: 0.8051 (p0) REVERT: J 91 LYS cc_start: 0.9136 (mttt) cc_final: 0.8783 (mtpp) REVERT: J 101 LYS cc_start: 0.8973 (mtpp) cc_final: 0.8586 (mtmm) REVERT: J 104 ASP cc_start: 0.8881 (m-30) cc_final: 0.8400 (m-30) REVERT: J 158 ASP cc_start: 0.8345 (t0) cc_final: 0.7794 (t0) REVERT: K 9 ILE cc_start: 0.9231 (pt) cc_final: 0.8822 (mt) REVERT: K 21 MET cc_start: 0.7028 (OUTLIER) cc_final: 0.6825 (mmm) REVERT: K 65 ARG cc_start: 0.7865 (mmm-85) cc_final: 0.7591 (mmt90) REVERT: K 74 GLU cc_start: 0.9171 (OUTLIER) cc_final: 0.8844 (pm20) REVERT: L 11 GLN cc_start: 0.8542 (mm110) cc_final: 0.8242 (mm-40) REVERT: L 104 LYS cc_start: 0.8826 (mtpm) cc_final: 0.7887 (mtpm) REVERT: L 105 ARG cc_start: 0.8477 (OUTLIER) cc_final: 0.8110 (mtp180) REVERT: M 85 LEU cc_start: 0.6509 (mt) cc_final: 0.6141 (mt) REVERT: N 55 ARG cc_start: 0.7703 (ttp-170) cc_final: 0.7373 (ttp-170) REVERT: N 76 LYS cc_start: 0.9004 (tttt) cc_final: 0.8752 (pptt) REVERT: N 114 ARG cc_start: 0.8547 (tpp-160) cc_final: 0.8299 (mmt-90) REVERT: N 121 ARG cc_start: 0.8808 (mtm180) cc_final: 0.8251 (mtm180) REVERT: O 50 LYS cc_start: 0.8490 (tttp) cc_final: 0.7910 (tptm) REVERT: O 60 MET cc_start: 0.8561 (mtt) cc_final: 0.7837 (mtt) REVERT: O 125 LYS cc_start: 0.8302 (tptm) cc_final: 0.8078 (tptt) REVERT: P 29 SER cc_start: 0.8973 (m) cc_final: 0.8289 (t) REVERT: P 31 GLU cc_start: 0.8721 (tt0) cc_final: 0.8108 (mp0) REVERT: P 32 GLN cc_start: 0.9070 (mt0) cc_final: 0.8610 (mt0) REVERT: P 83 MET cc_start: 0.8578 (tpt) cc_final: 0.8103 (tpt) REVERT: P 88 GLU cc_start: 0.8289 (mp0) cc_final: 0.7981 (mp0) REVERT: P 108 LYS cc_start: 0.8485 (mmmt) cc_final: 0.8185 (mmmm) REVERT: P 124 LYS cc_start: 0.9134 (tttt) cc_final: 0.8592 (ttpt) REVERT: Q 24 HIS cc_start: 0.8394 (t-170) cc_final: 0.8184 (t70) REVERT: Q 51 LEU cc_start: 0.9131 (OUTLIER) cc_final: 0.8888 (mp) REVERT: Q 97 GLN cc_start: 0.8849 (tm-30) cc_final: 0.8621 (tm-30) REVERT: Q 116 ASP cc_start: 0.7987 (t0) cc_final: 0.7708 (t0) REVERT: R 105 MET cc_start: 0.9104 (tpp) cc_final: 0.8505 (tpt) REVERT: S 34 LYS cc_start: 0.8885 (mttt) cc_final: 0.8530 (mtpp) REVERT: S 63 GLU cc_start: 0.8226 (mt-10) cc_final: 0.7825 (mt-10) REVERT: S 121 ARG cc_start: 0.8543 (mtt180) cc_final: 0.8333 (ttm170) REVERT: T 35 ASP cc_start: 0.8756 (t0) cc_final: 0.8527 (t0) REVERT: T 56 ARG cc_start: 0.9082 (tpp80) cc_final: 0.8600 (tpt-90) REVERT: T 67 ARG cc_start: 0.7099 (OUTLIER) cc_final: 0.6794 (ttt90) REVERT: T 76 THR cc_start: 0.7954 (m) cc_final: 0.7622 (p) REVERT: T 79 TYR cc_start: 0.8182 (m-80) cc_final: 0.7563 (m-80) REVERT: T 88 MET cc_start: 0.8700 (mtp) cc_final: 0.8445 (mtp) REVERT: T 117 GLN cc_start: 0.8962 (pt0) cc_final: 0.8393 (pp30) REVERT: T 133 ARG cc_start: 0.8702 (mtm-85) cc_final: 0.8105 (mtm-85) REVERT: T 137 GLN cc_start: 0.8920 (mt0) cc_final: 0.8664 (mp10) REVERT: T 142 ASN cc_start: 0.9087 (t0) cc_final: 0.8812 (t0) REVERT: U 46 LYS cc_start: 0.9238 (mtpp) cc_final: 0.8991 (mtmm) REVERT: U 47 ASN cc_start: 0.9434 (t0) cc_final: 0.9074 (m110) REVERT: U 51 LYS cc_start: 0.8407 (mmtt) cc_final: 0.7695 (ttmt) REVERT: U 59 LYS cc_start: 0.8801 (mptt) cc_final: 0.8530 (mptt) REVERT: U 92 HIS cc_start: 0.8431 (m90) cc_final: 0.8062 (m-70) REVERT: U 97 ILE cc_start: 0.8292 (mp) cc_final: 0.8008 (mp) REVERT: U 99 LYS cc_start: 0.9284 (ptpt) cc_final: 0.8617 (tptp) REVERT: V 7 GLU cc_start: 0.8602 (mp0) cc_final: 0.8080 (mp0) REVERT: V 16 LYS cc_start: 0.8979 (mtmt) cc_final: 0.8583 (mtpt) REVERT: V 47 ASN cc_start: 0.8870 (p0) cc_final: 0.8483 (p0) REVERT: V 49 GLN cc_start: 0.9208 (mm-40) cc_final: 0.8834 (mp10) REVERT: V 51 LYS cc_start: 0.9136 (mttt) cc_final: 0.8894 (mtmt) REVERT: V 61 ARG cc_start: 0.8466 (mtp85) cc_final: 0.7923 (mtp85) REVERT: V 76 ASP cc_start: 0.8758 (m-30) cc_final: 0.8214 (m-30) REVERT: W 5 ASN cc_start: 0.8669 (t0) cc_final: 0.8405 (t0) REVERT: W 23 ARG cc_start: 0.8611 (mmm160) cc_final: 0.8252 (mmm160) REVERT: W 24 GLN cc_start: 0.9077 (mt0) cc_final: 0.8832 (mt0) REVERT: W 36 ARG cc_start: 0.9141 (OUTLIER) cc_final: 0.8897 (mmt180) REVERT: W 49 GLU cc_start: 0.7471 (pt0) cc_final: 0.6234 (pt0) REVERT: W 51 GLU cc_start: 0.8172 (mm-30) cc_final: 0.7729 (mm-30) REVERT: W 86 LEU cc_start: 0.8998 (tp) cc_final: 0.8683 (tt) REVERT: W 90 GLN cc_start: 0.8793 (pt0) cc_final: 0.8249 (pt0) REVERT: W 91 ASN cc_start: 0.9238 (t0) cc_final: 0.9000 (t0) REVERT: X 5 ARG cc_start: 0.8119 (ttm170) cc_final: 0.7782 (ttm170) REVERT: X 8 ARG cc_start: 0.8260 (mtt180) cc_final: 0.7724 (mtp85) REVERT: X 48 LYS cc_start: 0.8954 (tttt) cc_final: 0.8716 (ttmt) REVERT: X 58 GLU cc_start: 0.8492 (mm-30) cc_final: 0.8234 (mm-30) REVERT: X 95 GLU cc_start: 0.8123 (tp30) cc_final: 0.7708 (tp30) REVERT: X 98 ASP cc_start: 0.7831 (m-30) cc_final: 0.7424 (m-30) REVERT: Y 10 ARG cc_start: 0.9260 (mtp180) cc_final: 0.8984 (mtm-85) REVERT: Y 77 ASP cc_start: 0.8655 (m-30) cc_final: 0.8453 (m-30) REVERT: Y 86 GLU cc_start: 0.8357 (mm-30) cc_final: 0.7961 (tp30) REVERT: Z 67 LEU cc_start: 0.8022 (tp) cc_final: 0.7672 (tp) REVERT: c 10 LYS cc_start: 0.8888 (mttt) cc_final: 0.8531 (mtpp) REVERT: c 52 GLU cc_start: 0.8684 (tt0) cc_final: 0.8401 (tp30) REVERT: c 54 ASP cc_start: 0.7376 (m-30) cc_final: 0.7070 (m-30) REVERT: g 3 GLU cc_start: 0.8537 (mm-30) cc_final: 0.8307 (mm-30) REVERT: g 5 MET cc_start: 0.8863 (mmt) cc_final: 0.8595 (mmm) REVERT: g 64 HIS cc_start: 0.7530 (OUTLIER) cc_final: 0.7304 (t70) REVERT: g 76 GLN cc_start: 0.8541 (tp-100) cc_final: 0.8152 (tp-100) REVERT: g 86 THR cc_start: 0.8848 (m) cc_final: 0.8509 (t) REVERT: g 107 ASP cc_start: 0.8368 (m-30) cc_final: 0.7609 (m-30) REVERT: g 143 GLN cc_start: 0.8582 (tp40) cc_final: 0.8363 (mm110) REVERT: g 191 HIS cc_start: 0.7656 (OUTLIER) cc_final: 0.7276 (t-90) REVERT: g 206 LEU cc_start: 0.8787 (mm) cc_final: 0.8321 (tp) REVERT: g 215 GLN cc_start: 0.8200 (mt0) cc_final: 0.7867 (mt0) REVERT: g 217 MET cc_start: 0.8096 (mmp) cc_final: 0.7488 (tpp) REVERT: g 219 TRP cc_start: 0.8615 (m100) cc_final: 0.7415 (m100) REVERT: g 241 PHE cc_start: 0.8488 (OUTLIER) cc_final: 0.8266 (m-10) REVERT: g 245 ARG cc_start: 0.7983 (OUTLIER) cc_final: 0.7731 (mtm-85) REVERT: g 285 GLN cc_start: 0.8375 (mm-40) cc_final: 0.8158 (tp40) REVERT: g 304 ASP cc_start: 0.7745 (t0) cc_final: 0.7453 (p0) REVERT: x 77 LYS cc_start: 0.8297 (OUTLIER) cc_final: 0.8044 (mtmm) REVERT: x 84 ARG cc_start: 0.9127 (mmp-170) cc_final: 0.8832 (mmm-85) REVERT: x 117 GLU cc_start: 0.7948 (OUTLIER) cc_final: 0.7372 (mm-30) REVERT: x 123 GLU cc_start: 0.8354 (mt-10) cc_final: 0.8059 (mp0) REVERT: x 126 ASP cc_start: 0.8578 (t0) cc_final: 0.8374 (t70) REVERT: x 154 ARG cc_start: 0.8339 (ttp-170) cc_final: 0.8082 (ptp90) REVERT: x 163 PHE cc_start: 0.7655 (OUTLIER) cc_final: 0.7416 (m-10) REVERT: x 189 LYS cc_start: 0.8776 (tmtp) cc_final: 0.8360 (tmtp) REVERT: x 208 LYS cc_start: 0.9109 (mmtp) cc_final: 0.8811 (mmtp) REVERT: x 217 ASN cc_start: 0.8435 (m-40) cc_final: 0.8157 (t0) REVERT: y 55 PHE cc_start: 0.8374 (m-10) cc_final: 0.8075 (m-80) REVERT: y 114 SER cc_start: 0.8719 (p) cc_final: 0.8296 (m) REVERT: y 241 MET cc_start: 0.8413 (mmt) cc_final: 0.7971 (mmm) REVERT: y 280 MET cc_start: 0.8136 (mmm) cc_final: 0.7864 (mmp) REVERT: y 308 MET cc_start: 0.8611 (mtp) cc_final: 0.8255 (mpp) REVERT: y 312 ARG cc_start: 0.6916 (ttm170) cc_final: 0.6500 (mtm110) outliers start: 194 outliers final: 120 residues processed: 1896 average time/residue: 0.8134 time to fit residues: 2545.1815 Evaluate side-chains 1848 residues out of total 4500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 142 poor density : 1706 time to evaluate : 4.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 PHE Chi-restraints excluded: chain A residue 41 ARG Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 125 THR Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 173 LEU Chi-restraints excluded: chain A residue 185 MET Chi-restraints excluded: chain B residue 56 LYS Chi-restraints excluded: chain B residue 210 VAL Chi-restraints excluded: chain C residue 65 LYS Chi-restraints excluded: chain C residue 134 ASN Chi-restraints excluded: chain C residue 156 ILE Chi-restraints excluded: chain C residue 160 LEU Chi-restraints excluded: chain C residue 165 VAL Chi-restraints excluded: chain C residue 174 ILE Chi-restraints excluded: chain C residue 192 LEU Chi-restraints excluded: chain C residue 221 ASP Chi-restraints excluded: chain C residue 222 CYS Chi-restraints excluded: chain C residue 227 ARG Chi-restraints excluded: chain D residue 55 THR Chi-restraints excluded: chain D residue 150 MET Chi-restraints excluded: chain D residue 158 ILE Chi-restraints excluded: chain D residue 168 VAL Chi-restraints excluded: chain D residue 198 ILE Chi-restraints excluded: chain D residue 208 VAL Chi-restraints excluded: chain E residue 44 LEU Chi-restraints excluded: chain E residue 146 THR Chi-restraints excluded: chain E residue 180 LEU Chi-restraints excluded: chain E residue 256 LEU Chi-restraints excluded: chain F residue 78 MET Chi-restraints excluded: chain F residue 79 HIS Chi-restraints excluded: chain F residue 98 GLU Chi-restraints excluded: chain F residue 166 ILE Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 153 VAL Chi-restraints excluded: chain G residue 212 LEU Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 100 ILE Chi-restraints excluded: chain H residue 122 LEU Chi-restraints excluded: chain H residue 130 LEU Chi-restraints excluded: chain H residue 145 ARG Chi-restraints excluded: chain I residue 61 ASP Chi-restraints excluded: chain I residue 69 SER Chi-restraints excluded: chain I residue 76 THR Chi-restraints excluded: chain I residue 157 LYS Chi-restraints excluded: chain I residue 159 SER Chi-restraints excluded: chain I residue 177 SER Chi-restraints excluded: chain J residue 12 THR Chi-restraints excluded: chain J residue 24 ARG Chi-restraints excluded: chain J residue 29 LEU Chi-restraints excluded: chain J residue 43 VAL Chi-restraints excluded: chain J residue 122 SER Chi-restraints excluded: chain K residue 21 MET Chi-restraints excluded: chain K residue 74 GLU Chi-restraints excluded: chain L residue 56 ILE Chi-restraints excluded: chain L residue 105 ARG Chi-restraints excluded: chain L residue 146 THR Chi-restraints excluded: chain N residue 26 LEU Chi-restraints excluded: chain N residue 143 SER Chi-restraints excluded: chain O residue 26 ASN Chi-restraints excluded: chain O residue 48 SER Chi-restraints excluded: chain O residue 81 VAL Chi-restraints excluded: chain P residue 65 LYS Chi-restraints excluded: chain Q residue 25 CYS Chi-restraints excluded: chain Q residue 31 LEU Chi-restraints excluded: chain Q residue 46 THR Chi-restraints excluded: chain Q residue 48 GLN Chi-restraints excluded: chain Q residue 51 LEU Chi-restraints excluded: chain R residue 16 ILE Chi-restraints excluded: chain R residue 22 THR Chi-restraints excluded: chain R residue 61 ILE Chi-restraints excluded: chain R residue 66 VAL Chi-restraints excluded: chain S residue 18 THR Chi-restraints excluded: chain S residue 71 MET Chi-restraints excluded: chain S residue 98 VAL Chi-restraints excluded: chain S residue 117 ILE Chi-restraints excluded: chain T residue 12 GLN Chi-restraints excluded: chain T residue 37 VAL Chi-restraints excluded: chain T residue 45 LEU Chi-restraints excluded: chain T residue 59 SER Chi-restraints excluded: chain T residue 67 ARG Chi-restraints excluded: chain T residue 96 SER Chi-restraints excluded: chain U residue 33 GLU Chi-restraints excluded: chain U residue 34 LYS Chi-restraints excluded: chain U residue 61 LEU Chi-restraints excluded: chain W residue 25 VAL Chi-restraints excluded: chain W residue 33 VAL Chi-restraints excluded: chain W residue 36 ARG Chi-restraints excluded: chain W residue 40 VAL Chi-restraints excluded: chain W residue 63 VAL Chi-restraints excluded: chain W residue 87 GLU Chi-restraints excluded: chain W residue 103 VAL Chi-restraints excluded: chain W residue 105 THR Chi-restraints excluded: chain Y residue 17 LEU Chi-restraints excluded: chain Y residue 25 ILE Chi-restraints excluded: chain Y residue 46 LYS Chi-restraints excluded: chain Y residue 55 ILE Chi-restraints excluded: chain Z residue 48 VAL Chi-restraints excluded: chain Z residue 69 THR Chi-restraints excluded: chain Z residue 92 LEU Chi-restraints excluded: chain Z residue 110 THR Chi-restraints excluded: chain Z residue 113 THR Chi-restraints excluded: chain b residue 53 VAL Chi-restraints excluded: chain b residue 74 THR Chi-restraints excluded: chain c residue 15 THR Chi-restraints excluded: chain c residue 32 VAL Chi-restraints excluded: chain f residue 121 CYS Chi-restraints excluded: chain g residue 24 THR Chi-restraints excluded: chain g residue 30 MET Chi-restraints excluded: chain g residue 64 HIS Chi-restraints excluded: chain g residue 66 VAL Chi-restraints excluded: chain g residue 111 VAL Chi-restraints excluded: chain g residue 128 THR Chi-restraints excluded: chain g residue 165 ILE Chi-restraints excluded: chain g residue 191 HIS Chi-restraints excluded: chain g residue 207 CYS Chi-restraints excluded: chain g residue 241 PHE Chi-restraints excluded: chain g residue 245 ARG Chi-restraints excluded: chain g residue 265 ILE Chi-restraints excluded: chain g residue 266 ILE Chi-restraints excluded: chain g residue 287 THR Chi-restraints excluded: chain x residue 77 LYS Chi-restraints excluded: chain x residue 78 ILE Chi-restraints excluded: chain x residue 88 LEU Chi-restraints excluded: chain x residue 117 GLU Chi-restraints excluded: chain x residue 118 ILE Chi-restraints excluded: chain x residue 150 LEU Chi-restraints excluded: chain x residue 163 PHE Chi-restraints excluded: chain x residue 214 SER Chi-restraints excluded: chain x residue 220 MET Chi-restraints excluded: chain x residue 225 ILE Chi-restraints excluded: chain x residue 244 VAL Chi-restraints excluded: chain y residue 48 VAL Chi-restraints excluded: chain y residue 126 SER Chi-restraints excluded: chain y residue 215 LYS Chi-restraints excluded: chain y residue 268 LEU Chi-restraints excluded: chain y residue 297 SER Chi-restraints excluded: chain y residue 307 HIS Chi-restraints excluded: chain y residue 316 VAL Chi-restraints excluded: chain y residue 328 THR Chi-restraints excluded: chain y residue 341 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 674 random chunks: chunk 628 optimal weight: 7.9990 chunk 73 optimal weight: 30.0000 chunk 371 optimal weight: 6.9990 chunk 476 optimal weight: 5.9990 chunk 368 optimal weight: 5.9990 chunk 548 optimal weight: 0.8980 chunk 364 optimal weight: 0.0470 chunk 649 optimal weight: 1.9990 chunk 406 optimal weight: 0.3980 chunk 396 optimal weight: 4.9990 chunk 299 optimal weight: 3.9990 overall best weight: 1.4682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 43 ASN B 149 GLN B 157 GLN B 177 GLN E 179 ASN ** F 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 163 GLN I 99 ASN J 132 GLN K 28 HIS K 61 GLN ** L 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 72 HIS M 73 GLN ** O 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 113 GLN Q 48 GLN S 19 ASN W 64 ASN W 120 HIS X 127 ASN Y 112 ASN ** Z 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 49 HIS d 26 ASN g 64 HIS g 237 ASN x 210 HIS ** y 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7919 moved from start: 0.3677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 82008 Z= 0.204 Angle : 0.671 14.624 118686 Z= 0.341 Chirality : 0.040 0.317 14646 Planarity : 0.005 0.116 8879 Dihedral : 23.736 179.292 31754 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 12.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 4.48 % Allowed : 22.42 % Favored : 73.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.95 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -1.20 (0.11), residues: 5145 helix: 0.09 (0.13), residues: 1593 sheet: -1.00 (0.16), residues: 942 loop : -1.24 (0.12), residues: 2610 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 55 HIS 0.013 0.001 HIS g 64 PHE 0.024 0.002 PHE C 269 TYR 0.041 0.002 TYR N 38 ARG 0.016 0.001 ARG Q 71 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10290 Ramachandran restraints generated. 5145 Oldfield, 0 Emsley, 5145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10290 Ramachandran restraints generated. 5145 Oldfield, 0 Emsley, 5145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1955 residues out of total 4500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 201 poor density : 1754 time to evaluate : 4.467 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 13 GLU cc_start: 0.8528 (pm20) cc_final: 0.8324 (pm20) REVERT: A 33 GLN cc_start: 0.9134 (mm-40) cc_final: 0.8688 (mm-40) REVERT: A 34 MET cc_start: 0.8164 (ttt) cc_final: 0.7910 (mtp) REVERT: A 35 GLU cc_start: 0.8887 (tt0) cc_final: 0.8466 (mt-10) REVERT: A 50 ASN cc_start: 0.8786 (t0) cc_final: 0.8376 (m110) REVERT: A 52 LYS cc_start: 0.7820 (ttmt) cc_final: 0.7383 (ttmt) REVERT: A 69 GLU cc_start: 0.8346 (tm-30) cc_final: 0.7969 (tm-30) REVERT: A 75 SER cc_start: 0.8933 (t) cc_final: 0.8571 (t) REVERT: A 99 ILE cc_start: 0.8778 (mt) cc_final: 0.8519 (mt) REVERT: A 169 HIS cc_start: 0.8909 (m-70) cc_final: 0.8626 (m-70) REVERT: A 173 LEU cc_start: 0.9137 (OUTLIER) cc_final: 0.8928 (pp) REVERT: A 181 GLU cc_start: 0.8284 (tp30) cc_final: 0.7936 (tp30) REVERT: A 185 MET cc_start: 0.9348 (OUTLIER) cc_final: 0.8861 (tpp) REVERT: B 29 ASP cc_start: 0.7634 (m-30) cc_final: 0.7253 (m-30) REVERT: B 63 LYS cc_start: 0.8815 (ttmm) cc_final: 0.8571 (mmtt) REVERT: B 76 ASN cc_start: 0.8724 (m-40) cc_final: 0.8225 (p0) REVERT: B 81 PHE cc_start: 0.8253 (p90) cc_final: 0.7979 (p90) REVERT: B 92 GLN cc_start: 0.8588 (mm-40) cc_final: 0.8271 (mm-40) REVERT: B 124 HIS cc_start: 0.7824 (p-80) cc_final: 0.7464 (p-80) REVERT: B 144 LYS cc_start: 0.9104 (tmtt) cc_final: 0.8541 (tmtt) REVERT: B 145 LYS cc_start: 0.9294 (tttt) cc_final: 0.8820 (tttp) REVERT: B 159 GLN cc_start: 0.8818 (mm-40) cc_final: 0.8586 (mm-40) REVERT: B 163 GLN cc_start: 0.9022 (mt0) cc_final: 0.8754 (mt0) REVERT: B 168 MET cc_start: 0.8770 (mtt) cc_final: 0.8499 (mtp) REVERT: B 170 GLU cc_start: 0.8915 (pp20) cc_final: 0.8588 (pp20) REVERT: B 202 GLN cc_start: 0.8089 (mm110) cc_final: 0.7751 (mt0) REVERT: B 208 HIS cc_start: 0.7975 (t-90) cc_final: 0.7259 (t-90) REVERT: B 211 PHE cc_start: 0.8587 (m-80) cc_final: 0.8349 (m-80) REVERT: B 217 MET cc_start: 0.8482 (tpt) cc_final: 0.8078 (tpp) REVERT: C 72 ASP cc_start: 0.8523 (m-30) cc_final: 0.8151 (m-30) REVERT: C 84 PHE cc_start: 0.8987 (m-80) cc_final: 0.8633 (m-80) REVERT: C 144 SER cc_start: 0.8513 (t) cc_final: 0.8261 (p) REVERT: C 224 THR cc_start: 0.9375 (m) cc_final: 0.9121 (p) REVERT: C 246 LYS cc_start: 0.9163 (mtpt) cc_final: 0.8870 (mtmt) REVERT: C 249 SER cc_start: 0.8970 (m) cc_final: 0.8691 (p) REVERT: D 54 ARG cc_start: 0.8309 (mpp-170) cc_final: 0.7894 (mmm160) REVERT: D 62 LYS cc_start: 0.8785 (mttt) cc_final: 0.8170 (mmmt) REVERT: D 81 GLU cc_start: 0.8739 (mp0) cc_final: 0.8438 (mp0) REVERT: D 117 ARG cc_start: 0.8948 (mmm160) cc_final: 0.8621 (mmm160) REVERT: D 123 LEU cc_start: 0.8790 (OUTLIER) cc_final: 0.8547 (mp) REVERT: D 125 PHE cc_start: 0.8872 (t80) cc_final: 0.8583 (t80) REVERT: D 127 MET cc_start: 0.9247 (mmt) cc_final: 0.8704 (mmt) REVERT: D 157 MET cc_start: 0.7767 (tpp) cc_final: 0.6828 (tpp) REVERT: D 173 ARG cc_start: 0.8190 (mmm160) cc_final: 0.7602 (mmm160) REVERT: D 178 ARG cc_start: 0.8370 (tpm170) cc_final: 0.8148 (tpm170) REVERT: D 189 MET cc_start: 0.7398 (tpp) cc_final: 0.5904 (mmm) REVERT: E 82 TYR cc_start: 0.8721 (t80) cc_final: 0.8515 (t80) REVERT: E 88 ASP cc_start: 0.8655 (m-30) cc_final: 0.8440 (m-30) REVERT: E 127 ARG cc_start: 0.8668 (ttm-80) cc_final: 0.8440 (ttm110) REVERT: E 130 PHE cc_start: 0.9270 (p90) cc_final: 0.9065 (p90) REVERT: E 237 SER cc_start: 0.8874 (t) cc_final: 0.8349 (p) REVERT: F 36 GLN cc_start: 0.8529 (tt0) cc_final: 0.8057 (tm-30) REVERT: F 43 GLU cc_start: 0.7191 (tp30) cc_final: 0.6888 (tp30) REVERT: F 79 HIS cc_start: 0.4950 (OUTLIER) cc_final: 0.4299 (t70) REVERT: F 98 GLU cc_start: 0.8920 (OUTLIER) cc_final: 0.7963 (mp0) REVERT: F 106 GLU cc_start: 0.8510 (mp0) cc_final: 0.8222 (mp0) REVERT: F 124 ASP cc_start: 0.8180 (t0) cc_final: 0.7678 (t0) REVERT: F 153 LEU cc_start: 0.9502 (mt) cc_final: 0.9170 (mm) REVERT: G 89 THR cc_start: 0.9303 (m) cc_final: 0.9039 (p) REVERT: G 91 GLU cc_start: 0.8259 (pp20) cc_final: 0.7906 (pp20) REVERT: G 96 SER cc_start: 0.8746 (m) cc_final: 0.8479 (t) REVERT: G 100 CYS cc_start: 0.8334 (p) cc_final: 0.8082 (p) REVERT: G 196 LYS cc_start: 0.9084 (mttt) cc_final: 0.8823 (mttm) REVERT: G 197 GLN cc_start: 0.8910 (mm-40) cc_final: 0.8516 (mm-40) REVERT: G 204 GLU cc_start: 0.8071 (tm-30) cc_final: 0.7741 (tm-30) REVERT: H 109 ARG cc_start: 0.5946 (mpt180) cc_final: 0.5579 (mpt180) REVERT: H 122 LEU cc_start: 0.5875 (OUTLIER) cc_final: 0.5667 (tm) REVERT: H 147 LYS cc_start: 0.8311 (mmtt) cc_final: 0.7938 (mmtt) REVERT: H 155 LYS cc_start: 0.8612 (mttp) cc_final: 0.8328 (mttp) REVERT: H 160 LYS cc_start: 0.7729 (tmtp) cc_final: 0.7399 (pptt) REVERT: H 171 GLU cc_start: 0.8256 (tm-30) cc_final: 0.7712 (tm-30) REVERT: H 179 LYS cc_start: 0.5525 (mptt) cc_final: 0.5216 (mmtm) REVERT: I 12 ARG cc_start: 0.7935 (mtt90) cc_final: 0.7459 (mtt90) REVERT: I 53 LYS cc_start: 0.9050 (mttt) cc_final: 0.8779 (mtmm) REVERT: I 75 LYS cc_start: 0.9058 (ttpt) cc_final: 0.8706 (ttmt) REVERT: I 94 LYS cc_start: 0.8806 (mttt) cc_final: 0.8536 (mmtm) REVERT: I 153 LYS cc_start: 0.9240 (mttt) cc_final: 0.9001 (mtmm) REVERT: I 163 GLU cc_start: 0.8540 (tm-30) cc_final: 0.8301 (tm-30) REVERT: I 194 GLU cc_start: 0.8626 (mp0) cc_final: 0.8319 (mp0) REVERT: I 197 PHE cc_start: 0.8920 (t80) cc_final: 0.8660 (t80) REVERT: J 7 TRP cc_start: 0.9004 (m-10) cc_final: 0.8726 (m-10) REVERT: J 28 GLU cc_start: 0.8784 (mt-10) cc_final: 0.8470 (mt-10) REVERT: J 65 GLU cc_start: 0.8851 (tm-30) cc_final: 0.8569 (tm-30) REVERT: J 79 ARG cc_start: 0.8703 (tpp80) cc_final: 0.8373 (mpp80) REVERT: J 101 LYS cc_start: 0.8965 (mtpp) cc_final: 0.8573 (mtmm) REVERT: J 104 ASP cc_start: 0.8866 (m-30) cc_final: 0.8389 (m-30) REVERT: J 158 ASP cc_start: 0.8328 (t0) cc_final: 0.7785 (t0) REVERT: K 8 ARG cc_start: 0.8182 (ttp80) cc_final: 0.7979 (ttp80) REVERT: K 9 ILE cc_start: 0.9240 (pt) cc_final: 0.8868 (mt) REVERT: K 25 LYS cc_start: 0.8440 (ttmm) cc_final: 0.8084 (ttmm) REVERT: K 65 ARG cc_start: 0.7969 (mmm-85) cc_final: 0.7537 (mtp85) REVERT: K 74 GLU cc_start: 0.9119 (OUTLIER) cc_final: 0.8861 (pm20) REVERT: L 11 GLN cc_start: 0.8558 (mm110) cc_final: 0.8261 (mm-40) REVERT: L 104 LYS cc_start: 0.8879 (mtpm) cc_final: 0.7985 (mtpm) REVERT: L 105 ARG cc_start: 0.8483 (OUTLIER) cc_final: 0.8156 (mtp180) REVERT: M 45 ARG cc_start: 0.7875 (OUTLIER) cc_final: 0.7615 (pmt100) REVERT: M 85 LEU cc_start: 0.6582 (mt) cc_final: 0.6180 (mt) REVERT: N 55 ARG cc_start: 0.7673 (ttp-170) cc_final: 0.7280 (ttp-170) REVERT: N 99 ARG cc_start: 0.8772 (tpp80) cc_final: 0.8127 (ttm170) REVERT: N 119 GLU cc_start: 0.7944 (mm-30) cc_final: 0.7722 (mm-30) REVERT: N 121 ARG cc_start: 0.8933 (mtm180) cc_final: 0.8406 (mtm180) REVERT: O 50 LYS cc_start: 0.8436 (tttp) cc_final: 0.8036 (tptm) REVERT: O 60 MET cc_start: 0.8596 (mtt) cc_final: 0.7821 (mtt) REVERT: O 98 ARG cc_start: 0.6520 (ptm160) cc_final: 0.5853 (ptm160) REVERT: O 125 LYS cc_start: 0.8295 (tptm) cc_final: 0.7951 (tptt) REVERT: P 16 THR cc_start: 0.8433 (OUTLIER) cc_final: 0.8183 (t) REVERT: P 29 SER cc_start: 0.8980 (m) cc_final: 0.8258 (t) REVERT: P 31 GLU cc_start: 0.8700 (tt0) cc_final: 0.8073 (mp0) REVERT: P 32 GLN cc_start: 0.9039 (mt0) cc_final: 0.8564 (mt0) REVERT: P 83 MET cc_start: 0.8638 (tpt) cc_final: 0.8173 (tpt) REVERT: P 88 GLU cc_start: 0.8305 (mp0) cc_final: 0.7954 (mp0) REVERT: P 108 LYS cc_start: 0.8485 (mmmt) cc_final: 0.8079 (mmmm) REVERT: P 124 LYS cc_start: 0.9145 (tttt) cc_final: 0.8608 (ttpt) REVERT: Q 51 LEU cc_start: 0.9188 (OUTLIER) cc_final: 0.8950 (mp) REVERT: Q 98 LYS cc_start: 0.9040 (tppt) cc_final: 0.8729 (tppt) REVERT: Q 105 LYS cc_start: 0.9431 (tttp) cc_final: 0.9154 (tttp) REVERT: Q 106 LYS cc_start: 0.9590 (tptm) cc_final: 0.9383 (tptp) REVERT: Q 116 ASP cc_start: 0.7961 (t0) cc_final: 0.7718 (t0) REVERT: R 40 ILE cc_start: 0.8778 (mt) cc_final: 0.8545 (mp) REVERT: S 63 GLU cc_start: 0.8206 (mt-10) cc_final: 0.7680 (mt-10) REVERT: S 110 ASP cc_start: 0.7518 (t0) cc_final: 0.7242 (t0) REVERT: S 121 ARG cc_start: 0.8523 (mtt180) cc_final: 0.8306 (ttm170) REVERT: T 35 ASP cc_start: 0.8764 (t0) cc_final: 0.8517 (t0) REVERT: T 67 ARG cc_start: 0.7126 (OUTLIER) cc_final: 0.6778 (ttt90) REVERT: T 76 THR cc_start: 0.7954 (m) cc_final: 0.7610 (p) REVERT: T 79 TYR cc_start: 0.8181 (m-80) cc_final: 0.7485 (m-80) REVERT: T 88 MET cc_start: 0.8713 (mtp) cc_final: 0.8449 (mtp) REVERT: T 117 GLN cc_start: 0.9045 (pt0) cc_final: 0.8604 (pp30) REVERT: T 129 ARG cc_start: 0.7705 (ttm-80) cc_final: 0.7448 (ttm-80) REVERT: T 133 ARG cc_start: 0.8714 (mtm-85) cc_final: 0.8193 (mtm-85) REVERT: T 137 GLN cc_start: 0.8955 (mt0) cc_final: 0.8572 (mp10) REVERT: T 142 ASN cc_start: 0.9113 (t0) cc_final: 0.8855 (t0) REVERT: U 46 LYS cc_start: 0.9245 (mtpp) cc_final: 0.9012 (mtmm) REVERT: U 47 ASN cc_start: 0.9433 (t0) cc_final: 0.9062 (m110) REVERT: U 51 LYS cc_start: 0.8453 (mmtt) cc_final: 0.7728 (ttmt) REVERT: U 59 LYS cc_start: 0.8777 (mptt) cc_final: 0.8528 (mptt) REVERT: U 92 HIS cc_start: 0.8482 (m90) cc_final: 0.8115 (m-70) REVERT: U 99 LYS cc_start: 0.9254 (ptpt) cc_final: 0.8696 (tptp) REVERT: V 2 GLN cc_start: 0.8522 (mt0) cc_final: 0.8182 (mm-40) REVERT: V 7 GLU cc_start: 0.8605 (mp0) cc_final: 0.8333 (mp0) REVERT: V 47 ASN cc_start: 0.8862 (p0) cc_final: 0.8446 (p0) REVERT: V 49 GLN cc_start: 0.9192 (mm-40) cc_final: 0.8800 (mp10) REVERT: V 51 LYS cc_start: 0.9127 (mttt) cc_final: 0.8885 (mtmt) REVERT: V 61 ARG cc_start: 0.8472 (mtp85) cc_final: 0.8194 (mtp85) REVERT: V 76 ASP cc_start: 0.8853 (m-30) cc_final: 0.8265 (m-30) REVERT: W 5 ASN cc_start: 0.8666 (t0) cc_final: 0.8401 (t0) REVERT: W 11 LEU cc_start: 0.9181 (mt) cc_final: 0.8865 (mt) REVERT: W 23 ARG cc_start: 0.8601 (mmm160) cc_final: 0.8235 (mmm160) REVERT: W 49 GLU cc_start: 0.7455 (pt0) cc_final: 0.6282 (pt0) REVERT: W 51 GLU cc_start: 0.8088 (mm-30) cc_final: 0.7703 (mm-30) REVERT: W 86 LEU cc_start: 0.9010 (tp) cc_final: 0.8736 (tt) REVERT: W 90 GLN cc_start: 0.8809 (pt0) cc_final: 0.8475 (pt0) REVERT: W 91 ASN cc_start: 0.9243 (t0) cc_final: 0.9002 (t0) REVERT: X 5 ARG cc_start: 0.8206 (ttm170) cc_final: 0.7910 (ttm170) REVERT: X 8 ARG cc_start: 0.8300 (mtt180) cc_final: 0.7795 (mtp85) REVERT: X 48 LYS cc_start: 0.9004 (tttt) cc_final: 0.8770 (ttmt) REVERT: X 58 GLU cc_start: 0.8505 (mm-30) cc_final: 0.8240 (mm-30) REVERT: X 95 GLU cc_start: 0.8149 (tp30) cc_final: 0.7735 (tp30) REVERT: X 98 ASP cc_start: 0.7904 (m-30) cc_final: 0.7526 (m-30) REVERT: Y 10 ARG cc_start: 0.9265 (mtp180) cc_final: 0.8972 (mtm-85) REVERT: Y 19 GLN cc_start: 0.9091 (mp10) cc_final: 0.8879 (mp10) REVERT: Y 77 ASP cc_start: 0.8649 (m-30) cc_final: 0.8436 (m-30) REVERT: Y 86 GLU cc_start: 0.8530 (mm-30) cc_final: 0.8056 (tp30) REVERT: c 31 ARG cc_start: 0.8776 (ttm-80) cc_final: 0.8348 (ttm-80) REVERT: c 52 GLU cc_start: 0.8717 (tt0) cc_final: 0.8421 (tp30) REVERT: c 54 ASP cc_start: 0.7337 (m-30) cc_final: 0.7035 (m-30) REVERT: e 15 GLN cc_start: 0.8854 (mt0) cc_final: 0.8626 (mm-40) REVERT: g 3 GLU cc_start: 0.8557 (OUTLIER) cc_final: 0.8146 (mm-30) REVERT: g 5 MET cc_start: 0.8886 (mmt) cc_final: 0.8577 (mmm) REVERT: g 86 THR cc_start: 0.8785 (m) cc_final: 0.8547 (t) REVERT: g 175 LYS cc_start: 0.7178 (mptt) cc_final: 0.6936 (mptt) REVERT: g 191 HIS cc_start: 0.7585 (OUTLIER) cc_final: 0.7303 (t-90) REVERT: g 206 LEU cc_start: 0.8786 (OUTLIER) cc_final: 0.8247 (tp) REVERT: g 215 GLN cc_start: 0.8215 (mt0) cc_final: 0.7914 (mt0) REVERT: g 225 LYS cc_start: 0.8473 (mmtm) cc_final: 0.8255 (mmtm) REVERT: g 285 GLN cc_start: 0.8611 (mm-40) cc_final: 0.8402 (tp40) REVERT: g 304 ASP cc_start: 0.7797 (t0) cc_final: 0.7523 (p0) REVERT: x 77 LYS cc_start: 0.8286 (OUTLIER) cc_final: 0.8081 (mtmm) REVERT: x 117 GLU cc_start: 0.7919 (OUTLIER) cc_final: 0.7363 (mm-30) REVERT: x 123 GLU cc_start: 0.8329 (mt-10) cc_final: 0.8092 (mp0) REVERT: x 126 ASP cc_start: 0.8590 (t0) cc_final: 0.8376 (t70) REVERT: x 132 LYS cc_start: 0.8288 (mmpt) cc_final: 0.8007 (mmpt) REVERT: x 163 PHE cc_start: 0.7601 (OUTLIER) cc_final: 0.7344 (m-10) REVERT: x 189 LYS cc_start: 0.8835 (tmtp) cc_final: 0.8406 (tmtp) REVERT: x 208 LYS cc_start: 0.9017 (mmtp) cc_final: 0.8744 (mmtp) REVERT: x 217 ASN cc_start: 0.8454 (m-40) cc_final: 0.8167 (t0) REVERT: y 114 SER cc_start: 0.8730 (p) cc_final: 0.8323 (m) REVERT: y 308 MET cc_start: 0.8620 (mtp) cc_final: 0.8245 (mpp) REVERT: y 312 ARG cc_start: 0.6893 (ttm170) cc_final: 0.6469 (mtm110) outliers start: 201 outliers final: 142 residues processed: 1825 average time/residue: 0.8078 time to fit residues: 2439.5235 Evaluate side-chains 1855 residues out of total 4500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 160 poor density : 1695 time to evaluate : 4.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 VAL Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 32 PHE Chi-restraints excluded: chain A residue 36 GLN Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 173 LEU Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain A residue 185 MET Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 56 LYS Chi-restraints excluded: chain B residue 75 GLN Chi-restraints excluded: chain B residue 207 LEU Chi-restraints excluded: chain B residue 210 VAL Chi-restraints excluded: chain C residue 65 LYS Chi-restraints excluded: chain C residue 130 ILE Chi-restraints excluded: chain C residue 156 ILE Chi-restraints excluded: chain C residue 160 LEU Chi-restraints excluded: chain C residue 165 VAL Chi-restraints excluded: chain C residue 174 ILE Chi-restraints excluded: chain C residue 221 ASP Chi-restraints excluded: chain C residue 222 CYS Chi-restraints excluded: chain D residue 16 ILE Chi-restraints excluded: chain D residue 55 THR Chi-restraints excluded: chain D residue 123 LEU Chi-restraints excluded: chain D residue 156 LEU Chi-restraints excluded: chain D residue 168 VAL Chi-restraints excluded: chain D residue 198 ILE Chi-restraints excluded: chain D residue 208 VAL Chi-restraints excluded: chain E residue 45 ILE Chi-restraints excluded: chain E residue 146 THR Chi-restraints excluded: chain E residue 256 LEU Chi-restraints excluded: chain F residue 28 VAL Chi-restraints excluded: chain F residue 78 MET Chi-restraints excluded: chain F residue 79 HIS Chi-restraints excluded: chain F residue 98 GLU Chi-restraints excluded: chain F residue 166 ILE Chi-restraints excluded: chain F residue 169 ILE Chi-restraints excluded: chain F residue 185 SER Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 153 VAL Chi-restraints excluded: chain G residue 212 LEU Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 100 ILE Chi-restraints excluded: chain H residue 122 LEU Chi-restraints excluded: chain H residue 130 LEU Chi-restraints excluded: chain H residue 145 ARG Chi-restraints excluded: chain H residue 151 SER Chi-restraints excluded: chain I residue 69 SER Chi-restraints excluded: chain I residue 76 THR Chi-restraints excluded: chain I residue 88 ASN Chi-restraints excluded: chain I residue 107 THR Chi-restraints excluded: chain I residue 157 LYS Chi-restraints excluded: chain I residue 159 SER Chi-restraints excluded: chain I residue 177 SER Chi-restraints excluded: chain J residue 12 THR Chi-restraints excluded: chain J residue 29 LEU Chi-restraints excluded: chain J residue 34 GLU Chi-restraints excluded: chain J residue 43 VAL Chi-restraints excluded: chain J residue 98 LEU Chi-restraints excluded: chain J residue 122 SER Chi-restraints excluded: chain J residue 144 ILE Chi-restraints excluded: chain K residue 74 GLU Chi-restraints excluded: chain K residue 79 LEU Chi-restraints excluded: chain L residue 40 ILE Chi-restraints excluded: chain L residue 56 ILE Chi-restraints excluded: chain L residue 74 SER Chi-restraints excluded: chain L residue 78 THR Chi-restraints excluded: chain L residue 105 ARG Chi-restraints excluded: chain L residue 146 THR Chi-restraints excluded: chain M residue 45 ARG Chi-restraints excluded: chain M residue 73 GLN Chi-restraints excluded: chain N residue 26 LEU Chi-restraints excluded: chain N residue 30 SER Chi-restraints excluded: chain N residue 143 SER Chi-restraints excluded: chain O residue 26 ASN Chi-restraints excluded: chain O residue 48 SER Chi-restraints excluded: chain O residue 91 THR Chi-restraints excluded: chain P residue 16 THR Chi-restraints excluded: chain P residue 65 LYS Chi-restraints excluded: chain P residue 105 VAL Chi-restraints excluded: chain Q residue 10 VAL Chi-restraints excluded: chain Q residue 25 CYS Chi-restraints excluded: chain Q residue 31 LEU Chi-restraints excluded: chain Q residue 48 GLN Chi-restraints excluded: chain Q residue 51 LEU Chi-restraints excluded: chain R residue 66 VAL Chi-restraints excluded: chain S residue 18 THR Chi-restraints excluded: chain S residue 71 MET Chi-restraints excluded: chain S residue 98 VAL Chi-restraints excluded: chain S residue 117 ILE Chi-restraints excluded: chain T residue 12 GLN Chi-restraints excluded: chain T residue 37 VAL Chi-restraints excluded: chain T residue 45 LEU Chi-restraints excluded: chain T residue 59 SER Chi-restraints excluded: chain T residue 67 ARG Chi-restraints excluded: chain T residue 96 SER Chi-restraints excluded: chain U residue 33 GLU Chi-restraints excluded: chain U residue 34 LYS Chi-restraints excluded: chain U residue 50 VAL Chi-restraints excluded: chain U residue 95 SER Chi-restraints excluded: chain W residue 14 ILE Chi-restraints excluded: chain W residue 33 VAL Chi-restraints excluded: chain W residue 36 ARG Chi-restraints excluded: chain W residue 40 VAL Chi-restraints excluded: chain W residue 63 VAL Chi-restraints excluded: chain W residue 87 GLU Chi-restraints excluded: chain W residue 94 LEU Chi-restraints excluded: chain W residue 103 VAL Chi-restraints excluded: chain W residue 105 THR Chi-restraints excluded: chain X residue 13 LEU Chi-restraints excluded: chain X residue 61 GLN Chi-restraints excluded: chain X residue 128 VAL Chi-restraints excluded: chain Y residue 17 LEU Chi-restraints excluded: chain Y residue 25 ILE Chi-restraints excluded: chain Y residue 55 ILE Chi-restraints excluded: chain Z residue 48 VAL Chi-restraints excluded: chain Z residue 69 THR Chi-restraints excluded: chain Z residue 92 LEU Chi-restraints excluded: chain Z residue 113 THR Chi-restraints excluded: chain b residue 53 VAL Chi-restraints excluded: chain b residue 77 CYS Chi-restraints excluded: chain c residue 15 THR Chi-restraints excluded: chain c residue 32 VAL Chi-restraints excluded: chain e residue 45 VAL Chi-restraints excluded: chain f residue 121 CYS Chi-restraints excluded: chain g residue 3 GLU Chi-restraints excluded: chain g residue 21 ILE Chi-restraints excluded: chain g residue 24 THR Chi-restraints excluded: chain g residue 30 MET Chi-restraints excluded: chain g residue 111 VAL Chi-restraints excluded: chain g residue 128 THR Chi-restraints excluded: chain g residue 165 ILE Chi-restraints excluded: chain g residue 191 HIS Chi-restraints excluded: chain g residue 206 LEU Chi-restraints excluded: chain g residue 207 CYS Chi-restraints excluded: chain g residue 245 ARG Chi-restraints excluded: chain g residue 265 ILE Chi-restraints excluded: chain g residue 266 ILE Chi-restraints excluded: chain g residue 287 THR Chi-restraints excluded: chain x residue 77 LYS Chi-restraints excluded: chain x residue 78 ILE Chi-restraints excluded: chain x residue 88 LEU Chi-restraints excluded: chain x residue 117 GLU Chi-restraints excluded: chain x residue 118 ILE Chi-restraints excluded: chain x residue 150 LEU Chi-restraints excluded: chain x residue 163 PHE Chi-restraints excluded: chain x residue 214 SER Chi-restraints excluded: chain x residue 220 MET Chi-restraints excluded: chain x residue 225 ILE Chi-restraints excluded: chain x residue 244 VAL Chi-restraints excluded: chain y residue 48 VAL Chi-restraints excluded: chain y residue 126 SER Chi-restraints excluded: chain y residue 215 LYS Chi-restraints excluded: chain y residue 268 LEU Chi-restraints excluded: chain y residue 307 HIS Chi-restraints excluded: chain y residue 328 THR Chi-restraints excluded: chain y residue 341 THR Chi-restraints excluded: chain y residue 359 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 674 random chunks: chunk 401 optimal weight: 10.0000 chunk 259 optimal weight: 3.9990 chunk 387 optimal weight: 0.0570 chunk 195 optimal weight: 4.9990 chunk 127 optimal weight: 9.9990 chunk 125 optimal weight: 10.0000 chunk 413 optimal weight: 1.9990 chunk 442 optimal weight: 10.0000 chunk 321 optimal weight: 10.0000 chunk 60 optimal weight: 7.9990 chunk 510 optimal weight: 8.9990 overall best weight: 3.8106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 43 ASN B 157 GLN B 177 GLN E 224 ASN ** F 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 163 GLN I 99 ASN I 181 GLN K 28 HIS ** K 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 48 GLN S 19 ASN ** T 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 127 ASN Y 106 GLN Y 112 ASN ** Z 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 49 HIS d 4 GLN d 26 ASN ** g 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 178 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** x 210 HIS y 85 GLN ** y 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 moved from start: 0.3691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.122 82008 Z= 0.374 Angle : 0.762 14.535 118686 Z= 0.388 Chirality : 0.045 0.356 14646 Planarity : 0.006 0.099 8879 Dihedral : 23.744 179.991 31754 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 15.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.10 % Favored : 93.90 % Rotamer: Outliers : 5.21 % Allowed : 22.07 % Favored : 72.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.95 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -1.33 (0.11), residues: 5145 helix: -0.09 (0.13), residues: 1597 sheet: -1.05 (0.16), residues: 950 loop : -1.26 (0.12), residues: 2598 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 55 HIS 0.015 0.001 HIS M 72 PHE 0.025 0.002 PHE b 47 TYR 0.046 0.002 TYR g 246 ARG 0.018 0.001 ARG F 135 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10290 Ramachandran restraints generated. 5145 Oldfield, 0 Emsley, 5145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10290 Ramachandran restraints generated. 5145 Oldfield, 0 Emsley, 5145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1936 residues out of total 4500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 234 poor density : 1702 time to evaluate : 4.449 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 GLN cc_start: 0.9033 (mm-40) cc_final: 0.8597 (mm-40) REVERT: A 35 GLU cc_start: 0.8942 (tt0) cc_final: 0.8604 (mt-10) REVERT: A 41 ARG cc_start: 0.8697 (OUTLIER) cc_final: 0.8344 (tpp80) REVERT: A 50 ASN cc_start: 0.8911 (t0) cc_final: 0.8436 (m110) REVERT: A 52 LYS cc_start: 0.7876 (ttmt) cc_final: 0.7421 (ttmt) REVERT: A 69 GLU cc_start: 0.8420 (tm-30) cc_final: 0.8209 (tm-30) REVERT: A 75 SER cc_start: 0.8769 (t) cc_final: 0.8513 (t) REVERT: A 156 TYR cc_start: 0.8723 (m-80) cc_final: 0.8431 (m-80) REVERT: A 169 HIS cc_start: 0.8906 (m-70) cc_final: 0.8561 (m-70) REVERT: A 173 LEU cc_start: 0.9228 (OUTLIER) cc_final: 0.8946 (pp) REVERT: A 181 GLU cc_start: 0.8353 (tp30) cc_final: 0.7948 (tp30) REVERT: B 29 ASP cc_start: 0.7516 (m-30) cc_final: 0.7038 (m-30) REVERT: B 42 ARG cc_start: 0.8365 (mmt90) cc_final: 0.8146 (mmt-90) REVERT: B 63 LYS cc_start: 0.8836 (ttmm) cc_final: 0.8295 (tppt) REVERT: B 76 ASN cc_start: 0.8791 (m-40) cc_final: 0.8228 (p0) REVERT: B 92 GLN cc_start: 0.8645 (mm-40) cc_final: 0.8260 (mm-40) REVERT: B 98 THR cc_start: 0.8578 (p) cc_final: 0.8264 (t) REVERT: B 124 HIS cc_start: 0.7859 (p-80) cc_final: 0.7502 (p-80) REVERT: B 145 LYS cc_start: 0.9287 (tttt) cc_final: 0.8760 (tttp) REVERT: B 159 GLN cc_start: 0.8835 (mm-40) cc_final: 0.8603 (mm-40) REVERT: B 163 GLN cc_start: 0.9046 (mt0) cc_final: 0.8793 (mt0) REVERT: B 168 MET cc_start: 0.8773 (mtt) cc_final: 0.8518 (mtp) REVERT: B 170 GLU cc_start: 0.8980 (pp20) cc_final: 0.8620 (pp20) REVERT: B 202 GLN cc_start: 0.8108 (mm110) cc_final: 0.7801 (mt0) REVERT: B 208 HIS cc_start: 0.8004 (t-90) cc_final: 0.7293 (t-90) REVERT: B 211 PHE cc_start: 0.8555 (m-80) cc_final: 0.8305 (m-80) REVERT: B 217 MET cc_start: 0.8522 (tpt) cc_final: 0.7927 (tpp) REVERT: C 77 SER cc_start: 0.9375 (t) cc_final: 0.8737 (p) REVERT: C 80 GLU cc_start: 0.9266 (mp0) cc_final: 0.8947 (mp0) REVERT: C 84 PHE cc_start: 0.8936 (m-80) cc_final: 0.8528 (m-80) REVERT: C 144 SER cc_start: 0.8561 (t) cc_final: 0.8306 (p) REVERT: C 224 THR cc_start: 0.9466 (m) cc_final: 0.9127 (p) REVERT: C 246 LYS cc_start: 0.9176 (mtpt) cc_final: 0.8777 (mtpp) REVERT: C 249 SER cc_start: 0.9019 (m) cc_final: 0.8748 (p) REVERT: D 4 GLN cc_start: 0.8746 (mm110) cc_final: 0.8341 (tp40) REVERT: D 54 ARG cc_start: 0.8320 (mpp-170) cc_final: 0.7901 (mmm160) REVERT: D 81 GLU cc_start: 0.8724 (mp0) cc_final: 0.8436 (mp0) REVERT: D 106 ARG cc_start: 0.8550 (ttp80) cc_final: 0.8298 (ttp80) REVERT: D 117 ARG cc_start: 0.8951 (mmm160) cc_final: 0.8610 (mmm160) REVERT: D 125 PHE cc_start: 0.8969 (t80) cc_final: 0.8541 (t80) REVERT: D 127 MET cc_start: 0.9349 (mmt) cc_final: 0.9034 (mmt) REVERT: D 138 VAL cc_start: 0.8480 (t) cc_final: 0.8208 (m) REVERT: D 157 MET cc_start: 0.7876 (tpp) cc_final: 0.7495 (tpp) REVERT: D 173 ARG cc_start: 0.8116 (mmm160) cc_final: 0.7662 (mmm160) REVERT: D 178 ARG cc_start: 0.8305 (tpm170) cc_final: 0.8093 (tpm170) REVERT: D 202 LYS cc_start: 0.8739 (pttm) cc_final: 0.8426 (pptt) REVERT: E 82 TYR cc_start: 0.8880 (t80) cc_final: 0.8672 (t80) REVERT: E 130 PHE cc_start: 0.9282 (p90) cc_final: 0.9066 (p90) REVERT: E 237 SER cc_start: 0.8787 (t) cc_final: 0.8342 (p) REVERT: F 43 GLU cc_start: 0.7238 (tp30) cc_final: 0.6953 (tp30) REVERT: F 79 HIS cc_start: 0.5675 (OUTLIER) cc_final: 0.5059 (t70) REVERT: F 98 GLU cc_start: 0.8921 (OUTLIER) cc_final: 0.7977 (mp0) REVERT: F 106 GLU cc_start: 0.8609 (mp0) cc_final: 0.8339 (mp0) REVERT: F 124 ASP cc_start: 0.8150 (t0) cc_final: 0.7663 (t0) REVERT: G 89 THR cc_start: 0.9365 (m) cc_final: 0.9008 (p) REVERT: G 91 GLU cc_start: 0.8401 (pp20) cc_final: 0.7985 (pp20) REVERT: G 92 ARG cc_start: 0.8873 (mtm-85) cc_final: 0.8529 (mtm-85) REVERT: G 96 SER cc_start: 0.8899 (m) cc_final: 0.8577 (t) REVERT: G 100 CYS cc_start: 0.8320 (p) cc_final: 0.8062 (p) REVERT: G 101 ILE cc_start: 0.9006 (mt) cc_final: 0.8802 (mt) REVERT: G 196 LYS cc_start: 0.9156 (mttt) cc_final: 0.8900 (mttm) REVERT: H 147 LYS cc_start: 0.8486 (mmtt) cc_final: 0.8077 (mmtt) REVERT: H 160 LYS cc_start: 0.7687 (tmtp) cc_final: 0.7461 (pptt) REVERT: H 171 GLU cc_start: 0.8132 (tm-30) cc_final: 0.7582 (tm-30) REVERT: H 179 LYS cc_start: 0.5573 (OUTLIER) cc_final: 0.5047 (mmtm) REVERT: I 12 ARG cc_start: 0.7905 (mtt90) cc_final: 0.7633 (mtt90) REVERT: I 53 LYS cc_start: 0.8968 (mttt) cc_final: 0.8703 (mtmm) REVERT: I 61 ASP cc_start: 0.7808 (m-30) cc_final: 0.7599 (m-30) REVERT: I 73 THR cc_start: 0.9153 (m) cc_final: 0.8756 (p) REVERT: I 75 LYS cc_start: 0.9047 (ttpt) cc_final: 0.8771 (ttmt) REVERT: I 94 LYS cc_start: 0.8864 (mttt) cc_final: 0.8510 (mmtm) REVERT: I 163 GLU cc_start: 0.8595 (tm-30) cc_final: 0.8196 (tm-30) REVERT: I 194 GLU cc_start: 0.8625 (mp0) cc_final: 0.8285 (mp0) REVERT: J 7 TRP cc_start: 0.9129 (m-10) cc_final: 0.8816 (m-10) REVERT: J 65 GLU cc_start: 0.8851 (tm-30) cc_final: 0.8569 (tm-30) REVERT: J 79 ARG cc_start: 0.8755 (tpp80) cc_final: 0.8368 (mpp80) REVERT: J 88 ASP cc_start: 0.8462 (m-30) cc_final: 0.7956 (t70) REVERT: J 92 MET cc_start: 0.8441 (mtp) cc_final: 0.8234 (ttm) REVERT: J 101 LYS cc_start: 0.8970 (mtpp) cc_final: 0.8471 (mtmm) REVERT: J 104 ASP cc_start: 0.8869 (m-30) cc_final: 0.8244 (m-30) REVERT: J 158 ASP cc_start: 0.8443 (t0) cc_final: 0.7963 (t0) REVERT: K 9 ILE cc_start: 0.9323 (pt) cc_final: 0.9011 (mt) REVERT: K 65 ARG cc_start: 0.7982 (mmm-85) cc_final: 0.7654 (mmm-85) REVERT: K 70 TYR cc_start: 0.7891 (m-80) cc_final: 0.7657 (m-80) REVERT: K 74 GLU cc_start: 0.9143 (OUTLIER) cc_final: 0.8892 (pm20) REVERT: L 11 GLN cc_start: 0.8620 (mm110) cc_final: 0.8302 (mm-40) REVERT: L 103 GLU cc_start: 0.8449 (pt0) cc_final: 0.7973 (pt0) REVERT: L 104 LYS cc_start: 0.8978 (OUTLIER) cc_final: 0.8350 (mtpm) REVERT: L 107 LYS cc_start: 0.8599 (mtmt) cc_final: 0.8328 (mttp) REVERT: L 135 SER cc_start: 0.8532 (t) cc_final: 0.8253 (t) REVERT: M 12 MET cc_start: 0.4406 (ptt) cc_final: 0.3847 (ptt) REVERT: M 45 ARG cc_start: 0.7957 (OUTLIER) cc_final: 0.7679 (pmt100) REVERT: M 88 TRP cc_start: 0.6795 (m100) cc_final: 0.6415 (m100) REVERT: O 50 LYS cc_start: 0.8565 (tttp) cc_final: 0.8327 (tttp) REVERT: O 51 GLU cc_start: 0.7216 (mt-10) cc_final: 0.6749 (mp0) REVERT: O 60 MET cc_start: 0.8431 (mtt) cc_final: 0.7773 (mtt) REVERT: O 125 LYS cc_start: 0.8242 (tptm) cc_final: 0.8000 (tptt) REVERT: O 138 ASP cc_start: 0.7426 (m-30) cc_final: 0.7142 (m-30) REVERT: P 16 THR cc_start: 0.8446 (OUTLIER) cc_final: 0.8140 (t) REVERT: P 29 SER cc_start: 0.8945 (m) cc_final: 0.8292 (t) REVERT: P 31 GLU cc_start: 0.8739 (tt0) cc_final: 0.8129 (mp0) REVERT: P 32 GLN cc_start: 0.8997 (mt0) cc_final: 0.8553 (mt0) REVERT: P 83 MET cc_start: 0.8762 (tpt) cc_final: 0.8211 (tpt) REVERT: P 108 LYS cc_start: 0.8567 (mmmt) cc_final: 0.8267 (mmmm) REVERT: P 124 LYS cc_start: 0.9273 (tttt) cc_final: 0.8699 (ttpt) REVERT: Q 99 TYR cc_start: 0.8895 (m-80) cc_final: 0.8680 (m-80) REVERT: Q 106 LYS cc_start: 0.9614 (tptm) cc_final: 0.9349 (tptp) REVERT: Q 116 ASP cc_start: 0.8193 (t0) cc_final: 0.7903 (t0) REVERT: R 21 TYR cc_start: 0.8894 (t80) cc_final: 0.8666 (t80) REVERT: R 23 ARG cc_start: 0.8433 (mtm-85) cc_final: 0.8184 (mtm180) REVERT: R 59 LYS cc_start: 0.8553 (tptp) cc_final: 0.8351 (tptp) REVERT: S 83 PHE cc_start: 0.8879 (m-80) cc_final: 0.8493 (m-80) REVERT: S 110 ASP cc_start: 0.7649 (t0) cc_final: 0.7315 (t0) REVERT: S 121 ARG cc_start: 0.8575 (mtt180) cc_final: 0.8342 (ttm170) REVERT: T 35 ASP cc_start: 0.8807 (t0) cc_final: 0.8556 (t0) REVERT: T 67 ARG cc_start: 0.7033 (OUTLIER) cc_final: 0.6676 (ttt90) REVERT: T 76 THR cc_start: 0.8128 (m) cc_final: 0.7780 (p) REVERT: T 79 TYR cc_start: 0.8183 (m-80) cc_final: 0.7400 (m-80) REVERT: T 88 MET cc_start: 0.8710 (mtp) cc_final: 0.8426 (mtp) REVERT: T 133 ARG cc_start: 0.8579 (mtm-85) cc_final: 0.8142 (mtm-85) REVERT: T 137 GLN cc_start: 0.8880 (mt0) cc_final: 0.8539 (mp10) REVERT: T 142 ASN cc_start: 0.9156 (t0) cc_final: 0.8903 (t0) REVERT: U 40 ILE cc_start: 0.9240 (tt) cc_final: 0.9030 (mt) REVERT: U 41 ARG cc_start: 0.8854 (tmt-80) cc_final: 0.8608 (ttp-110) REVERT: U 44 LYS cc_start: 0.9691 (mmmm) cc_final: 0.9367 (mtmm) REVERT: U 46 LYS cc_start: 0.9256 (mtpp) cc_final: 0.9055 (mtmm) REVERT: U 47 ASN cc_start: 0.9453 (t0) cc_final: 0.9098 (m110) REVERT: U 51 LYS cc_start: 0.8407 (mmtt) cc_final: 0.7656 (ttmt) REVERT: U 55 ARG cc_start: 0.8338 (mtt90) cc_final: 0.7999 (mtt-85) REVERT: U 59 LYS cc_start: 0.8830 (mptt) cc_final: 0.8524 (mptt) REVERT: U 99 LYS cc_start: 0.9263 (ptpt) cc_final: 0.8737 (tptp) REVERT: U 100 GLN cc_start: 0.9163 (pt0) cc_final: 0.8854 (pt0) REVERT: V 7 GLU cc_start: 0.8725 (mp0) cc_final: 0.8174 (mp0) REVERT: V 49 GLN cc_start: 0.9221 (mm-40) cc_final: 0.8727 (mp10) REVERT: V 51 LYS cc_start: 0.9079 (mttt) cc_final: 0.8786 (mtmt) REVERT: V 59 ILE cc_start: 0.9074 (mt) cc_final: 0.8804 (mt) REVERT: V 76 ASP cc_start: 0.8772 (m-30) cc_final: 0.8169 (m-30) REVERT: W 5 ASN cc_start: 0.8848 (t0) cc_final: 0.8567 (t0) REVERT: W 23 ARG cc_start: 0.8601 (mmm160) cc_final: 0.8253 (mmm160) REVERT: W 24 GLN cc_start: 0.9009 (mt0) cc_final: 0.8769 (mt0) REVERT: W 49 GLU cc_start: 0.7504 (pt0) cc_final: 0.6360 (pt0) REVERT: W 51 GLU cc_start: 0.8093 (mm-30) cc_final: 0.7772 (mm-30) REVERT: W 86 LEU cc_start: 0.9049 (tp) cc_final: 0.8712 (tt) REVERT: W 91 ASN cc_start: 0.9257 (t0) cc_final: 0.9003 (t0) REVERT: X 5 ARG cc_start: 0.8462 (ttm170) cc_final: 0.8231 (ttm170) REVERT: X 8 ARG cc_start: 0.8322 (mtt180) cc_final: 0.7881 (mtp85) REVERT: X 48 LYS cc_start: 0.9091 (tttt) cc_final: 0.8799 (ttmt) REVERT: X 58 GLU cc_start: 0.8451 (mm-30) cc_final: 0.8168 (mm-30) REVERT: X 95 GLU cc_start: 0.8270 (tp30) cc_final: 0.7776 (tp30) REVERT: X 98 ASP cc_start: 0.7886 (m-30) cc_final: 0.7404 (m-30) REVERT: Y 19 GLN cc_start: 0.9127 (mp10) cc_final: 0.8901 (mp10) REVERT: Z 44 LEU cc_start: 0.8491 (tp) cc_final: 0.8280 (tt) REVERT: Z 112 ASN cc_start: 0.7356 (m-40) cc_final: 0.7146 (m-40) REVERT: c 10 LYS cc_start: 0.8820 (mttt) cc_final: 0.8410 (mtpp) REVERT: c 13 ARG cc_start: 0.7460 (tpp80) cc_final: 0.7240 (tpp80) REVERT: c 26 GLN cc_start: 0.8178 (pt0) cc_final: 0.7153 (pm20) REVERT: c 31 ARG cc_start: 0.8821 (ttm-80) cc_final: 0.8563 (ttm-80) REVERT: c 52 GLU cc_start: 0.8732 (tt0) cc_final: 0.8397 (tp30) REVERT: g 3 GLU cc_start: 0.8600 (OUTLIER) cc_final: 0.8262 (mm-30) REVERT: g 5 MET cc_start: 0.9006 (mmt) cc_final: 0.8655 (mmt) REVERT: g 76 GLN cc_start: 0.8581 (tp-100) cc_final: 0.8336 (tp-100) REVERT: g 86 THR cc_start: 0.8697 (m) cc_final: 0.8492 (t) REVERT: g 143 GLN cc_start: 0.8740 (OUTLIER) cc_final: 0.8376 (mm110) REVERT: g 191 HIS cc_start: 0.7472 (OUTLIER) cc_final: 0.7236 (t-90) REVERT: g 206 LEU cc_start: 0.8886 (OUTLIER) cc_final: 0.8306 (tp) REVERT: g 219 TRP cc_start: 0.8684 (OUTLIER) cc_final: 0.8202 (m100) REVERT: g 285 GLN cc_start: 0.8573 (mm-40) cc_final: 0.8339 (tp40) REVERT: g 304 ASP cc_start: 0.7874 (t0) cc_final: 0.7576 (p0) REVERT: x 77 LYS cc_start: 0.8248 (OUTLIER) cc_final: 0.7871 (mtmm) REVERT: x 94 LYS cc_start: 0.9228 (OUTLIER) cc_final: 0.8874 (ttmp) REVERT: x 117 GLU cc_start: 0.7982 (OUTLIER) cc_final: 0.7428 (mm-30) REVERT: x 123 GLU cc_start: 0.8383 (mt-10) cc_final: 0.8080 (mp0) REVERT: x 126 ASP cc_start: 0.8560 (t0) cc_final: 0.8352 (t70) REVERT: x 145 GLN cc_start: 0.8707 (mm-40) cc_final: 0.8432 (mm-40) REVERT: x 163 PHE cc_start: 0.7736 (OUTLIER) cc_final: 0.7415 (m-10) REVERT: x 189 LYS cc_start: 0.8955 (tmtp) cc_final: 0.8508 (tmtp) REVERT: x 208 LYS cc_start: 0.9133 (mmtp) cc_final: 0.8855 (mmtp) REVERT: x 217 ASN cc_start: 0.8382 (m-40) cc_final: 0.8077 (m-40) REVERT: y 114 SER cc_start: 0.8716 (p) cc_final: 0.8284 (m) REVERT: y 241 MET cc_start: 0.8299 (mmt) cc_final: 0.7997 (mmm) REVERT: y 294 LYS cc_start: 0.8062 (mtmt) cc_final: 0.7748 (mtmt) REVERT: y 308 MET cc_start: 0.8475 (mtp) cc_final: 0.8054 (mpp) REVERT: y 312 ARG cc_start: 0.6989 (ttm170) cc_final: 0.6596 (mtm110) outliers start: 234 outliers final: 178 residues processed: 1786 average time/residue: 0.8115 time to fit residues: 2414.5280 Evaluate side-chains 1849 residues out of total 4500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 197 poor density : 1652 time to evaluate : 4.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 32 PHE Chi-restraints excluded: chain A residue 36 GLN Chi-restraints excluded: chain A residue 41 ARG Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 173 LEU Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain A residue 185 MET Chi-restraints excluded: chain A residue 200 ASP Chi-restraints excluded: chain B residue 56 LYS Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 75 GLN Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 207 LEU Chi-restraints excluded: chain B residue 210 VAL Chi-restraints excluded: chain C residue 65 LYS Chi-restraints excluded: chain C residue 108 LYS Chi-restraints excluded: chain C residue 130 ILE Chi-restraints excluded: chain C residue 156 ILE Chi-restraints excluded: chain C residue 160 LEU Chi-restraints excluded: chain C residue 165 VAL Chi-restraints excluded: chain C residue 174 ILE Chi-restraints excluded: chain C residue 192 LEU Chi-restraints excluded: chain C residue 221 ASP Chi-restraints excluded: chain C residue 222 CYS Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain D residue 16 ILE Chi-restraints excluded: chain D residue 55 THR Chi-restraints excluded: chain D residue 168 VAL Chi-restraints excluded: chain D residue 188 ILE Chi-restraints excluded: chain D residue 198 ILE Chi-restraints excluded: chain D residue 208 VAL Chi-restraints excluded: chain E residue 32 SER Chi-restraints excluded: chain E residue 52 LEU Chi-restraints excluded: chain E residue 146 THR Chi-restraints excluded: chain E residue 192 ILE Chi-restraints excluded: chain E residue 224 ASN Chi-restraints excluded: chain E residue 256 LEU Chi-restraints excluded: chain F residue 33 ILE Chi-restraints excluded: chain F residue 78 MET Chi-restraints excluded: chain F residue 79 HIS Chi-restraints excluded: chain F residue 90 VAL Chi-restraints excluded: chain F residue 98 GLU Chi-restraints excluded: chain F residue 166 ILE Chi-restraints excluded: chain F residue 169 ILE Chi-restraints excluded: chain F residue 185 SER Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 50 VAL Chi-restraints excluded: chain G residue 153 VAL Chi-restraints excluded: chain G residue 212 LEU Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 100 ILE Chi-restraints excluded: chain H residue 122 LEU Chi-restraints excluded: chain H residue 130 LEU Chi-restraints excluded: chain H residue 145 ARG Chi-restraints excluded: chain H residue 151 SER Chi-restraints excluded: chain H residue 179 LYS Chi-restraints excluded: chain I residue 69 SER Chi-restraints excluded: chain I residue 76 THR Chi-restraints excluded: chain I residue 88 ASN Chi-restraints excluded: chain I residue 157 LYS Chi-restraints excluded: chain I residue 159 SER Chi-restraints excluded: chain I residue 177 SER Chi-restraints excluded: chain J residue 12 THR Chi-restraints excluded: chain J residue 29 LEU Chi-restraints excluded: chain J residue 34 GLU Chi-restraints excluded: chain J residue 43 VAL Chi-restraints excluded: chain J residue 91 LYS Chi-restraints excluded: chain J residue 95 ASP Chi-restraints excluded: chain J residue 98 LEU Chi-restraints excluded: chain J residue 122 SER Chi-restraints excluded: chain J residue 144 ILE Chi-restraints excluded: chain K residue 74 GLU Chi-restraints excluded: chain K residue 79 LEU Chi-restraints excluded: chain L residue 40 ILE Chi-restraints excluded: chain L residue 46 THR Chi-restraints excluded: chain L residue 66 VAL Chi-restraints excluded: chain L residue 74 SER Chi-restraints excluded: chain L residue 78 THR Chi-restraints excluded: chain L residue 104 LYS Chi-restraints excluded: chain L residue 105 ARG Chi-restraints excluded: chain L residue 121 GLN Chi-restraints excluded: chain L residue 146 THR Chi-restraints excluded: chain M residue 45 ARG Chi-restraints excluded: chain N residue 29 THR Chi-restraints excluded: chain N residue 30 SER Chi-restraints excluded: chain N residue 32 ASP Chi-restraints excluded: chain N residue 143 SER Chi-restraints excluded: chain O residue 26 ASN Chi-restraints excluded: chain O residue 48 SER Chi-restraints excluded: chain O residue 91 THR Chi-restraints excluded: chain O residue 95 ILE Chi-restraints excluded: chain O residue 105 THR Chi-restraints excluded: chain P residue 16 THR Chi-restraints excluded: chain P residue 65 LYS Chi-restraints excluded: chain P residue 72 LYS Chi-restraints excluded: chain P residue 96 VAL Chi-restraints excluded: chain P residue 105 VAL Chi-restraints excluded: chain P residue 122 THR Chi-restraints excluded: chain Q residue 10 VAL Chi-restraints excluded: chain Q residue 25 CYS Chi-restraints excluded: chain Q residue 31 LEU Chi-restraints excluded: chain Q residue 121 VAL Chi-restraints excluded: chain R residue 9 VAL Chi-restraints excluded: chain R residue 66 VAL Chi-restraints excluded: chain S residue 12 ILE Chi-restraints excluded: chain S residue 18 THR Chi-restraints excluded: chain S residue 33 ILE Chi-restraints excluded: chain S residue 71 MET Chi-restraints excluded: chain S residue 98 VAL Chi-restraints excluded: chain S residue 117 ILE Chi-restraints excluded: chain T residue 4 VAL Chi-restraints excluded: chain T residue 12 GLN Chi-restraints excluded: chain T residue 37 VAL Chi-restraints excluded: chain T residue 45 LEU Chi-restraints excluded: chain T residue 59 SER Chi-restraints excluded: chain T residue 67 ARG Chi-restraints excluded: chain T residue 96 SER Chi-restraints excluded: chain U residue 32 LEU Chi-restraints excluded: chain U residue 33 GLU Chi-restraints excluded: chain U residue 39 LEU Chi-restraints excluded: chain U residue 61 LEU Chi-restraints excluded: chain W residue 14 ILE Chi-restraints excluded: chain W residue 25 VAL Chi-restraints excluded: chain W residue 27 ILE Chi-restraints excluded: chain W residue 33 VAL Chi-restraints excluded: chain W residue 36 ARG Chi-restraints excluded: chain W residue 40 VAL Chi-restraints excluded: chain W residue 47 ILE Chi-restraints excluded: chain W residue 63 VAL Chi-restraints excluded: chain W residue 94 LEU Chi-restraints excluded: chain W residue 103 VAL Chi-restraints excluded: chain W residue 105 THR Chi-restraints excluded: chain W residue 106 THR Chi-restraints excluded: chain X residue 13 LEU Chi-restraints excluded: chain X residue 70 VAL Chi-restraints excluded: chain X residue 77 ASN Chi-restraints excluded: chain X residue 81 ILE Chi-restraints excluded: chain X residue 128 VAL Chi-restraints excluded: chain Y residue 17 LEU Chi-restraints excluded: chain Y residue 25 ILE Chi-restraints excluded: chain Y residue 55 ILE Chi-restraints excluded: chain Z residue 48 VAL Chi-restraints excluded: chain Z residue 69 THR Chi-restraints excluded: chain Z residue 92 LEU Chi-restraints excluded: chain Z residue 110 THR Chi-restraints excluded: chain Z residue 113 THR Chi-restraints excluded: chain b residue 53 VAL Chi-restraints excluded: chain b residue 77 CYS Chi-restraints excluded: chain c residue 15 THR Chi-restraints excluded: chain c residue 32 VAL Chi-restraints excluded: chain e residue 29 THR Chi-restraints excluded: chain e residue 45 VAL Chi-restraints excluded: chain f residue 121 CYS Chi-restraints excluded: chain g residue 3 GLU Chi-restraints excluded: chain g residue 21 ILE Chi-restraints excluded: chain g residue 24 THR Chi-restraints excluded: chain g residue 30 MET Chi-restraints excluded: chain g residue 111 VAL Chi-restraints excluded: chain g residue 143 GLN Chi-restraints excluded: chain g residue 165 ILE Chi-restraints excluded: chain g residue 173 LEU Chi-restraints excluded: chain g residue 189 ILE Chi-restraints excluded: chain g residue 191 HIS Chi-restraints excluded: chain g residue 206 LEU Chi-restraints excluded: chain g residue 207 CYS Chi-restraints excluded: chain g residue 219 TRP Chi-restraints excluded: chain g residue 245 ARG Chi-restraints excluded: chain g residue 261 LEU Chi-restraints excluded: chain g residue 265 ILE Chi-restraints excluded: chain g residue 266 ILE Chi-restraints excluded: chain g residue 287 THR Chi-restraints excluded: chain x residue 77 LYS Chi-restraints excluded: chain x residue 78 ILE Chi-restraints excluded: chain x residue 88 LEU Chi-restraints excluded: chain x residue 94 LYS Chi-restraints excluded: chain x residue 117 GLU Chi-restraints excluded: chain x residue 118 ILE Chi-restraints excluded: chain x residue 119 ARG Chi-restraints excluded: chain x residue 127 VAL Chi-restraints excluded: chain x residue 150 LEU Chi-restraints excluded: chain x residue 163 PHE Chi-restraints excluded: chain x residue 220 MET Chi-restraints excluded: chain x residue 241 ILE Chi-restraints excluded: chain x residue 244 VAL Chi-restraints excluded: chain y residue 48 VAL Chi-restraints excluded: chain y residue 126 SER Chi-restraints excluded: chain y residue 215 LYS Chi-restraints excluded: chain y residue 268 LEU Chi-restraints excluded: chain y residue 297 SER Chi-restraints excluded: chain y residue 307 HIS Chi-restraints excluded: chain y residue 328 THR Chi-restraints excluded: chain y residue 341 THR Chi-restraints excluded: chain y residue 359 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 766, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 60.9561 > 50: distance: 73 - 77: 17.320 distance: 77 - 78: 15.298 distance: 78 - 79: 23.469 distance: 78 - 81: 10.400 distance: 79 - 80: 35.245 distance: 79 - 88: 29.237 distance: 81 - 82: 9.286 distance: 82 - 83: 19.223 distance: 82 - 84: 6.178 distance: 83 - 85: 8.563 distance: 84 - 86: 6.332 distance: 85 - 87: 3.557 distance: 86 - 87: 6.436 distance: 88 - 89: 14.291 distance: 88 - 170: 8.605 distance: 89 - 90: 6.852 distance: 89 - 92: 10.650 distance: 90 - 91: 26.924 distance: 90 - 96: 15.597 distance: 91 - 167: 26.812 distance: 92 - 93: 9.421 distance: 93 - 94: 10.922 distance: 94 - 95: 17.055 distance: 96 - 97: 9.956 distance: 97 - 98: 13.733 distance: 97 - 100: 16.087 distance: 98 - 99: 24.462 distance: 98 - 103: 17.104 distance: 100 - 101: 18.370 distance: 100 - 102: 15.809 distance: 103 - 104: 19.704 distance: 103 - 150: 9.567 distance: 104 - 105: 12.363 distance: 104 - 107: 9.251 distance: 105 - 106: 13.991 distance: 105 - 111: 9.966 distance: 106 - 147: 31.817 distance: 107 - 108: 14.759 distance: 108 - 109: 18.599 distance: 108 - 110: 19.749 distance: 111 - 112: 15.505 distance: 112 - 113: 20.914 distance: 112 - 115: 24.801 distance: 113 - 114: 26.730 distance: 113 - 122: 30.807 distance: 115 - 116: 18.567 distance: 116 - 117: 11.237 distance: 117 - 118: 5.496 distance: 118 - 119: 20.832 distance: 119 - 120: 24.951 distance: 119 - 121: 19.371 distance: 122 - 123: 22.442 distance: 123 - 124: 21.714 distance: 123 - 126: 43.689 distance: 124 - 125: 33.395 distance: 124 - 130: 29.987 distance: 126 - 127: 12.477 distance: 127 - 128: 32.566 distance: 127 - 129: 32.016 distance: 130 - 131: 15.697 distance: 131 - 132: 13.997 distance: 131 - 134: 37.094 distance: 132 - 133: 13.856 distance: 132 - 138: 10.352 distance: 134 - 135: 12.445 distance: 135 - 136: 11.854 distance: 135 - 137: 49.579 distance: 138 - 139: 15.715 distance: 139 - 140: 19.027 distance: 139 - 142: 20.067 distance: 140 - 141: 22.291 distance: 140 - 147: 18.958 distance: 142 - 143: 10.867 distance: 143 - 144: 12.410 distance: 144 - 145: 27.582 distance: 144 - 146: 20.167 distance: 147 - 148: 15.151 distance: 148 - 149: 15.705 distance: 148 - 151: 13.091 distance: 149 - 150: 9.195 distance: 149 - 158: 10.186 distance: 151 - 152: 3.076 distance: 152 - 153: 12.718 distance: 153 - 154: 11.226 distance: 154 - 155: 24.265 distance: 155 - 156: 18.174 distance: 155 - 157: 23.881 distance: 158 - 159: 12.302 distance: 158 - 198: 22.332 distance: 159 - 160: 10.285 distance: 159 - 162: 18.884 distance: 160 - 161: 12.510 distance: 160 - 167: 16.543 distance: 161 - 195: 3.639 distance: 162 - 163: 16.227 distance: 163 - 164: 21.962 distance: 164 - 165: 15.814 distance: 165 - 166: 28.208