Starting phenix.real_space_refine on Thu May 29 08:23:59 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/4v1a_2787/05_2025/4v1a_2787_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/4v1a_2787/05_2025/4v1a_2787.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/4v1a_2787/05_2025/4v1a_2787.map" default_real_map = "/net/cci-nas-00/data/ceres_data/4v1a_2787/05_2025/4v1a_2787.map" model { file = "/net/cci-nas-00/data/ceres_data/4v1a_2787/05_2025/4v1a_2787_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/4v1a_2787/05_2025/4v1a_2787_neut.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.004 sd= 0.025 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: 5 Type Number sf(0) Gaussians Zn 1 6.06 5 S 124 5.16 5 C 20336 2.51 5 N 5766 2.21 5 O 5690 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 31917 Number of models: 1 Model: "" Number of chains: 27 Chain: "a" Number of atoms: 3173 Number of conformers: 1 Conformer: "" Number of residues, atoms: 393, 3173 Classifications: {'peptide': 393} Link IDs: {'PTRANS': 35, 'TRANS': 357} Chain: "b" Number of atoms: 2952 Number of conformers: 1 Conformer: "" Number of residues, atoms: 354, 2952 Classifications: {'peptide': 354} Link IDs: {'PTRANS': 32, 'TRANS': 321} Chain: "c" Number of atoms: 2408 Number of conformers: 1 Conformer: "" Number of residues, atoms: 295, 2408 Classifications: {'peptide': 295} Link IDs: {'PTRANS': 15, 'TRANS': 279} Chain: "d" Number of atoms: 832 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 832 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 11, 'TRANS': 87} Chain: "e" Number of atoms: 968 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 968 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 11, 'TRANS': 109} Chain: "f" Number of atoms: 332 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 332 Classifications: {'peptide': 42} Link IDs: {'PTRANS': 5, 'TRANS': 36} Chain: "f" Number of atoms: 520 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 520 Classifications: {'peptide': 66} Link IDs: {'PTRANS': 5, 'TRANS': 60} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 48 Planarities with less than four sites: {'UNK:plan-1': 24} Unresolved non-hydrogen planarities: 24 Chain: "g" Number of atoms: 1167 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 1167 Classifications: {'peptide': 148} Link IDs: {'PTRANS': 10, 'TRANS': 137} Chain: "h" Number of atoms: 2319 Number of conformers: 1 Conformer: "" Number of residues, atoms: 289, 2319 Classifications: {'peptide': 289} Link IDs: {'PTRANS': 18, 'TRANS': 270} Chain: "i" Number of atoms: 1979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 242, 1979 Classifications: {'peptide': 242} Link IDs: {'PTRANS': 20, 'TRANS': 221} Chain: "j" Number of atoms: 1775 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1775 Classifications: {'peptide': 217} Link IDs: {'PTRANS': 9, 'TRANS': 207} Chain breaks: 2 Chain: "k" Number of atoms: 1050 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1050 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 4, 'TRANS': 126} Chain breaks: 2 Chain: "l" Number of atoms: 1097 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 1097 Classifications: {'peptide': 133} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 116} Chain: "m" Number of atoms: 893 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 893 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 8, 'TRANS': 100} Chain: "n" Number of atoms: 837 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 837 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 4, 'TRANS': 92} Chain: "o" Number of atoms: 747 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 747 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 6, 'TRANS': 87} Chain: "p" Number of atoms: 742 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 742 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 2, 'TRANS': 94} Chain: "q" Number of atoms: 336 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 336 Classifications: {'peptide': 37} Link IDs: {'PTRANS': 3, 'TRANS': 33} Chain: "t" Number of atoms: 780 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 780 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 5, 'TRANS': 88} Chain: "u" Number of atoms: 956 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 956 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 5, 'TRANS': 113} Chain breaks: 1 Chain: "u" Number of atoms: 252 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 252 Classifications: {'peptide': 32} Link IDs: {'TRANS': 31} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Planarities with less than four sites: {'UNK:plan-1': 10} Unresolved non-hydrogen planarities: 10 Chain: "v" Number of atoms: 996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 996 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 12, 'TRANS': 106} Chain: "v" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 72 Classifications: {'peptide': 12} Link IDs: {'TRANS': 11} Chain breaks: 1 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Planarities with less than four sites: {'UNK:plan-1': 12} Unresolved non-hydrogen planarities: 12 Chain: "w" Number of atoms: 3126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 387, 3126 Classifications: {'peptide': 387} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 360} Chain: "x" Number of atoms: 1325 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1325 Classifications: {'peptide': 162} Link IDs: {'PTRANS': 18, 'TRANS': 143} Chain: "z" Number of atoms: 282 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 282 Classifications: {'peptide': 47} Link IDs: {'TRANS': 46} Chain breaks: 5 Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 94 Planarities with less than four sites: {'UNK:plan-1': 47} Unresolved non-hydrogen planarities: 47 Chain: "x" 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 30586 SG CYS x 70 104.313 101.405 191.425 1.00100.37 S ATOM 30607 SG CYS x 73 108.012 102.136 191.452 1.00 79.09 S ATOM 30904 SG CYS x 108 106.515 100.013 188.707 1.00 59.61 S Time building chain proxies: 16.27, per 1000 atoms: 0.51 Number of scatterers: 31917 At special positions: 0 Unit cell: (264.6, 218.4, 229.6, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 1 29.99 S 124 16.00 O 5690 8.00 N 5766 7.00 C 20336 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 Links applied TRANS " UNK f 77 " - " PRO f 76 " " UNK u 164 " - " PRO u 163 " " UNK v 144 " - " ARG v 143 " Time building additional restraints: 7.16 Conformation dependent library (CDL) restraints added in 3.5 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN x 500 " pdb="ZN ZN x 500 " - pdb=" SG CYS x 70 " pdb="ZN ZN x 500 " - pdb=" SG CYS x 73 " pdb="ZN ZN x 500 " - pdb=" SG CYS x 108 " 7570 Ramachandran restraints generated. 3785 Oldfield, 0 Emsley, 3785 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7508 Finding SS restraints... Secondary structure from input PDB file: 141 helices and 34 sheets defined 43.2% alpha, 18.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.09 Creating SS restraints... Processing helix chain 'a' and resid 47 through 51 Processing helix chain 'a' and resid 60 through 63 Processing helix chain 'a' and resid 92 through 96 Processing helix chain 'a' and resid 115 through 125 Processing helix chain 'a' and resid 133 through 142 Processing helix chain 'a' and resid 149 through 163 removed outlier: 3.607A pdb=" N LEU a 155 " --> pdb=" O ASP a 151 " (cutoff:3.500A) Processing helix chain 'a' and resid 172 through 190 Proline residue: a 178 - end of helix removed outlier: 3.545A pdb=" N SER a 190 " --> pdb=" O GLN a 186 " (cutoff:3.500A) Processing helix chain 'a' and resid 191 through 194 Processing helix chain 'a' and resid 197 through 199 No H-bonds generated for 'chain 'a' and resid 197 through 199' Processing helix chain 'a' and resid 241 through 250 Processing helix chain 'a' and resid 305 through 329 removed outlier: 3.614A pdb=" N ARG a 310 " --> pdb=" O PRO a 306 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLN a 324 " --> pdb=" O SER a 320 " (cutoff:3.500A) Processing helix chain 'a' and resid 407 through 419 removed outlier: 4.283A pdb=" N PHE a 411 " --> pdb=" O GLN a 407 " (cutoff:3.500A) Processing helix chain 'b' and resid 44 through 48 Processing helix chain 'b' and resid 53 through 67 removed outlier: 3.711A pdb=" N LYS b 67 " --> pdb=" O GLN b 63 " (cutoff:3.500A) Processing helix chain 'b' and resid 73 through 78 removed outlier: 3.648A pdb=" N HIS b 77 " --> pdb=" O THR b 73 " (cutoff:3.500A) Processing helix chain 'b' and resid 98 through 115 removed outlier: 3.708A pdb=" N GLN b 102 " --> pdb=" O SER b 98 " (cutoff:3.500A) Processing helix chain 'b' and resid 116 through 125 removed outlier: 3.564A pdb=" N GLU b 120 " --> pdb=" O ASN b 116 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LEU b 125 " --> pdb=" O ARG b 121 " (cutoff:3.500A) Processing helix chain 'b' and resid 131 through 142 Processing helix chain 'b' and resid 143 through 155 removed outlier: 3.756A pdb=" N GLN b 149 " --> pdb=" O PRO b 145 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ARG b 150 " --> pdb=" O TYR b 146 " (cutoff:3.500A) Processing helix chain 'b' and resid 196 through 200 removed outlier: 4.076A pdb=" N GLN b 200 " --> pdb=" O GLU b 197 " (cutoff:3.500A) Processing helix chain 'b' and resid 299 through 308 Processing helix chain 'b' and resid 326 through 334 removed outlier: 3.579A pdb=" N HIS b 332 " --> pdb=" O THR b 328 " (cutoff:3.500A) Processing helix chain 'b' and resid 362 through 369 removed outlier: 3.607A pdb=" N TYR b 369 " --> pdb=" O LEU b 366 " (cutoff:3.500A) Processing helix chain 'c' and resid 33 through 54 removed outlier: 3.537A pdb=" N ILE c 38 " --> pdb=" O PRO c 34 " (cutoff:3.500A) Processing helix chain 'c' and resid 84 through 90 Processing helix chain 'c' and resid 93 through 100 removed outlier: 3.547A pdb=" N CYS c 97 " --> pdb=" O SER c 93 " (cutoff:3.500A) Processing helix chain 'c' and resid 132 through 153 removed outlier: 3.573A pdb=" N MET c 147 " --> pdb=" O CYS c 143 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N CYS c 149 " --> pdb=" O MET c 145 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ARG c 153 " --> pdb=" O CYS c 149 " (cutoff:3.500A) Processing helix chain 'c' and resid 184 through 187 Processing helix chain 'c' and resid 192 through 209 removed outlier: 3.745A pdb=" N LYS c 209 " --> pdb=" O ALA c 205 " (cutoff:3.500A) Processing helix chain 'c' and resid 220 through 228 removed outlier: 3.961A pdb=" N GLU c 225 " --> pdb=" O LYS c 221 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N ILE c 226 " --> pdb=" O VAL c 222 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N PHE c 227 " --> pdb=" O ALA c 223 " (cutoff:3.500A) Processing helix chain 'c' and resid 230 through 244 removed outlier: 3.769A pdb=" N ASN c 244 " --> pdb=" O LYS c 240 " (cutoff:3.500A) Processing helix chain 'c' and resid 305 through 316 removed outlier: 3.757A pdb=" N ASN c 310 " --> pdb=" O PHE c 306 " (cutoff:3.500A) Processing helix chain 'd' and resid 91 through 95 Processing helix chain 'd' and resid 95 through 100 removed outlier: 4.000A pdb=" N GLU d 98 " --> pdb=" O LEU d 95 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N ARG d 99 " --> pdb=" O ASN d 96 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLN d 100 " --> pdb=" O LYS d 97 " (cutoff:3.500A) No H-bonds generated for 'chain 'd' and resid 95 through 100' Processing helix chain 'd' and resid 107 through 154 removed outlier: 3.528A pdb=" N GLU d 130 " --> pdb=" O GLN d 126 " (cutoff:3.500A) Processing helix chain 'd' and resid 155 through 161 Processing helix chain 'd' and resid 165 through 169 removed outlier: 3.700A pdb=" N LEU d 168 " --> pdb=" O ASP d 165 " (cutoff:3.500A) Processing helix chain 'e' and resid 52 through 55 Processing helix chain 'e' and resid 85 through 93 removed outlier: 3.629A pdb=" N THR e 93 " --> pdb=" O LEU e 89 " (cutoff:3.500A) Processing helix chain 'e' and resid 93 through 104 removed outlier: 4.173A pdb=" N ALA e 97 " --> pdb=" O THR e 93 " (cutoff:3.500A) Processing helix chain 'e' and resid 112 through 116 Processing helix chain 'f' and resid 68 through 72 Processing helix chain 'f' and resid 88 through 95 Processing helix chain 'f' and resid 104 through 116 Processing helix chain 'f' and resid 127 through 133 removed outlier: 3.770A pdb=" N ARG f 133 " --> pdb=" O TYR f 129 " (cutoff:3.500A) Processing helix chain 'g' and resid 13 through 17 removed outlier: 3.952A pdb=" N HIS g 16 " --> pdb=" O SER g 13 " (cutoff:3.500A) Processing helix chain 'g' and resid 37 through 39 No H-bonds generated for 'chain 'g' and resid 37 through 39' Processing helix chain 'g' and resid 40 through 49 Processing helix chain 'g' and resid 49 through 58 removed outlier: 4.584A pdb=" N ASP g 53 " --> pdb=" O ARG g 49 " (cutoff:3.500A) Processing helix chain 'g' and resid 93 through 106 removed outlier: 3.956A pdb=" N ASP g 106 " --> pdb=" O GLN g 102 " (cutoff:3.500A) Processing helix chain 'g' and resid 139 through 143 removed outlier: 3.706A pdb=" N GLY g 142 " --> pdb=" O THR g 139 " (cutoff:3.500A) Processing helix chain 'h' and resid 34 through 53 removed outlier: 3.686A pdb=" N LYS h 43 " --> pdb=" O TYR h 39 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N GLU h 44 " --> pdb=" O ARG h 40 " (cutoff:3.500A) Processing helix chain 'h' and resid 67 through 79 removed outlier: 3.506A pdb=" N GLY h 76 " --> pdb=" O ILE h 72 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LEU h 79 " --> pdb=" O PHE h 75 " (cutoff:3.500A) Processing helix chain 'h' and resid 84 through 92 Processing helix chain 'h' and resid 94 through 108 Processing helix chain 'h' and resid 112 through 118 Processing helix chain 'h' and resid 122 through 145 Processing helix chain 'h' and resid 149 through 161 Processing helix chain 'h' and resid 162 through 173 Processing helix chain 'h' and resid 174 through 179 removed outlier: 3.527A pdb=" N LEU h 178 " --> pdb=" O ALA h 174 " (cutoff:3.500A) Processing helix chain 'h' and resid 187 through 206 removed outlier: 3.535A pdb=" N GLN h 193 " --> pdb=" O PRO h 189 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N VAL h 198 " --> pdb=" O THR h 194 " (cutoff:3.500A) Processing helix chain 'h' and resid 207 through 219 removed outlier: 3.625A pdb=" N LEU h 213 " --> pdb=" O GLU h 209 " (cutoff:3.500A) Processing helix chain 'h' and resid 220 through 224 Processing helix chain 'h' and resid 227 through 233 removed outlier: 3.650A pdb=" N MET h 231 " --> pdb=" O GLU h 227 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N THR h 233 " --> pdb=" O PHE h 229 " (cutoff:3.500A) Processing helix chain 'h' and resid 236 through 248 Processing helix chain 'h' and resid 288 through 306 Processing helix chain 'i' and resid 93 through 98 Processing helix chain 'i' and resid 100 through 115 removed outlier: 3.989A pdb=" N ALA i 106 " --> pdb=" O LYS i 102 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ASN i 115 " --> pdb=" O ARG i 111 " (cutoff:3.500A) Processing helix chain 'i' and resid 115 through 129 Processing helix chain 'i' and resid 136 through 155 removed outlier: 3.554A pdb=" N LYS i 140 " --> pdb=" O ASP i 136 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N PHE i 145 " --> pdb=" O ALA i 141 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ILE i 146 " --> pdb=" O LYS i 142 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LEU i 150 " --> pdb=" O ILE i 146 " (cutoff:3.500A) Processing helix chain 'i' and resid 156 through 164 removed outlier: 3.665A pdb=" N LEU i 160 " --> pdb=" O ASP i 156 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N THR i 162 " --> pdb=" O ASP i 158 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N VAL i 164 " --> pdb=" O LEU i 160 " (cutoff:3.500A) Processing helix chain 'i' and resid 167 through 177 removed outlier: 4.563A pdb=" N ASP i 171 " --> pdb=" O ASN i 167 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N MET i 172 " --> pdb=" O CYS i 168 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ILE i 176 " --> pdb=" O MET i 172 " (cutoff:3.500A) Processing helix chain 'j' and resid 64 through 81 Processing helix chain 'j' and resid 85 through 104 removed outlier: 3.943A pdb=" N GLU j 94 " --> pdb=" O ARG j 90 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ALA j 99 " --> pdb=" O ALA j 95 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LYS j 100 " --> pdb=" O GLN j 96 " (cutoff:3.500A) Processing helix chain 'j' and resid 116 through 130 Processing helix chain 'j' and resid 183 through 197 removed outlier: 3.553A pdb=" N SER j 196 " --> pdb=" O LEU j 192 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N GLU j 197 " --> pdb=" O ALA j 193 " (cutoff:3.500A) Processing helix chain 'j' and resid 256 through 264 removed outlier: 3.579A pdb=" N ASP j 262 " --> pdb=" O GLU j 258 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N LEU j 264 " --> pdb=" O LEU j 260 " (cutoff:3.500A) Processing helix chain 'j' and resid 266 through 271 Processing helix chain 'k' and resid 99 through 117 Processing helix chain 'k' and resid 163 through 177 removed outlier: 3.795A pdb=" N GLU k 172 " --> pdb=" O GLU k 168 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ILE k 173 " --> pdb=" O ILE k 169 " (cutoff:3.500A) Processing helix chain 'l' and resid 42 through 44 No H-bonds generated for 'chain 'l' and resid 42 through 44' Processing helix chain 'l' and resid 45 through 50 removed outlier: 3.611A pdb=" N ARG l 50 " --> pdb=" O HIS l 46 " (cutoff:3.500A) Processing helix chain 'l' and resid 116 through 133 removed outlier: 3.609A pdb=" N LEU l 120 " --> pdb=" O ASP l 116 " (cutoff:3.500A) Proline residue: l 130 - end of helix Processing helix chain 'l' and resid 153 through 164 Processing helix chain 'm' and resid 66 through 80 Processing helix chain 'm' and resid 94 through 109 Processing helix chain 'm' and resid 115 through 120 Processing helix chain 'm' and resid 123 through 132 removed outlier: 4.071A pdb=" N VAL m 127 " --> pdb=" O ARG m 123 " (cutoff:3.500A) Processing helix chain 'm' and resid 139 through 146 Processing helix chain 'n' and resid 48 through 53 Processing helix chain 'n' and resid 59 through 64 Processing helix chain 'n' and resid 69 through 74 Processing helix chain 'n' and resid 86 through 98 Processing helix chain 'n' and resid 99 through 102 Processing helix chain 'n' and resid 103 through 124 Processing helix chain 'o' and resid 24 through 32 Processing helix chain 'o' and resid 41 through 46 removed outlier: 3.513A pdb=" N GLU o 45 " --> pdb=" O GLY o 41 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N LEU o 46 " --> pdb=" O PRO o 42 " (cutoff:3.500A) No H-bonds generated for 'chain 'o' and resid 41 through 46' Processing helix chain 'o' and resid 60 through 109 removed outlier: 3.686A pdb=" N GLU o 103 " --> pdb=" O LEU o 99 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N GLN o 106 " --> pdb=" O GLU o 102 " (cutoff:3.500A) Processing helix chain 'p' and resid 2 through 7 Processing helix chain 'p' and resid 8 through 11 removed outlier: 5.733A pdb=" N ARG p 11 " --> pdb=" O LEU p 8 " (cutoff:3.500A) No H-bonds generated for 'chain 'p' and resid 8 through 11' Processing helix chain 'p' and resid 27 through 38 Processing helix chain 'p' and resid 39 through 46 removed outlier: 3.947A pdb=" N ASN p 46 " --> pdb=" O VAL p 42 " (cutoff:3.500A) Processing helix chain 'p' and resid 82 through 95 removed outlier: 3.549A pdb=" N LEU p 87 " --> pdb=" O ALA p 83 " (cutoff:3.500A) Processing helix chain 'q' and resid 117 through 132 removed outlier: 3.696A pdb=" N LEU q 121 " --> pdb=" O TYR q 117 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N HIS q 129 " --> pdb=" O ASN q 125 " (cutoff:3.500A) Processing helix chain 't' and resid 28 through 50 Processing helix chain 't' and resid 64 through 80 removed outlier: 3.750A pdb=" N PHE t 71 " --> pdb=" O ARG t 67 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N GLN t 78 " --> pdb=" O LEU t 74 " (cutoff:3.500A) Processing helix chain 't' and resid 87 through 94 removed outlier: 4.107A pdb=" N GLN t 91 " --> pdb=" O ARG t 87 " (cutoff:3.500A) Processing helix chain 't' and resid 95 through 99 removed outlier: 3.501A pdb=" N THR t 98 " --> pdb=" O LEU t 95 " (cutoff:3.500A) Processing helix chain 'u' and resid 44 through 49 Processing helix chain 'u' and resid 54 through 58 removed outlier: 3.673A pdb=" N ALA u 58 " --> pdb=" O SER u 55 " (cutoff:3.500A) Processing helix chain 'u' and resid 72 through 76 Processing helix chain 'u' and resid 111 through 118 Processing helix chain 'u' and resid 141 through 162 removed outlier: 3.743A pdb=" N ASN u 145 " --> pdb=" O TYR u 141 " (cutoff:3.500A) Processing helix chain 'u' and resid 170 through 189 removed outlier: 3.768A pdb=" N LEU u 174 " --> pdb=" O UNK u 170 " (cutoff:3.500A) removed outlier: 5.493A pdb=" N ARG u 176 " --> pdb=" O UNK u 172 " (cutoff:3.500A) removed outlier: 4.848A pdb=" N SER u 177 " --> pdb=" O UNK u 173 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LEU u 187 " --> pdb=" O ASN u 183 " (cutoff:3.500A) Processing helix chain 'v' and resid 48 through 52 Processing helix chain 'v' and resid 53 through 64 removed outlier: 3.630A pdb=" N ALA v 57 " --> pdb=" O SER v 53 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ALA v 58 " --> pdb=" O PRO v 54 " (cutoff:3.500A) Processing helix chain 'v' and resid 71 through 76 removed outlier: 3.599A pdb=" N TRP v 76 " --> pdb=" O GLY v 73 " (cutoff:3.500A) Processing helix chain 'v' and resid 78 through 93 Processing helix chain 'v' and resid 95 through 154 removed outlier: 3.650A pdb=" N VAL v 105 " --> pdb=" O GLU v 101 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N GLN v 106 " --> pdb=" O SER v 102 " (cutoff:3.500A) Proline residue: v 129 - end of helix Processing helix chain 'w' and resid 55 through 72 Processing helix chain 'w' and resid 75 through 85 removed outlier: 3.582A pdb=" N LYS w 79 " --> pdb=" O SER w 75 " (cutoff:3.500A) Processing helix chain 'w' and resid 101 through 111 removed outlier: 4.143A pdb=" N TRP w 105 " --> pdb=" O ASN w 101 " (cutoff:3.500A) Processing helix chain 'w' and resid 132 through 149 removed outlier: 3.684A pdb=" N LEU w 136 " --> pdb=" O ASP w 132 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N CYS w 143 " --> pdb=" O ALA w 139 " (cutoff:3.500A) Processing helix chain 'w' and resid 162 through 184 removed outlier: 3.655A pdb=" N SER w 168 " --> pdb=" O GLU w 164 " (cutoff:3.500A) Proline residue: w 169 - end of helix removed outlier: 3.885A pdb=" N GLY w 180 " --> pdb=" O ALA w 176 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LEU w 181 " --> pdb=" O SER w 177 " (cutoff:3.500A) Processing helix chain 'w' and resid 186 through 191 removed outlier: 3.622A pdb=" N ALA w 191 " --> pdb=" O VAL w 188 " (cutoff:3.500A) Processing helix chain 'w' and resid 261 through 265 Processing helix chain 'w' and resid 297 through 300 Processing helix chain 'w' and resid 301 through 308 Processing helix chain 'w' and resid 312 through 337 removed outlier: 3.788A pdb=" N PHE w 318 " --> pdb=" O ILE w 314 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N PHE w 327 " --> pdb=" O ILE w 323 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N GLN w 333 " --> pdb=" O TRP w 329 " (cutoff:3.500A) Processing helix chain 'w' and resid 340 through 344 removed outlier: 3.749A pdb=" N ASP w 344 " --> pdb=" O SER w 341 " (cutoff:3.500A) Processing helix chain 'w' and resid 374 through 381 removed outlier: 4.521A pdb=" N ASN w 380 " --> pdb=" O GLN w 376 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ASN w 381 " --> pdb=" O ALA w 377 " (cutoff:3.500A) Processing helix chain 'w' and resid 408 through 420 removed outlier: 3.960A pdb=" N LEU w 412 " --> pdb=" O ASN w 408 " (cutoff:3.500A) Processing helix chain 'x' and resid 70 through 75 removed outlier: 3.855A pdb=" N TRP x 75 " --> pdb=" O PRO x 71 " (cutoff:3.500A) Processing helix chain 'x' and resid 85 through 90 removed outlier: 3.513A pdb=" N LEU x 89 " --> pdb=" O ASP x 85 " (cutoff:3.500A) Processing helix chain 'x' and resid 101 through 106 Processing helix chain 'x' and resid 108 through 125 Processing helix chain 'x' and resid 128 through 132 removed outlier: 3.941A pdb=" N ARG x 132 " --> pdb=" O PRO x 129 " (cutoff:3.500A) Processing helix chain 'x' and resid 135 through 139 removed outlier: 3.672A pdb=" N PHE x 139 " --> pdb=" O PRO x 136 " (cutoff:3.500A) Processing helix chain 'x' and resid 178 through 182 Processing helix chain 'z' and resid 9 through 35 Processing helix chain 'z' and resid 201 through 210 Processing sheet with id=AA, first strand: chain 'a' and resid 208 through 215 removed outlier: 4.982A pdb=" N LEU a 219 " --> pdb=" O ALA a 103 " (cutoff:3.500A) removed outlier: 10.217A pdb=" N GLN a 102 " --> pdb=" O VAL a 270 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N VAL a 270 " --> pdb=" O GLN a 102 " (cutoff:3.500A) Processing sheet with id=AB, first strand: chain 'a' and resid 126 through 129 removed outlier: 6.498A pdb=" N ASN a 372 " --> pdb=" O ASN a 360 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N ASN a 360 " --> pdb=" O ASN a 372 " (cutoff:3.500A) removed outlier: 5.079A pdb=" N ALA a 374 " --> pdb=" O GLN a 358 " (cutoff:3.500A) removed outlier: 7.098A pdb=" N GLN a 358 " --> pdb=" O ALA a 374 " (cutoff:3.500A) removed outlier: 5.555A pdb=" N VAL a 376 " --> pdb=" O VAL a 356 " (cutoff:3.500A) removed outlier: 7.590A pdb=" N VAL a 356 " --> pdb=" O VAL a 376 " (cutoff:3.500A) removed outlier: 4.956A pdb=" N SER a 378 " --> pdb=" O PHE a 354 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N PHE a 354 " --> pdb=" O SER a 378 " (cutoff:3.500A) removed outlier: 10.052A pdb=" N PHE a 352 " --> pdb=" O SER a 344 " (cutoff:3.500A) removed outlier: 11.444A pdb=" N SER a 344 " --> pdb=" O PHE a 352 " (cutoff:3.500A) removed outlier: 10.836A pdb=" N PHE a 354 " --> pdb=" O VAL a 342 " (cutoff:3.500A) removed outlier: 11.807A pdb=" N VAL a 342 " --> pdb=" O PHE a 354 " (cutoff:3.500A) removed outlier: 10.099A pdb=" N VAL a 356 " --> pdb=" O VAL a 340 " (cutoff:3.500A) removed outlier: 10.822A pdb=" N VAL a 340 " --> pdb=" O VAL a 356 " (cutoff:3.500A) removed outlier: 10.410A pdb=" N GLN a 358 " --> pdb=" O GLN a 338 " (cutoff:3.500A) removed outlier: 11.380A pdb=" N GLN a 338 " --> pdb=" O GLN a 358 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N ASN a 360 " --> pdb=" O LEU a 336 " (cutoff:3.500A) removed outlier: 12.069A pdb=" N CYS a 287 " --> pdb=" O PRO a 339 " (cutoff:3.500A) removed outlier: 9.215A pdb=" N VAL a 341 " --> pdb=" O CYS a 287 " (cutoff:3.500A) removed outlier: 6.014A pdb=" N HIS a 289 " --> pdb=" O VAL a 341 " (cutoff:3.500A) removed outlier: 5.710A pdb=" N ALA a 232 " --> pdb=" O PRO a 288 " (cutoff:3.500A) Processing sheet with id=AC, first strand: chain 'a' and resid 385 through 387 removed outlier: 3.847A pdb=" N HIS a 385 " --> pdb=" O ILE a 404 " (cutoff:3.500A) Processing sheet with id=AD, first strand: chain 'a' and resid 391 through 393 removed outlier: 6.764A pdb=" N VAL a 391 " --> pdb=" O VAL a 398 " (cutoff:3.500A) Processing sheet with id=BA, first strand: chain 'b' and resid 88 through 89 Processing sheet with id=BB, first strand: chain 'b' and resid 203 through 205 removed outlier: 4.546A pdb=" N VAL b 175 " --> pdb=" O VAL b 187 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N LYS u 190 " --> pdb=" O LEU b 184 " (cutoff:3.500A) Processing sheet with id=BC, first strand: chain 'b' and resid 191 through 192 removed outlier: 4.087A pdb=" N ASN b 191 " --> pdb=" O PHE b 318 " (cutoff:3.500A) removed outlier: 6.001A pdb=" N LYS b 274 " --> pdb=" O PRO b 313 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N GLY b 315 " --> pdb=" O LEU b 272 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N TRP b 214 " --> pdb=" O THR b 238 " (cutoff:3.500A) removed outlier: 5.064A pdb=" N THR b 238 " --> pdb=" O TRP b 214 " (cutoff:3.500A) removed outlier: 7.106A pdb=" N LEU b 216 " --> pdb=" O LEU b 236 " (cutoff:3.500A) removed outlier: 4.866A pdb=" N LEU b 236 " --> pdb=" O LEU b 216 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N LEU b 218 " --> pdb=" O HIS b 234 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N LEU b 236 " --> pdb=" O THR b 251 " (cutoff:3.500A) Processing sheet with id=CA, first strand: chain 'c' and resid 108 through 111 removed outlier: 3.902A pdb=" N LEU c 102 " --> pdb=" O LEU c 125 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N THR c 74 " --> pdb=" O HIS c 66 " (cutoff:3.500A) Processing sheet with id=CB, first strand: chain 'c' and resid 161 through 163 removed outlier: 4.724A pdb=" N LEU c 182 " --> pdb=" O LEU c 289 " (cutoff:3.500A) removed outlier: 7.135A pdb=" N LEU c 289 " --> pdb=" O LEU c 182 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N VAL c 290 " --> pdb=" O HIS c 281 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N HIS c 281 " --> pdb=" O VAL c 290 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N ARG c 292 " --> pdb=" O ALA c 279 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N ALA c 279 " --> pdb=" O ARG c 292 " (cutoff:3.500A) removed outlier: 7.197A pdb=" N GLN c 294 " --> pdb=" O VAL c 277 " (cutoff:3.500A) removed outlier: 5.208A pdb=" N VAL c 277 " --> pdb=" O GLN c 294 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N LEU c 296 " --> pdb=" O TYR c 275 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N TYR c 275 " --> pdb=" O LEU c 296 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N LEU c 298 " --> pdb=" O PHE c 273 " (cutoff:3.500A) Processing sheet with id=CC, first strand: chain 'c' and resid 214 through 219 Processing sheet with id=DA, first strand: chain 'd' and resid 172 through 174 removed outlier: 7.614A pdb=" N THR k 152 " --> pdb=" O PRO k 128 " (cutoff:3.500A) removed outlier: 7.299A pdb=" N GLU k 154 " --> pdb=" O ALA k 126 " (cutoff:3.500A) removed outlier: 5.002A pdb=" N ALA k 126 " --> pdb=" O GLU k 154 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N VAL k 156 " --> pdb=" O SER k 124 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N SER k 124 " --> pdb=" O VAL k 156 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N GLN k 158 " --> pdb=" O GLU k 122 " (cutoff:3.500A) Processing sheet with id=EA, first strand: chain 'e' and resid 40 through 42 Processing sheet with id=FA, first strand: chain 'f' and resid 48 through 51 Processing sheet with id=FB, first strand: chain 'f' and resid 73 through 74 removed outlier: 5.744A pdb=" N SER h 255 " --> pdb=" O TYR h 275 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N TYR h 275 " --> pdb=" O SER h 255 " (cutoff:3.500A) removed outlier: 5.312A pdb=" N LEU h 257 " --> pdb=" O GLY h 273 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N GLY h 273 " --> pdb=" O LEU h 257 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ARG h 259 " --> pdb=" O PHE h 271 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N TYR h 270 " --> pdb=" O PRO h 285 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N VAL h 272 " --> pdb=" O GLU h 283 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N GLU h 283 " --> pdb=" O VAL h 272 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N LEU h 274 " --> pdb=" O ILE h 281 " (cutoff:3.500A) Processing sheet with id=GA, first strand: chain 'g' and resid 84 through 88 removed outlier: 6.868A pdb=" N ARG g 74 " --> pdb=" O PHE g 31 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N PHE g 31 " --> pdb=" O ARG g 74 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N VAL g 76 " --> pdb=" O LEU g 29 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N LEU g 29 " --> pdb=" O VAL g 76 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N GLU g 78 " --> pdb=" O GLN g 27 " (cutoff:3.500A) Processing sheet with id=IA, first strand: chain 'i' and resid 180 through 187 removed outlier: 30.827A pdb=" N THR i 180 " --> pdb=" O THR i 213 " (cutoff:3.500A) removed outlier: 26.782A pdb=" N ARG i 215 " --> pdb=" O THR i 180 " (cutoff:3.500A) removed outlier: 23.216A pdb=" N ARG i 182 " --> pdb=" O ARG i 215 " (cutoff:3.500A) removed outlier: 18.368A pdb=" N HIS i 217 " --> pdb=" O ARG i 182 " (cutoff:3.500A) removed outlier: 13.111A pdb=" N SER i 184 " --> pdb=" O HIS i 217 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N ARG i 219 " --> pdb=" O SER i 184 " (cutoff:3.500A) removed outlier: 9.030A pdb=" N THR i 221 " --> pdb=" O VAL i 186 " (cutoff:3.500A) Processing sheet with id=IB, first strand: chain 'i' and resid 193 through 201 removed outlier: 5.719A pdb=" N VAL i 194 " --> pdb=" O ARG i 215 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N ARG i 215 " --> pdb=" O VAL i 194 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N GLN i 196 " --> pdb=" O THR i 213 " (cutoff:3.500A) Processing sheet with id=IC, first strand: chain 'i' and resid 259 through 265 removed outlier: 6.718A pdb=" N TRP i 259 " --> pdb=" O HIS i 251 " (cutoff:3.500A) removed outlier: 8.147A pdb=" N HIS i 251 " --> pdb=" O TRP i 259 " (cutoff:3.500A) removed outlier: 5.340A pdb=" N MET i 261 " --> pdb=" O GLU i 249 " (cutoff:3.500A) removed outlier: 5.627A pdb=" N GLU i 249 " --> pdb=" O MET i 261 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N TYR i 209 " --> pdb=" O CYS i 199 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N CYS i 199 " --> pdb=" O TYR i 209 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N GLN i 211 " --> pdb=" O VAL i 197 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N VAL i 197 " --> pdb=" O GLN i 211 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N THR i 213 " --> pdb=" O VAL i 195 " (cutoff:3.500A) Processing sheet with id=ID, first strand: chain 'i' and resid 259 through 265 removed outlier: 6.718A pdb=" N TRP i 259 " --> pdb=" O HIS i 251 " (cutoff:3.500A) removed outlier: 8.147A pdb=" N HIS i 251 " --> pdb=" O TRP i 259 " (cutoff:3.500A) removed outlier: 5.340A pdb=" N MET i 261 " --> pdb=" O GLU i 249 " (cutoff:3.500A) removed outlier: 5.627A pdb=" N GLU i 249 " --> pdb=" O MET i 261 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N THR i 180 " --> pdb=" O ALA i 223 " (cutoff:3.500A) removed outlier: 7.484A pdb=" N ARG i 182 " --> pdb=" O TYR i 225 " (cutoff:3.500A) Processing sheet with id=JA, first strand: chain 'j' and resid 175 through 177 removed outlier: 6.547A pdb=" N GLY j 211 " --> pdb=" O VAL j 231 " (cutoff:3.500A) removed outlier: 8.100A pdb=" N TYR j 213 " --> pdb=" O PHE j 233 " (cutoff:3.500A) removed outlier: 14.530A pdb=" N LYS j 235 " --> pdb=" O TYR j 213 " (cutoff:3.500A) removed outlier: 21.069A pdb=" N PHE j 215 " --> pdb=" O LYS j 235 " (cutoff:3.500A) removed outlier: 26.338A pdb=" N LEU j 237 " --> pdb=" O PHE j 215 " (cutoff:3.500A) Processing sheet with id=JB, first strand: chain 'j' and resid 175 through 177 removed outlier: 4.965A pdb=" N LEU j 238 " --> pdb=" O LYS j 203 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N LYS j 203 " --> pdb=" O LEU j 238 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N THR j 240 " --> pdb=" O GLU j 201 " (cutoff:3.500A) Processing sheet with id=JC, first strand: chain 'j' and resid 211 through 215 removed outlier: 6.779A pdb=" N ALA j 229 " --> pdb=" O TYR j 213 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N VAL j 231 " --> pdb=" O PHE j 215 " (cutoff:3.500A) Processing sheet with id=JD, first strand: chain 'j' and resid 168 through 172 removed outlier: 4.577A pdb=" N HIS j 251 " --> pdb=" O ARG j 162 " (cutoff:3.500A) Processing sheet with id=KA, first strand: chain 'k' and resid 80 through 81 Processing sheet with id=KB, first strand: chain 'k' and resid 145 through 149 removed outlier: 3.622A pdb=" N ALA k 148 " --> pdb=" O VAL k 134 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N VAL k 134 " --> pdb=" O ALA k 148 " (cutoff:3.500A) Processing sheet with id=LA, first strand: chain 'l' and resid 84 through 86 Processing sheet with id=LB, first strand: chain 'l' and resid 96 through 101 Processing sheet with id=PA, first strand: chain 'p' and resid 50 through 55 removed outlier: 3.659A pdb=" N SER p 50 " --> pdb=" O LYS p 14 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLN p 15 " --> pdb=" O LEU p 67 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N GLY x 51 " --> pdb=" O ARG p 77 " (cutoff:3.500A) Processing sheet with id=UA, first strand: chain 'u' and resid 77 through 83 removed outlier: 3.565A pdb=" N ASN u 95 " --> pdb=" O SER u 83 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N PHE u 102 " --> pdb=" O LEU u 132 " (cutoff:3.500A) Processing sheet with id=WA, first strand: chain 'w' and resid 200 through 210 removed outlier: 5.200A pdb=" N HIS w 201 " --> pdb=" O ASP w 229 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N ASP w 229 " --> pdb=" O HIS w 201 " (cutoff:3.500A) removed outlier: 5.663A pdb=" N PHE w 203 " --> pdb=" O ILE w 227 " (cutoff:3.500A) removed outlier: 7.440A pdb=" N ILE w 227 " --> pdb=" O PHE w 203 " (cutoff:3.500A) removed outlier: 5.635A pdb=" N LEU w 205 " --> pdb=" O TYR w 225 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N TYR w 225 " --> pdb=" O LEU w 205 " (cutoff:3.500A) removed outlier: 5.257A pdb=" N GLY w 207 " --> pdb=" O LEU w 223 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LEU w 223 " --> pdb=" O GLY w 207 " (cutoff:3.500A) Processing sheet with id=WB, first strand: chain 'w' and resid 112 through 116 Processing sheet with id=WC, first strand: chain 'w' and resid 112 through 116 removed outlier: 9.531A pdb=" N VAL w 350 " --> pdb=" O TYR w 288 " (cutoff:3.500A) removed outlier: 5.881A pdb=" N HIS w 290 " --> pdb=" O VAL w 350 " (cutoff:3.500A) removed outlier: 4.958A pdb=" N GLY w 289 " --> pdb=" O ILE w 237 " (cutoff:3.500A) removed outlier: 5.656A pdb=" N ILE w 237 " --> pdb=" O GLY w 289 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N THR w 291 " --> pdb=" O ILE w 235 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ASN w 233 " --> pdb=" O PHE w 293 " (cutoff:3.500A) Processing sheet with id=WD, first strand: chain 'w' and resid 393 through 394 Processing sheet with id=WE, first strand: chain 'w' and resid 396 through 400 removed outlier: 6.907A pdb=" N TYR w 396 " --> pdb=" O PHE w 407 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N PHE w 407 " --> pdb=" O TYR w 396 " (cutoff:3.500A) removed outlier: 7.353A pdb=" N THR w 398 " --> pdb=" O LYS w 405 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N LYS w 405 " --> pdb=" O THR w 398 " (cutoff:3.500A) 1342 hydrogen bonds defined for protein. 3750 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 9.34 Time building geometry restraints manager: 8.55 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.34: 10182 1.34 - 1.47: 7285 1.47 - 1.60: 15026 1.60 - 1.73: 31 1.73 - 1.86: 187 Bond restraints: 32711 Sorted by residual: bond pdb=" CA UNK z 34 " pdb=" C UNK z 34 " ideal model delta sigma weight residual 1.525 1.627 -0.102 2.10e-02 2.27e+03 2.34e+01 bond pdb=" CA UNK z 30 " pdb=" C UNK z 30 " ideal model delta sigma weight residual 1.525 1.626 -0.101 2.10e-02 2.27e+03 2.33e+01 bond pdb=" CA UNK v 153 " pdb=" C UNK v 153 " ideal model delta sigma weight residual 1.525 1.626 -0.101 2.10e-02 2.27e+03 2.30e+01 bond pdb=" CA UNK z 20 " pdb=" C UNK z 20 " ideal model delta sigma weight residual 1.525 1.622 -0.097 2.10e-02 2.27e+03 2.13e+01 bond pdb=" CA UNK v 149 " pdb=" C UNK v 149 " ideal model delta sigma weight residual 1.525 1.620 -0.095 2.10e-02 2.27e+03 2.04e+01 ... (remaining 32706 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.19: 42913 3.19 - 6.38: 1257 6.38 - 9.57: 77 9.57 - 12.76: 7 12.76 - 15.95: 1 Bond angle restraints: 44255 Sorted by residual: angle pdb=" C GLY h 284 " pdb=" N PRO h 285 " pdb=" CA PRO h 285 " ideal model delta sigma weight residual 120.31 130.89 -10.58 9.80e-01 1.04e+00 1.17e+02 angle pdb=" C GLY e 26 " pdb=" N PRO e 27 " pdb=" CA PRO e 27 " ideal model delta sigma weight residual 120.21 129.69 -9.48 9.60e-01 1.09e+00 9.75e+01 angle pdb=" C ALA j 208 " pdb=" N PRO j 209 " pdb=" CA PRO j 209 " ideal model delta sigma weight residual 119.99 130.01 -10.02 1.08e+00 8.57e-01 8.61e+01 angle pdb=" C ARG t 25 " pdb=" N PRO t 26 " pdb=" CA PRO t 26 " ideal model delta sigma weight residual 120.14 129.76 -9.62 1.06e+00 8.90e-01 8.23e+01 angle pdb=" C CYS p 21 " pdb=" N PRO p 22 " pdb=" CA PRO p 22 " ideal model delta sigma weight residual 119.47 129.48 -10.01 1.16e+00 7.43e-01 7.44e+01 ... (remaining 44250 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.71: 17953 16.71 - 33.42: 1581 33.42 - 50.12: 375 50.12 - 66.83: 109 66.83 - 83.54: 8 Dihedral angle restraints: 20026 sinusoidal: 8493 harmonic: 11533 Sorted by residual: dihedral pdb=" CA ASP w 357 " pdb=" C ASP w 357 " pdb=" N GLY w 358 " pdb=" CA GLY w 358 " ideal model delta harmonic sigma weight residual -180.00 -140.73 -39.27 0 5.00e+00 4.00e-02 6.17e+01 dihedral pdb=" CA GLU b 210 " pdb=" C GLU b 210 " pdb=" N GLY b 211 " pdb=" CA GLY b 211 " ideal model delta harmonic sigma weight residual 180.00 141.19 38.81 0 5.00e+00 4.00e-02 6.03e+01 dihedral pdb=" CA ASN n 65 " pdb=" C ASN n 65 " pdb=" N PHE n 66 " pdb=" CA PHE n 66 " ideal model delta harmonic sigma weight residual -180.00 -141.60 -38.40 0 5.00e+00 4.00e-02 5.90e+01 ... (remaining 20023 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.072: 4037 0.072 - 0.144: 614 0.144 - 0.216: 59 0.216 - 0.288: 3 0.288 - 0.360: 2 Chirality restraints: 4715 Sorted by residual: chirality pdb=" CA PHE b 78 " pdb=" N PHE b 78 " pdb=" C PHE b 78 " pdb=" CB PHE b 78 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.24e+00 chirality pdb=" CA ASN x 164 " pdb=" N ASN x 164 " pdb=" C ASN x 164 " pdb=" CB ASN x 164 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.62e+00 chirality pdb=" CA ILE g 113 " pdb=" N ILE g 113 " pdb=" C ILE g 113 " pdb=" CB ILE g 113 " both_signs ideal model delta sigma weight residual False 2.43 2.67 -0.24 2.00e-01 2.50e+01 1.43e+00 ... (remaining 4712 not shown) Planarity restraints: 5776 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO d 180 " -0.077 5.00e-02 4.00e+02 1.19e-01 2.26e+01 pdb=" N PRO d 181 " 0.206 5.00e-02 4.00e+02 pdb=" CA PRO d 181 " -0.071 5.00e-02 4.00e+02 pdb=" CD PRO d 181 " -0.057 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE b 357 " -0.045 5.00e-02 4.00e+02 6.86e-02 7.54e+00 pdb=" N PRO b 358 " 0.119 5.00e-02 4.00e+02 pdb=" CA PRO b 358 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO b 358 " -0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS h 63 " 0.042 5.00e-02 4.00e+02 6.30e-02 6.35e+00 pdb=" N PRO h 64 " -0.109 5.00e-02 4.00e+02 pdb=" CA PRO h 64 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO h 64 " 0.034 5.00e-02 4.00e+02 ... (remaining 5773 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.63: 277 2.63 - 3.20: 27105 3.20 - 3.77: 45116 3.77 - 4.33: 61639 4.33 - 4.90: 97302 Nonbonded interactions: 231439 Sorted by model distance: nonbonded pdb=" NH1 ARG a 173 " pdb=" O ASP a 348 " model vdw 2.067 3.120 nonbonded pdb=" NH1 ARG a 162 " pdb=" OH TYR a 383 " model vdw 2.115 3.120 nonbonded pdb=" N ASP o 48 " pdb=" OD1 ASP o 48 " model vdw 2.121 3.120 nonbonded pdb=" OG SER g 34 " pdb=" O CYS g 70 " model vdw 2.129 3.040 nonbonded pdb=" O GLU a 244 " pdb=" OG1 THR a 248 " model vdw 2.131 3.040 ... (remaining 231434 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: 0.670 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: 0.030 Extract box with map and model: 1.050 Check model and map are aligned: 0.190 Set scattering table: 0.250 Process input model: 65.750 Find NCS groups from input model: 0.560 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 71.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7758 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 : 0.009 0.102 32717 Z= 0.502 Angle : 1.285 15.947 44264 Z= 0.869 Chirality : 0.051 0.360 4715 Planarity : 0.005 0.119 5773 Dihedral : 13.808 83.541 12509 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 12.17 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.57 % Favored : 95.30 % Rotamer: Outliers : 6.03 % Allowed : 8.12 % Favored : 85.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.71 % Cis-general : 0.00 % Twisted Proline : 0.36 % Twisted General : 0.08 % 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: -2.62 (0.11), residues: 3785 helix: -2.58 (0.10), residues: 1348 sheet: -0.20 (0.20), residues: 514 loop : -1.45 (0.12), residues: 1923 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP t 101 HIS 0.008 0.001 HIS n 120 PHE 0.043 0.002 PHE l 153 TYR 0.030 0.003 TYR o 40 ARG 0.006 0.001 ARG b 99 Details of bonding type rmsd link_TRANS : bond 0.00455 ( 3) link_TRANS : angle 0.64601 ( 9) hydrogen bonds : bond 0.16837 ( 1304) hydrogen bonds : angle 8.51554 ( 3750) metal coordination : bond 0.01051 ( 3) covalent geometry : bond 0.00850 (32711) covalent geometry : angle 1.28528 (44255) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7570 Ramachandran restraints generated. 3785 Oldfield, 0 Emsley, 3785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7570 Ramachandran restraints generated. 3785 Oldfield, 0 Emsley, 3785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1305 residues out of total 3397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 205 poor density : 1100 time to evaluate : 3.673 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: a 35 VAL cc_start: 0.8645 (OUTLIER) cc_final: 0.8404 (p) REVERT: a 110 ARG cc_start: 0.8413 (mmt180) cc_final: 0.6343 (mtt90) REVERT: a 151 ASP cc_start: 0.7665 (OUTLIER) cc_final: 0.6823 (t0) REVERT: a 263 MET cc_start: 0.8628 (tpp) cc_final: 0.8255 (ttm) REVERT: a 368 GLU cc_start: 0.7978 (mt-10) cc_final: 0.7568 (mm-30) REVERT: b 52 ARG cc_start: 0.7878 (mtt180) cc_final: 0.7264 (ttt90) REVERT: b 63 GLN cc_start: 0.8358 (mt0) cc_final: 0.8048 (mt0) REVERT: b 229 ASP cc_start: 0.7612 (m-30) cc_final: 0.7054 (p0) REVERT: b 281 PHE cc_start: 0.2940 (OUTLIER) cc_final: 0.1637 (p90) REVERT: b 324 ASP cc_start: 0.7686 (OUTLIER) cc_final: 0.7157 (t0) REVERT: b 356 ARG cc_start: 0.8382 (ttt180) cc_final: 0.7850 (ttp-170) REVERT: c 90 MET cc_start: 0.8011 (OUTLIER) cc_final: 0.7043 (ptt) REVERT: c 159 TYR cc_start: 0.7044 (m-80) cc_final: 0.6830 (m-80) REVERT: c 277 VAL cc_start: 0.8777 (t) cc_final: 0.8566 (m) REVERT: d 83 ILE cc_start: 0.1698 (OUTLIER) cc_final: 0.1281 (mt) REVERT: d 119 LYS cc_start: 0.6251 (mttt) cc_final: 0.5203 (tptt) REVERT: d 126 GLN cc_start: 0.7587 (tt0) cc_final: 0.6710 (mm110) REVERT: d 154 SER cc_start: 0.5798 (t) cc_final: 0.5003 (m) REVERT: e 28 ARG cc_start: 0.8644 (ttt180) cc_final: 0.7415 (mpt180) REVERT: e 67 LYS cc_start: 0.7129 (OUTLIER) cc_final: 0.6593 (tmmt) REVERT: e 69 LYS cc_start: 0.7804 (mmtp) cc_final: 0.6506 (pttm) REVERT: e 71 TYR cc_start: 0.7914 (m-80) cc_final: 0.6177 (t80) REVERT: e 85 THR cc_start: 0.8826 (m) cc_final: 0.8260 (p) REVERT: e 127 GLN cc_start: 0.8309 (OUTLIER) cc_final: 0.7696 (mt0) REVERT: e 131 LYS cc_start: 0.8505 (tptt) cc_final: 0.7674 (mttt) REVERT: f 56 ARG cc_start: 0.7962 (mtt180) cc_final: 0.7178 (tpm170) REVERT: f 128 GLN cc_start: 0.8707 (mm-40) cc_final: 0.5701 (pm20) REVERT: f 132 ARG cc_start: 0.8784 (mmt180) cc_final: 0.7172 (mmt90) REVERT: f 134 ARG cc_start: 0.8473 (ttt-90) cc_final: 0.7669 (mmt180) REVERT: f 140 LYS cc_start: 0.8717 (tttt) cc_final: 0.8417 (mptt) REVERT: g 12 THR cc_start: 0.8809 (m) cc_final: 0.8592 (m) REVERT: g 14 VAL cc_start: 0.8673 (OUTLIER) cc_final: 0.8467 (t) REVERT: g 70 CYS cc_start: 0.8304 (OUTLIER) cc_final: 0.7997 (p) REVERT: g 112 VAL cc_start: 0.8437 (OUTLIER) cc_final: 0.8087 (p) REVERT: g 117 LYS cc_start: 0.8893 (pttt) cc_final: 0.8065 (mmtm) REVERT: g 144 ARG cc_start: 0.7222 (mmt180) cc_final: 0.6720 (mtt180) REVERT: h 36 ARG cc_start: 0.7295 (mtt180) cc_final: 0.5956 (mtm180) REVERT: h 59 ARG cc_start: 0.6579 (mtt180) cc_final: 0.6361 (mtt-85) REVERT: h 78 ARG cc_start: 0.8811 (OUTLIER) cc_final: 0.8494 (ptp90) REVERT: h 138 THR cc_start: 0.9243 (m) cc_final: 0.8719 (p) REVERT: h 163 GLU cc_start: 0.7859 (tp30) cc_final: 0.7531 (tt0) REVERT: h 234 ILE cc_start: 0.8099 (OUTLIER) cc_final: 0.7523 (tp) REVERT: h 235 THR cc_start: 0.8322 (p) cc_final: 0.7923 (t) REVERT: i 142 LYS cc_start: 0.7580 (tttt) cc_final: 0.7244 (tmtt) REVERT: i 143 ASP cc_start: 0.8390 (t0) cc_final: 0.8124 (m-30) REVERT: i 172 MET cc_start: 0.7345 (ptp) cc_final: 0.6657 (mmt) REVERT: i 175 ASP cc_start: 0.7531 (m-30) cc_final: 0.6422 (t70) REVERT: i 207 ASN cc_start: 0.6499 (m-40) cc_final: 0.5800 (m110) REVERT: i 208 ILE cc_start: 0.6524 (OUTLIER) cc_final: 0.6263 (mt) REVERT: i 209 TYR cc_start: 0.6448 (m-80) cc_final: 0.6218 (m-80) REVERT: i 218 THR cc_start: 0.7266 (m) cc_final: 0.6604 (p) REVERT: i 227 ARG cc_start: 0.7411 (ptm160) cc_final: 0.5836 (tpp-160) REVERT: i 240 ARG cc_start: 0.7167 (tpt170) cc_final: 0.6557 (ptt90) REVERT: i 245 TYR cc_start: 0.6485 (t80) cc_final: 0.6108 (t80) REVERT: i 278 LYS cc_start: 0.7880 (pttt) cc_final: 0.6529 (tptt) REVERT: i 291 GLU cc_start: 0.6770 (tt0) cc_final: 0.6083 (mm-30) REVERT: j 120 LEU cc_start: 0.7369 (mt) cc_final: 0.6511 (mm) REVERT: j 124 TRP cc_start: 0.4855 (m-10) cc_final: 0.4464 (t-100) REVERT: j 209 PRO cc_start: 0.4542 (Cg_endo) cc_final: 0.4021 (Cg_exo) REVERT: j 264 LEU cc_start: 0.5700 (OUTLIER) cc_final: 0.5012 (mp) REVERT: j 274 ARG cc_start: 0.6677 (OUTLIER) cc_final: 0.6192 (tmm-80) REVERT: k 58 ARG cc_start: 0.7982 (ttt180) cc_final: 0.7076 (tpm170) REVERT: k 108 GLN cc_start: 0.7680 (tt0) cc_final: 0.7357 (mm110) REVERT: k 151 THR cc_start: 0.6928 (OUTLIER) cc_final: 0.6633 (p) REVERT: k 182 VAL cc_start: 0.5953 (t) cc_final: 0.5686 (m) REVERT: k 193 ASP cc_start: 0.5551 (t0) cc_final: 0.4914 (m-30) REVERT: l 93 ASN cc_start: 0.9060 (OUTLIER) cc_final: 0.7947 (m-40) REVERT: m 57 GLN cc_start: 0.4523 (pt0) cc_final: 0.4147 (mp10) REVERT: m 68 GLN cc_start: 0.8095 (mm-40) cc_final: 0.7528 (mp10) REVERT: m 77 GLU cc_start: 0.7982 (pt0) cc_final: 0.7302 (pt0) REVERT: m 135 VAL cc_start: 0.8515 (OUTLIER) cc_final: 0.8292 (p) REVERT: m 142 ASP cc_start: 0.7284 (m-30) cc_final: 0.6881 (t70) REVERT: n 46 ARG cc_start: 0.8293 (OUTLIER) cc_final: 0.5606 (mtp180) REVERT: n 66 PHE cc_start: 0.8842 (OUTLIER) cc_final: 0.8630 (m-80) REVERT: n 75 LYS cc_start: 0.7751 (mmtt) cc_final: 0.7029 (tmtt) REVERT: n 95 LYS cc_start: 0.9158 (tttt) cc_final: 0.8921 (ttpp) REVERT: n 96 ARG cc_start: 0.8612 (mtp180) cc_final: 0.8040 (ttt180) REVERT: n 101 ARG cc_start: 0.8629 (mtp-110) cc_final: 0.7700 (mmp-170) REVERT: n 128 ARG cc_start: 0.7654 (mmt90) cc_final: 0.4799 (mtt180) REVERT: o 61 LYS cc_start: 0.8437 (mmtt) cc_final: 0.7814 (pttm) REVERT: p 18 VAL cc_start: 0.7968 (t) cc_final: 0.7650 (p) REVERT: p 84 GLN cc_start: 0.4880 (pt0) cc_final: 0.4649 (tt0) REVERT: t 9 ARG cc_start: 0.8151 (OUTLIER) cc_final: 0.5468 (ptt180) REVERT: t 11 ARG cc_start: 0.8270 (mtt180) cc_final: 0.7355 (tpt170) REVERT: t 44 GLU cc_start: 0.9076 (tt0) cc_final: 0.8619 (tp30) REVERT: t 60 ARG cc_start: 0.8357 (mmt90) cc_final: 0.7534 (mmp-170) REVERT: t 96 LEU cc_start: 0.8663 (mt) cc_final: 0.8362 (mt) REVERT: u 43 TYR cc_start: 0.6710 (m-80) cc_final: 0.6450 (m-80) REVERT: u 59 TRP cc_start: 0.7020 (m100) cc_final: 0.4216 (t60) REVERT: u 61 LEU cc_start: 0.6091 (mt) cc_final: 0.5849 (mp) REVERT: u 77 THR cc_start: 0.9061 (m) cc_final: 0.8617 (p) REVERT: u 121 LYS cc_start: 0.7848 (mttt) cc_final: 0.7533 (mtmm) REVERT: u 125 ARG cc_start: 0.7421 (ptp-170) cc_final: 0.6888 (mtm-85) REVERT: u 137 GLU cc_start: 0.7157 (OUTLIER) cc_final: 0.6912 (mt-10) REVERT: u 186 ARG cc_start: 0.5941 (mtt-85) cc_final: 0.5190 (ttp-170) REVERT: v 36 GLU cc_start: 0.7625 (mt-10) cc_final: 0.7392 (tm-30) REVERT: v 59 LYS cc_start: 0.8128 (tttt) cc_final: 0.7662 (mmtt) REVERT: w 52 THR cc_start: 0.9107 (m) cc_final: 0.8705 (p) REVERT: w 56 LYS cc_start: 0.9107 (mttt) cc_final: 0.8879 (mttt) REVERT: w 59 ARG cc_start: 0.8633 (OUTLIER) cc_final: 0.8250 (tpt170) REVERT: w 86 MET cc_start: 0.8308 (mmp) cc_final: 0.6696 (mtt) REVERT: w 141 CYS cc_start: 0.7908 (m) cc_final: 0.7379 (p) REVERT: w 142 ASP cc_start: 0.6690 (m-30) cc_final: 0.6403 (m-30) REVERT: w 166 ILE cc_start: 0.8061 (OUTLIER) cc_final: 0.7719 (tp) REVERT: w 271 GLN cc_start: 0.8263 (OUTLIER) cc_final: 0.7353 (tm-30) REVERT: x 36 ARG cc_start: 0.6266 (OUTLIER) cc_final: 0.4256 (pmt-80) REVERT: x 56 THR cc_start: 0.7341 (OUTLIER) cc_final: 0.6572 (t) REVERT: x 114 LYS cc_start: 0.9056 (mttt) cc_final: 0.8823 (mttp) REVERT: x 121 MET cc_start: 0.9324 (OUTLIER) cc_final: 0.9074 (mtp) REVERT: x 140 VAL cc_start: 0.2326 (t) cc_final: 0.2089 (t) REVERT: x 152 THR cc_start: 0.9339 (OUTLIER) cc_final: 0.9066 (p) REVERT: x 168 ARG cc_start: 0.8143 (ttm170) cc_final: 0.6883 (mtt180) outliers start: 205 outliers final: 49 residues processed: 1252 average time/residue: 0.5095 time to fit residues: 935.2729 Evaluate side-chains 629 residues out of total 3397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 550 time to evaluate : 3.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 35 VAL Chi-restraints excluded: chain a residue 151 ASP Chi-restraints excluded: chain a residue 175 THR Chi-restraints excluded: chain a residue 225 SER Chi-restraints excluded: chain b residue 281 PHE Chi-restraints excluded: chain b residue 324 ASP Chi-restraints excluded: chain c residue 56 THR Chi-restraints excluded: chain c residue 90 MET Chi-restraints excluded: chain c residue 106 ASP Chi-restraints excluded: chain c residue 140 TRP Chi-restraints excluded: chain c residue 222 VAL Chi-restraints excluded: chain c residue 260 VAL Chi-restraints excluded: chain c residue 272 CYS Chi-restraints excluded: chain c residue 280 VAL Chi-restraints excluded: chain c residue 285 THR Chi-restraints excluded: chain d residue 83 ILE Chi-restraints excluded: chain e residue 67 LYS Chi-restraints excluded: chain e residue 127 GLN Chi-restraints excluded: chain f residue 52 THR Chi-restraints excluded: chain f residue 59 VAL Chi-restraints excluded: chain f residue 109 ILE Chi-restraints excluded: chain g residue 6 THR Chi-restraints excluded: chain g residue 14 VAL Chi-restraints excluded: chain g residue 33 LEU Chi-restraints excluded: chain g residue 39 SER Chi-restraints excluded: chain g residue 61 VAL Chi-restraints excluded: chain g residue 70 CYS Chi-restraints excluded: chain g residue 94 VAL Chi-restraints excluded: chain g residue 108 SER Chi-restraints excluded: chain g residue 112 VAL Chi-restraints excluded: chain g residue 114 ARG Chi-restraints excluded: chain g residue 126 ILE Chi-restraints excluded: chain g residue 138 THR Chi-restraints excluded: chain h residue 33 LYS Chi-restraints excluded: chain h residue 51 LEU Chi-restraints excluded: chain h residue 78 ARG Chi-restraints excluded: chain h residue 211 THR Chi-restraints excluded: chain h residue 231 MET Chi-restraints excluded: chain h residue 233 THR Chi-restraints excluded: chain h residue 234 ILE Chi-restraints excluded: chain i residue 151 CYS Chi-restraints excluded: chain i residue 186 VAL Chi-restraints excluded: chain i residue 208 ILE Chi-restraints excluded: chain i residue 242 VAL Chi-restraints excluded: chain j residue 55 ARG Chi-restraints excluded: chain j residue 264 LEU Chi-restraints excluded: chain j residue 274 ARG Chi-restraints excluded: chain j residue 276 LEU Chi-restraints excluded: chain j residue 277 LEU Chi-restraints excluded: chain k residue 151 THR Chi-restraints excluded: chain l residue 93 ASN Chi-restraints excluded: chain l residue 137 VAL Chi-restraints excluded: chain m residue 90 ILE Chi-restraints excluded: chain m residue 135 VAL Chi-restraints excluded: chain n residue 46 ARG Chi-restraints excluded: chain n residue 56 VAL Chi-restraints excluded: chain n residue 66 PHE Chi-restraints excluded: chain n residue 92 ILE Chi-restraints excluded: chain n residue 105 ASP Chi-restraints excluded: chain t residue 9 ARG Chi-restraints excluded: chain t residue 45 ASN Chi-restraints excluded: chain u residue 79 SER Chi-restraints excluded: chain u residue 137 GLU Chi-restraints excluded: chain v residue 64 HIS Chi-restraints excluded: chain w residue 59 ARG Chi-restraints excluded: chain w residue 166 ILE Chi-restraints excluded: chain w residue 271 GLN Chi-restraints excluded: chain w residue 274 ASN Chi-restraints excluded: chain w residue 287 CYS Chi-restraints excluded: chain w residue 395 LEU Chi-restraints excluded: chain x residue 36 ARG Chi-restraints excluded: chain x residue 38 VAL Chi-restraints excluded: chain x residue 54 THR Chi-restraints excluded: chain x residue 56 THR Chi-restraints excluded: chain x residue 70 CYS Chi-restraints excluded: chain x residue 111 GLU Chi-restraints excluded: chain x residue 119 VAL Chi-restraints excluded: chain x residue 121 MET Chi-restraints excluded: chain x residue 152 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 371 random chunks: chunk 313 optimal weight: 9.9990 chunk 281 optimal weight: 6.9990 chunk 156 optimal weight: 9.9990 chunk 96 optimal weight: 6.9990 chunk 189 optimal weight: 10.0000 chunk 150 optimal weight: 6.9990 chunk 290 optimal weight: 2.9990 chunk 112 optimal weight: 9.9990 chunk 176 optimal weight: 20.0000 chunk 216 optimal weight: 2.9990 chunk 336 optimal weight: 5.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 108 HIS a 150 GLN a 156 ASN a 207 ASN a 223 HIS a 274 ASN a 289 HIS a 360 ASN a 420 HIS b 116 ASN b 163 HIS b 220 ASN b 224 HIS b 266 HIS ** b 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 308 GLN c 274 GLN c 305 HIS ** d 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 158 HIS e 50 GLN f 44 ASN g 81 ASN g 107 GLN g 131 HIS h 118 ASN h 204 GLN i 107 GLN i 157 HIS ** i 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 87 HIS ** j 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 116 HIS k 136 GLN k 177 ASN l 93 ASN l 141 ASN l 156 GLN m 119 HIS n 69 HIS n 100 ASN n 124 HIS p 19 GLN p 57 HIS p 72 HIS p 93 HIS q 129 HIS t 34 ASN t 45 ASN t 85 HIS ** u 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** u 145 ASN v 79 GLN v 138 GLN w 101 ASN w 148 HIS w 173 GLN ** w 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 321 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** w 385 ASN w 391 GLN ** w 421 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** x 65 ASN x 164 ASN x 184 ASN Total number of N/Q/H flips: 57 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.138341 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.117096 restraints weight = 82736.476| |-----------------------------------------------------------------------------| r_work (start): 0.3682 rms_B_bonded: 3.41 r_work: 0.3406 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.3406 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7880 moved from start: 0.3798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 32717 Z= 0.208 Angle : 0.751 12.242 44264 Z= 0.388 Chirality : 0.045 0.237 4715 Planarity : 0.007 0.105 5773 Dihedral : 8.436 81.466 4584 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 10.57 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.91 % Favored : 96.96 % Rotamer: Outliers : 6.15 % Allowed : 16.04 % Favored : 77.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.73 (0.13), residues: 3785 helix: -0.28 (0.13), residues: 1379 sheet: 0.17 (0.20), residues: 545 loop : -0.74 (0.13), residues: 1861 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP t 101 HIS 0.012 0.002 HIS x 131 PHE 0.027 0.002 PHE j 215 TYR 0.035 0.002 TYR i 245 ARG 0.014 0.001 ARG b 121 Details of bonding type rmsd link_TRANS : bond 0.00117 ( 3) link_TRANS : angle 0.57151 ( 9) hydrogen bonds : bond 0.04895 ( 1304) hydrogen bonds : angle 5.69063 ( 3750) metal coordination : bond 0.00212 ( 3) covalent geometry : bond 0.00480 (32711) covalent geometry : angle 0.75118 (44255) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7570 Ramachandran restraints generated. 3785 Oldfield, 0 Emsley, 3785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7570 Ramachandran restraints generated. 3785 Oldfield, 0 Emsley, 3785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 836 residues out of total 3397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 209 poor density : 627 time to evaluate : 3.487 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: a 110 ARG cc_start: 0.8317 (mmt180) cc_final: 0.6395 (mtm180) REVERT: a 263 MET cc_start: 0.8678 (tpp) cc_final: 0.7939 (ttm) REVERT: b 52 ARG cc_start: 0.8110 (mtt180) cc_final: 0.7709 (ptm160) REVERT: b 154 TYR cc_start: 0.8302 (t80) cc_final: 0.7896 (t80) REVERT: b 184 LEU cc_start: 0.7738 (OUTLIER) cc_final: 0.7472 (pp) REVERT: b 229 ASP cc_start: 0.7566 (m-30) cc_final: 0.7168 (p0) REVERT: b 254 TYR cc_start: 0.6940 (t80) cc_final: 0.6715 (t80) REVERT: b 281 PHE cc_start: 0.2544 (OUTLIER) cc_final: 0.1390 (p90) REVERT: b 324 ASP cc_start: 0.7362 (OUTLIER) cc_final: 0.6682 (t70) REVERT: b 356 ARG cc_start: 0.8223 (ttt180) cc_final: 0.7906 (ttp-170) REVERT: c 90 MET cc_start: 0.7774 (OUTLIER) cc_final: 0.7069 (ptt) REVERT: c 131 ASP cc_start: 0.7248 (t0) cc_final: 0.6790 (p0) REVERT: d 119 LYS cc_start: 0.6458 (mttt) cc_final: 0.5583 (tptt) REVERT: d 126 GLN cc_start: 0.7718 (tt0) cc_final: 0.6807 (mm110) REVERT: d 140 LEU cc_start: 0.7417 (mt) cc_final: 0.6873 (tp) REVERT: d 148 GLN cc_start: 0.7953 (tp-100) cc_final: 0.6857 (pt0) REVERT: e 28 ARG cc_start: 0.8694 (ttt180) cc_final: 0.7419 (mpt180) REVERT: e 85 THR cc_start: 0.8659 (m) cc_final: 0.8207 (p) REVERT: e 115 TYR cc_start: 0.7836 (m-80) cc_final: 0.7530 (m-80) REVERT: e 131 LYS cc_start: 0.8247 (tptt) cc_final: 0.7488 (mttt) REVERT: f 56 ARG cc_start: 0.8128 (mtt180) cc_final: 0.6905 (tpm170) REVERT: f 128 GLN cc_start: 0.8353 (mm-40) cc_final: 0.5737 (pm20) REVERT: f 132 ARG cc_start: 0.8929 (mmt180) cc_final: 0.7012 (mtt180) REVERT: f 134 ARG cc_start: 0.8278 (ttt-90) cc_final: 0.7658 (mmt180) REVERT: f 140 LYS cc_start: 0.8595 (tttt) cc_final: 0.8366 (mptt) REVERT: g 12 THR cc_start: 0.8448 (m) cc_final: 0.8211 (m) REVERT: g 117 LYS cc_start: 0.8772 (pttt) cc_final: 0.8038 (mmtt) REVERT: g 122 ASP cc_start: 0.7545 (m-30) cc_final: 0.7276 (m-30) REVERT: h 36 ARG cc_start: 0.6957 (mtt180) cc_final: 0.6113 (mtm180) REVERT: h 138 THR cc_start: 0.9341 (m) cc_final: 0.8552 (p) REVERT: h 235 THR cc_start: 0.8387 (p) cc_final: 0.8032 (t) REVERT: i 118 SER cc_start: 0.5055 (OUTLIER) cc_final: 0.4362 (t) REVERT: i 139 GLU cc_start: 0.8335 (mm-30) cc_final: 0.7371 (pt0) REVERT: i 140 LYS cc_start: 0.7944 (ttpt) cc_final: 0.7098 (ptmm) REVERT: i 143 ASP cc_start: 0.8446 (t0) cc_final: 0.8108 (m-30) REVERT: i 145 PHE cc_start: 0.7357 (OUTLIER) cc_final: 0.6743 (t80) REVERT: i 172 MET cc_start: 0.7606 (ptp) cc_final: 0.6557 (mmt) REVERT: i 209 TYR cc_start: 0.6546 (m-80) cc_final: 0.6339 (m-80) REVERT: i 240 ARG cc_start: 0.7123 (tpt170) cc_final: 0.6477 (ptt90) REVERT: i 245 TYR cc_start: 0.6093 (t80) cc_final: 0.5746 (t80) REVERT: i 291 GLU cc_start: 0.5854 (tt0) cc_final: 0.5577 (mm-30) REVERT: j 124 TRP cc_start: 0.5292 (m-10) cc_final: 0.4709 (t-100) REVERT: j 157 LEU cc_start: 0.5652 (OUTLIER) cc_final: 0.5435 (mt) REVERT: j 209 PRO cc_start: 0.4702 (Cg_endo) cc_final: 0.4444 (Cg_exo) REVERT: j 240 THR cc_start: 0.7960 (OUTLIER) cc_final: 0.7750 (p) REVERT: k 58 ARG cc_start: 0.7835 (ttt180) cc_final: 0.6816 (tpm170) REVERT: k 98 TYR cc_start: 0.5787 (OUTLIER) cc_final: 0.5338 (m-80) REVERT: k 108 GLN cc_start: 0.7754 (tt0) cc_final: 0.7391 (tp-100) REVERT: k 130 LYS cc_start: 0.6824 (mptt) cc_final: 0.5523 (mtpt) REVERT: k 151 THR cc_start: 0.7206 (OUTLIER) cc_final: 0.6186 (p) REVERT: k 185 SER cc_start: 0.8070 (m) cc_final: 0.7809 (p) REVERT: k 193 ASP cc_start: 0.5531 (t0) cc_final: 0.5012 (m-30) REVERT: m 57 GLN cc_start: 0.5202 (pt0) cc_final: 0.4619 (mp10) REVERT: m 68 GLN cc_start: 0.8248 (mm-40) cc_final: 0.7440 (mp10) REVERT: m 125 ARG cc_start: 0.7782 (ptm160) cc_final: 0.7259 (ttm110) REVERT: m 137 ASP cc_start: 0.5973 (t0) cc_final: 0.5149 (m-30) REVERT: m 140 LYS cc_start: 0.6638 (mmtt) cc_final: 0.6327 (mttp) REVERT: m 142 ASP cc_start: 0.7285 (m-30) cc_final: 0.6870 (t70) REVERT: m 143 GLU cc_start: 0.7676 (pt0) cc_final: 0.7434 (pt0) REVERT: n 46 ARG cc_start: 0.8338 (OUTLIER) cc_final: 0.4543 (ttt-90) REVERT: n 75 LYS cc_start: 0.7558 (mmtt) cc_final: 0.7030 (tmtt) REVERT: n 92 ILE cc_start: 0.9252 (OUTLIER) cc_final: 0.8756 (mt) REVERT: n 96 ARG cc_start: 0.8839 (mtp180) cc_final: 0.8249 (ttt180) REVERT: n 101 ARG cc_start: 0.8532 (OUTLIER) cc_final: 0.7685 (mmm160) REVERT: n 128 ARG cc_start: 0.7346 (mmt90) cc_final: 0.4507 (mtt180) REVERT: o 61 LYS cc_start: 0.8249 (mmtt) cc_final: 0.7639 (pttt) REVERT: p 52 ILE cc_start: 0.7196 (mt) cc_final: 0.6959 (mm) REVERT: t 9 ARG cc_start: 0.8043 (OUTLIER) cc_final: 0.5605 (ptt180) REVERT: t 11 ARG cc_start: 0.7500 (mtt180) cc_final: 0.7260 (mmp-170) REVERT: t 33 GLN cc_start: 0.8543 (mm-40) cc_final: 0.8258 (mt0) REVERT: t 37 ARG cc_start: 0.7651 (ttp80) cc_final: 0.7420 (ptt90) REVERT: t 39 LEU cc_start: 0.8827 (mt) cc_final: 0.8546 (mt) REVERT: t 60 ARG cc_start: 0.8119 (mmt90) cc_final: 0.7505 (mmp-170) REVERT: t 98 THR cc_start: 0.7866 (OUTLIER) cc_final: 0.7627 (m) REVERT: u 43 TYR cc_start: 0.6750 (m-80) cc_final: 0.6100 (m-80) REVERT: u 59 TRP cc_start: 0.7239 (m100) cc_final: 0.4487 (t60) REVERT: u 118 LEU cc_start: 0.8477 (mt) cc_final: 0.8054 (mt) REVERT: u 159 GLU cc_start: 0.8089 (pp20) cc_final: 0.7524 (pp20) REVERT: u 186 ARG cc_start: 0.5809 (mtt-85) cc_final: 0.5178 (ttp-170) REVERT: v 59 LYS cc_start: 0.8601 (tttt) cc_final: 0.8268 (tppt) REVERT: v 82 LEU cc_start: 0.8607 (tt) cc_final: 0.7938 (mt) REVERT: w 52 THR cc_start: 0.9168 (OUTLIER) cc_final: 0.8775 (p) REVERT: w 59 ARG cc_start: 0.8562 (OUTLIER) cc_final: 0.8245 (tpt170) REVERT: w 86 MET cc_start: 0.7864 (mmp) cc_final: 0.6522 (mtt) REVERT: w 141 CYS cc_start: 0.7744 (m) cc_final: 0.7368 (p) REVERT: w 163 ARG cc_start: 0.6404 (mmp80) cc_final: 0.5864 (tmm160) REVERT: w 216 ARG cc_start: 0.8971 (OUTLIER) cc_final: 0.7594 (mtt-85) REVERT: w 271 GLN cc_start: 0.8215 (OUTLIER) cc_final: 0.6405 (tt0) REVERT: x 38 VAL cc_start: 0.5735 (OUTLIER) cc_final: 0.5441 (p) REVERT: x 111 GLU cc_start: 0.7930 (OUTLIER) cc_final: 0.7649 (mm-30) REVERT: x 170 ASN cc_start: 0.8739 (OUTLIER) cc_final: 0.8439 (p0) outliers start: 209 outliers final: 117 residues processed: 772 average time/residue: 0.4731 time to fit residues: 560.1149 Evaluate side-chains 644 residues out of total 3397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 139 poor density : 505 time to evaluate : 3.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 117 VAL Chi-restraints excluded: chain a residue 128 LEU Chi-restraints excluded: chain a residue 167 THR Chi-restraints excluded: chain a residue 180 ILE Chi-restraints excluded: chain a residue 203 CYS Chi-restraints excluded: chain a residue 225 SER Chi-restraints excluded: chain a residue 248 THR Chi-restraints excluded: chain a residue 268 CYS Chi-restraints excluded: chain a residue 277 THR Chi-restraints excluded: chain a residue 396 VAL Chi-restraints excluded: chain b residue 32 LEU Chi-restraints excluded: chain b residue 40 ILE Chi-restraints excluded: chain b residue 43 SER Chi-restraints excluded: chain b residue 184 LEU Chi-restraints excluded: chain b residue 281 PHE Chi-restraints excluded: chain b residue 324 ASP Chi-restraints excluded: chain c residue 43 ASP Chi-restraints excluded: chain c residue 56 THR Chi-restraints excluded: chain c residue 83 SER Chi-restraints excluded: chain c residue 90 MET Chi-restraints excluded: chain c residue 140 TRP Chi-restraints excluded: chain c residue 177 CYS Chi-restraints excluded: chain c residue 222 VAL Chi-restraints excluded: chain c residue 236 PHE Chi-restraints excluded: chain c residue 256 ASP Chi-restraints excluded: chain c residue 260 VAL Chi-restraints excluded: chain c residue 280 VAL Chi-restraints excluded: chain c residue 285 THR Chi-restraints excluded: chain d residue 85 ILE Chi-restraints excluded: chain d residue 89 ILE Chi-restraints excluded: chain d residue 104 VAL Chi-restraints excluded: chain d residue 111 SER Chi-restraints excluded: chain d residue 150 LEU Chi-restraints excluded: chain d residue 173 ARG Chi-restraints excluded: chain e residue 19 SER Chi-restraints excluded: chain e residue 39 THR Chi-restraints excluded: chain e residue 49 VAL Chi-restraints excluded: chain e residue 120 THR Chi-restraints excluded: chain e residue 127 GLN Chi-restraints excluded: chain f residue 59 VAL Chi-restraints excluded: chain f residue 108 MET Chi-restraints excluded: chain f residue 114 LYS Chi-restraints excluded: chain g residue 6 THR Chi-restraints excluded: chain g residue 14 VAL Chi-restraints excluded: chain g residue 33 LEU Chi-restraints excluded: chain g residue 39 SER Chi-restraints excluded: chain g residue 61 VAL Chi-restraints excluded: chain g residue 62 VAL Chi-restraints excluded: chain g residue 94 VAL Chi-restraints excluded: chain g residue 108 SER Chi-restraints excluded: chain g residue 112 VAL Chi-restraints excluded: chain g residue 113 ILE Chi-restraints excluded: chain g residue 114 ARG Chi-restraints excluded: chain g residue 121 THR Chi-restraints excluded: chain g residue 126 ILE Chi-restraints excluded: chain g residue 138 THR Chi-restraints excluded: chain h residue 33 LYS Chi-restraints excluded: chain h residue 77 HIS Chi-restraints excluded: chain h residue 151 GLU Chi-restraints excluded: chain h residue 154 THR Chi-restraints excluded: chain h residue 158 ASP Chi-restraints excluded: chain h residue 215 ILE Chi-restraints excluded: chain h residue 265 THR Chi-restraints excluded: chain h residue 307 PHE Chi-restraints excluded: chain i residue 88 TYR Chi-restraints excluded: chain i residue 112 LEU Chi-restraints excluded: chain i residue 116 VAL Chi-restraints excluded: chain i residue 118 SER Chi-restraints excluded: chain i residue 134 ILE Chi-restraints excluded: chain i residue 145 PHE Chi-restraints excluded: chain i residue 151 CYS Chi-restraints excluded: chain i residue 177 ARG Chi-restraints excluded: chain i residue 186 VAL Chi-restraints excluded: chain i residue 238 VAL Chi-restraints excluded: chain i residue 246 VAL Chi-restraints excluded: chain i residue 253 VAL Chi-restraints excluded: chain j residue 60 THR Chi-restraints excluded: chain j residue 84 TYR Chi-restraints excluded: chain j residue 139 GLU Chi-restraints excluded: chain j residue 157 LEU Chi-restraints excluded: chain j residue 240 THR Chi-restraints excluded: chain j residue 253 VAL Chi-restraints excluded: chain j residue 276 LEU Chi-restraints excluded: chain k residue 98 TYR Chi-restraints excluded: chain k residue 151 THR Chi-restraints excluded: chain k residue 174 ILE Chi-restraints excluded: chain l residue 39 VAL Chi-restraints excluded: chain l residue 42 VAL Chi-restraints excluded: chain l residue 65 HIS Chi-restraints excluded: chain l residue 99 ASP Chi-restraints excluded: chain l residue 135 THR Chi-restraints excluded: chain l residue 137 VAL Chi-restraints excluded: chain l residue 156 GLN Chi-restraints excluded: chain m residue 90 ILE Chi-restraints excluded: chain m residue 127 VAL Chi-restraints excluded: chain n residue 37 THR Chi-restraints excluded: chain n residue 44 VAL Chi-restraints excluded: chain n residue 46 ARG Chi-restraints excluded: chain n residue 56 VAL Chi-restraints excluded: chain n residue 91 CYS Chi-restraints excluded: chain n residue 92 ILE Chi-restraints excluded: chain n residue 101 ARG Chi-restraints excluded: chain o residue 78 VAL Chi-restraints excluded: chain o residue 99 LEU Chi-restraints excluded: chain p residue 50 SER Chi-restraints excluded: chain t residue 9 ARG Chi-restraints excluded: chain t residue 12 ILE Chi-restraints excluded: chain t residue 32 LYS Chi-restraints excluded: chain t residue 49 LEU Chi-restraints excluded: chain t residue 55 THR Chi-restraints excluded: chain t residue 98 THR Chi-restraints excluded: chain t residue 101 TRP Chi-restraints excluded: chain u residue 104 LEU Chi-restraints excluded: chain u residue 110 ILE Chi-restraints excluded: chain u residue 114 VAL Chi-restraints excluded: chain u residue 153 LEU Chi-restraints excluded: chain w residue 52 THR Chi-restraints excluded: chain w residue 59 ARG Chi-restraints excluded: chain w residue 63 VAL Chi-restraints excluded: chain w residue 97 THR Chi-restraints excluded: chain w residue 166 ILE Chi-restraints excluded: chain w residue 188 VAL Chi-restraints excluded: chain w residue 205 LEU Chi-restraints excluded: chain w residue 216 ARG Chi-restraints excluded: chain w residue 271 GLN Chi-restraints excluded: chain w residue 282 THR Chi-restraints excluded: chain w residue 287 CYS Chi-restraints excluded: chain w residue 316 VAL Chi-restraints excluded: chain w residue 356 THR Chi-restraints excluded: chain w residue 395 LEU Chi-restraints excluded: chain w residue 412 LEU Chi-restraints excluded: chain w residue 419 LEU Chi-restraints excluded: chain x residue 38 VAL Chi-restraints excluded: chain x residue 54 THR Chi-restraints excluded: chain x residue 86 VAL Chi-restraints excluded: chain x residue 104 ILE Chi-restraints excluded: chain x residue 111 GLU Chi-restraints excluded: chain x residue 170 ASN Chi-restraints excluded: chain x residue 193 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 371 random chunks: chunk 88 optimal weight: 5.9990 chunk 261 optimal weight: 9.9990 chunk 181 optimal weight: 10.0000 chunk 154 optimal weight: 10.0000 chunk 7 optimal weight: 9.9990 chunk 99 optimal weight: 0.8980 chunk 234 optimal weight: 0.8980 chunk 207 optimal weight: 5.9990 chunk 36 optimal weight: 2.9990 chunk 199 optimal weight: 8.9990 chunk 12 optimal weight: 0.9980 overall best weight: 2.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 94 HIS b 191 ASN ** b 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 158 HIS f 71 HIS g 107 GLN i 107 GLN ** i 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 116 HIS l 73 GLN ** u 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** v 79 GLN w 228 ASN ** w 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 321 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 421 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** x 65 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.154441 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.130786 restraints weight = 74640.219| |-----------------------------------------------------------------------------| r_work (start): 0.3648 rms_B_bonded: 2.76 r_work: 0.3407 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3407 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7829 moved from start: 0.4399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 32717 Z= 0.136 Angle : 0.635 12.661 44264 Z= 0.328 Chirality : 0.042 0.243 4715 Planarity : 0.005 0.057 5773 Dihedral : 7.207 82.588 4511 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.30 % Favored : 96.64 % Rotamer: Outliers : 4.53 % Allowed : 17.63 % Favored : 77.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.04 (0.13), residues: 3785 helix: 0.54 (0.14), residues: 1386 sheet: 0.33 (0.21), residues: 545 loop : -0.48 (0.14), residues: 1854 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP c 110 HIS 0.009 0.001 HIS k 116 PHE 0.022 0.001 PHE j 215 TYR 0.024 0.001 TYR i 245 ARG 0.005 0.000 ARG m 104 Details of bonding type rmsd link_TRANS : bond 0.00088 ( 3) link_TRANS : angle 0.34252 ( 9) hydrogen bonds : bond 0.04143 ( 1304) hydrogen bonds : angle 5.11744 ( 3750) metal coordination : bond 0.00265 ( 3) covalent geometry : bond 0.00305 (32711) covalent geometry : angle 0.63553 (44255) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7570 Ramachandran restraints generated. 3785 Oldfield, 0 Emsley, 3785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7570 Ramachandran restraints generated. 3785 Oldfield, 0 Emsley, 3785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 714 residues out of total 3397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 154 poor density : 560 time to evaluate : 3.506 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: a 141 ASP cc_start: 0.8022 (m-30) cc_final: 0.7761 (t0) REVERT: a 263 MET cc_start: 0.8653 (tpp) cc_final: 0.7888 (ttm) REVERT: b 52 ARG cc_start: 0.7991 (mtt180) cc_final: 0.7630 (ttt180) REVERT: b 53 SER cc_start: 0.8126 (OUTLIER) cc_final: 0.7911 (p) REVERT: b 154 TYR cc_start: 0.8380 (t80) cc_final: 0.8107 (t80) REVERT: b 184 LEU cc_start: 0.7801 (OUTLIER) cc_final: 0.7487 (pp) REVERT: b 229 ASP cc_start: 0.7605 (m-30) cc_final: 0.7171 (p0) REVERT: b 281 PHE cc_start: 0.2242 (OUTLIER) cc_final: 0.1285 (p90) REVERT: b 356 ARG cc_start: 0.8229 (ttt180) cc_final: 0.7992 (ttp-170) REVERT: c 90 MET cc_start: 0.7754 (OUTLIER) cc_final: 0.7360 (tmm) REVERT: c 131 ASP cc_start: 0.7036 (t0) cc_final: 0.6653 (p0) REVERT: d 83 ILE cc_start: 0.1966 (OUTLIER) cc_final: 0.1633 (mt) REVERT: d 126 GLN cc_start: 0.7767 (tt0) cc_final: 0.6790 (mm110) REVERT: d 127 ARG cc_start: 0.8205 (ttm-80) cc_final: 0.8002 (ttm-80) REVERT: d 140 LEU cc_start: 0.7495 (OUTLIER) cc_final: 0.7072 (tp) REVERT: d 148 GLN cc_start: 0.7907 (tp-100) cc_final: 0.6874 (pt0) REVERT: e 28 ARG cc_start: 0.8437 (ttt180) cc_final: 0.7023 (mpt180) REVERT: e 71 TYR cc_start: 0.8148 (m-80) cc_final: 0.6406 (t80) REVERT: e 85 THR cc_start: 0.8706 (m) cc_final: 0.8385 (p) REVERT: e 115 TYR cc_start: 0.7404 (m-80) cc_final: 0.7159 (m-80) REVERT: e 118 GLU cc_start: 0.5230 (pm20) cc_final: 0.4923 (pm20) REVERT: e 131 LYS cc_start: 0.8177 (tptt) cc_final: 0.7433 (mttt) REVERT: f 56 ARG cc_start: 0.8099 (mtt180) cc_final: 0.6787 (tpm170) REVERT: f 128 GLN cc_start: 0.8469 (mm-40) cc_final: 0.6107 (pm20) REVERT: f 132 ARG cc_start: 0.8864 (mmt180) cc_final: 0.7074 (mtt180) REVERT: f 134 ARG cc_start: 0.8257 (ttt-90) cc_final: 0.7636 (mmt-90) REVERT: f 140 LYS cc_start: 0.8479 (tttt) cc_final: 0.8192 (mptt) REVERT: g 36 ASP cc_start: 0.7436 (m-30) cc_final: 0.7187 (p0) REVERT: g 114 ARG cc_start: 0.8741 (OUTLIER) cc_final: 0.8370 (ttt-90) REVERT: g 117 LYS cc_start: 0.8757 (pttt) cc_final: 0.8058 (mmmt) REVERT: h 36 ARG cc_start: 0.6817 (mtt180) cc_final: 0.5998 (mtm180) REVERT: h 235 THR cc_start: 0.8264 (p) cc_final: 0.7938 (t) REVERT: i 139 GLU cc_start: 0.8480 (mm-30) cc_final: 0.7454 (pt0) REVERT: i 143 ASP cc_start: 0.8528 (t0) cc_final: 0.8051 (m-30) REVERT: i 145 PHE cc_start: 0.7284 (OUTLIER) cc_final: 0.6803 (t80) REVERT: i 165 THR cc_start: 0.7982 (t) cc_final: 0.7599 (m) REVERT: i 172 MET cc_start: 0.7330 (ptp) cc_final: 0.6706 (mmt) REVERT: i 175 ASP cc_start: 0.6515 (m-30) cc_final: 0.5667 (t70) REVERT: i 209 TYR cc_start: 0.6543 (m-80) cc_final: 0.5872 (m-10) REVERT: i 220 GLN cc_start: 0.6665 (mt0) cc_final: 0.6283 (mt0) REVERT: i 240 ARG cc_start: 0.7075 (tpt170) cc_final: 0.6335 (ptt90) REVERT: i 245 TYR cc_start: 0.6061 (t80) cc_final: 0.5705 (t80) REVERT: i 291 GLU cc_start: 0.6206 (tt0) cc_final: 0.5751 (mm-30) REVERT: j 120 LEU cc_start: 0.7733 (mt) cc_final: 0.6784 (mm) REVERT: j 124 TRP cc_start: 0.5002 (m-10) cc_final: 0.4651 (t-100) REVERT: k 58 ARG cc_start: 0.7747 (ttt180) cc_final: 0.6673 (tpm170) REVERT: k 108 GLN cc_start: 0.7506 (tt0) cc_final: 0.7276 (tp-100) REVERT: k 119 ILE cc_start: 0.7618 (OUTLIER) cc_final: 0.7393 (mp) REVERT: k 132 MET cc_start: 0.6603 (tmm) cc_final: 0.5526 (ptt) REVERT: k 151 THR cc_start: 0.7110 (OUTLIER) cc_final: 0.6100 (p) REVERT: k 159 ILE cc_start: 0.8409 (OUTLIER) cc_final: 0.7496 (tt) REVERT: m 57 GLN cc_start: 0.5746 (pt0) cc_final: 0.5146 (mp10) REVERT: m 68 GLN cc_start: 0.8126 (mm-40) cc_final: 0.7395 (mp10) REVERT: m 77 GLU cc_start: 0.8073 (pt0) cc_final: 0.7575 (pt0) REVERT: m 89 ASP cc_start: 0.8593 (m-30) cc_final: 0.8206 (m-30) REVERT: m 125 ARG cc_start: 0.7687 (ptm160) cc_final: 0.7184 (ttm110) REVERT: m 129 ASP cc_start: 0.7867 (m-30) cc_final: 0.7643 (m-30) REVERT: m 137 ASP cc_start: 0.5944 (t0) cc_final: 0.5238 (m-30) REVERT: m 142 ASP cc_start: 0.7446 (m-30) cc_final: 0.6992 (t70) REVERT: n 46 ARG cc_start: 0.8468 (OUTLIER) cc_final: 0.4541 (ttt-90) REVERT: n 62 ILE cc_start: 0.8976 (mt) cc_final: 0.8765 (mt) REVERT: n 75 LYS cc_start: 0.7432 (mmtt) cc_final: 0.6969 (tmtt) REVERT: n 92 ILE cc_start: 0.9212 (OUTLIER) cc_final: 0.8823 (mt) REVERT: n 96 ARG cc_start: 0.8617 (mtp180) cc_final: 0.8198 (ttp80) REVERT: n 128 ARG cc_start: 0.7066 (mmt90) cc_final: 0.4520 (mtt180) REVERT: o 61 LYS cc_start: 0.8100 (mmtt) cc_final: 0.7847 (mtmt) REVERT: p 40 GLU cc_start: 0.6273 (mp0) cc_final: 0.5543 (mp0) REVERT: p 85 GLU cc_start: 0.5967 (tt0) cc_final: 0.5294 (mm-30) REVERT: q 107 LEU cc_start: 0.8587 (mm) cc_final: 0.8012 (mp) REVERT: t 9 ARG cc_start: 0.7781 (ttt90) cc_final: 0.5207 (ptt180) REVERT: t 60 ARG cc_start: 0.8196 (mmt90) cc_final: 0.7601 (mmp-170) REVERT: t 98 THR cc_start: 0.7897 (OUTLIER) cc_final: 0.7547 (m) REVERT: u 43 TYR cc_start: 0.6684 (m-80) cc_final: 0.6448 (m-80) REVERT: u 59 TRP cc_start: 0.7434 (m100) cc_final: 0.4771 (t60) REVERT: u 82 ARG cc_start: 0.7547 (mmm160) cc_final: 0.6369 (ttp80) REVERT: u 118 LEU cc_start: 0.8363 (mt) cc_final: 0.7860 (mt) REVERT: u 148 ASP cc_start: 0.8011 (t70) cc_final: 0.7488 (t70) REVERT: u 159 GLU cc_start: 0.8269 (pp20) cc_final: 0.7696 (pp20) REVERT: u 186 ARG cc_start: 0.5894 (mtt-85) cc_final: 0.5154 (ptt180) REVERT: w 52 THR cc_start: 0.9144 (OUTLIER) cc_final: 0.8803 (p) REVERT: w 59 ARG cc_start: 0.8491 (tmt170) cc_final: 0.8173 (tpt170) REVERT: w 86 MET cc_start: 0.7849 (mmp) cc_final: 0.6348 (mtt) REVERT: w 141 CYS cc_start: 0.7793 (m) cc_final: 0.7370 (p) REVERT: w 163 ARG cc_start: 0.6265 (mmp80) cc_final: 0.5732 (ttp80) REVERT: w 271 GLN cc_start: 0.8183 (OUTLIER) cc_final: 0.6752 (tt0) REVERT: x 111 GLU cc_start: 0.8019 (OUTLIER) cc_final: 0.7786 (mm-30) REVERT: x 163 TYR cc_start: 0.8415 (m-80) cc_final: 0.8200 (m-80) outliers start: 154 outliers final: 89 residues processed: 669 average time/residue: 0.4405 time to fit residues: 455.4726 Evaluate side-chains 592 residues out of total 3397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 486 time to evaluate : 3.558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 117 VAL Chi-restraints excluded: chain a residue 180 ILE Chi-restraints excluded: chain a residue 248 THR Chi-restraints excluded: chain a residue 396 VAL Chi-restraints excluded: chain b residue 32 LEU Chi-restraints excluded: chain b residue 40 ILE Chi-restraints excluded: chain b residue 53 SER Chi-restraints excluded: chain b residue 127 THR Chi-restraints excluded: chain b residue 184 LEU Chi-restraints excluded: chain b residue 281 PHE Chi-restraints excluded: chain c residue 56 THR Chi-restraints excluded: chain c residue 90 MET Chi-restraints excluded: chain c residue 140 TRP Chi-restraints excluded: chain c residue 177 CYS Chi-restraints excluded: chain c residue 222 VAL Chi-restraints excluded: chain c residue 236 PHE Chi-restraints excluded: chain c residue 256 ASP Chi-restraints excluded: chain c residue 260 VAL Chi-restraints excluded: chain c residue 280 VAL Chi-restraints excluded: chain c residue 285 THR Chi-restraints excluded: chain d residue 83 ILE Chi-restraints excluded: chain d residue 89 ILE Chi-restraints excluded: chain d residue 140 LEU Chi-restraints excluded: chain d residue 173 ARG Chi-restraints excluded: chain e residue 19 SER Chi-restraints excluded: chain e residue 39 THR Chi-restraints excluded: chain e residue 49 VAL Chi-restraints excluded: chain e residue 127 GLN Chi-restraints excluded: chain f residue 59 VAL Chi-restraints excluded: chain f residue 108 MET Chi-restraints excluded: chain g residue 6 THR Chi-restraints excluded: chain g residue 14 VAL Chi-restraints excluded: chain g residue 62 VAL Chi-restraints excluded: chain g residue 94 VAL Chi-restraints excluded: chain g residue 112 VAL Chi-restraints excluded: chain g residue 113 ILE Chi-restraints excluded: chain g residue 114 ARG Chi-restraints excluded: chain g residue 121 THR Chi-restraints excluded: chain g residue 126 ILE Chi-restraints excluded: chain g residue 138 THR Chi-restraints excluded: chain h residue 33 LYS Chi-restraints excluded: chain h residue 50 LEU Chi-restraints excluded: chain h residue 151 GLU Chi-restraints excluded: chain h residue 307 PHE Chi-restraints excluded: chain i residue 88 TYR Chi-restraints excluded: chain i residue 134 ILE Chi-restraints excluded: chain i residue 145 PHE Chi-restraints excluded: chain i residue 162 THR Chi-restraints excluded: chain i residue 177 ARG Chi-restraints excluded: chain i residue 186 VAL Chi-restraints excluded: chain i residue 196 GLN Chi-restraints excluded: chain i residue 221 THR Chi-restraints excluded: chain i residue 238 VAL Chi-restraints excluded: chain j residue 60 THR Chi-restraints excluded: chain j residue 84 TYR Chi-restraints excluded: chain j residue 130 HIS Chi-restraints excluded: chain j residue 139 GLU Chi-restraints excluded: chain j residue 253 VAL Chi-restraints excluded: chain j residue 276 LEU Chi-restraints excluded: chain k residue 116 HIS Chi-restraints excluded: chain k residue 119 ILE Chi-restraints excluded: chain k residue 151 THR Chi-restraints excluded: chain k residue 159 ILE Chi-restraints excluded: chain k residue 174 ILE Chi-restraints excluded: chain l residue 39 VAL Chi-restraints excluded: chain l residue 42 VAL Chi-restraints excluded: chain l residue 81 SER Chi-restraints excluded: chain l residue 99 ASP Chi-restraints excluded: chain l residue 134 LYS Chi-restraints excluded: chain l residue 135 THR Chi-restraints excluded: chain m residue 83 VAL Chi-restraints excluded: chain m residue 127 VAL Chi-restraints excluded: chain m residue 133 VAL Chi-restraints excluded: chain n residue 44 VAL Chi-restraints excluded: chain n residue 46 ARG Chi-restraints excluded: chain n residue 56 VAL Chi-restraints excluded: chain n residue 92 ILE Chi-restraints excluded: chain n residue 105 ASP Chi-restraints excluded: chain o residue 78 VAL Chi-restraints excluded: chain o residue 79 LEU Chi-restraints excluded: chain o residue 99 LEU Chi-restraints excluded: chain p residue 27 VAL Chi-restraints excluded: chain t residue 12 ILE Chi-restraints excluded: chain t residue 32 LYS Chi-restraints excluded: chain t residue 98 THR Chi-restraints excluded: chain t residue 101 TRP Chi-restraints excluded: chain u residue 104 LEU Chi-restraints excluded: chain u residue 114 VAL Chi-restraints excluded: chain w residue 52 THR Chi-restraints excluded: chain w residue 92 VAL Chi-restraints excluded: chain w residue 97 THR Chi-restraints excluded: chain w residue 166 ILE Chi-restraints excluded: chain w residue 189 LEU Chi-restraints excluded: chain w residue 205 LEU Chi-restraints excluded: chain w residue 209 GLU Chi-restraints excluded: chain w residue 271 GLN Chi-restraints excluded: chain w residue 282 THR Chi-restraints excluded: chain w residue 287 CYS Chi-restraints excluded: chain w residue 316 VAL Chi-restraints excluded: chain w residue 345 VAL Chi-restraints excluded: chain w residue 395 LEU Chi-restraints excluded: chain x residue 54 THR Chi-restraints excluded: chain x residue 56 THR Chi-restraints excluded: chain x residue 104 ILE Chi-restraints excluded: chain x residue 111 GLU Chi-restraints excluded: chain x residue 193 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 371 random chunks: chunk 179 optimal weight: 10.0000 chunk 197 optimal weight: 6.9990 chunk 228 optimal weight: 10.0000 chunk 315 optimal weight: 10.0000 chunk 276 optimal weight: 30.0000 chunk 98 optimal weight: 4.9990 chunk 170 optimal weight: 0.8980 chunk 204 optimal weight: 40.0000 chunk 168 optimal weight: 10.0000 chunk 231 optimal weight: 4.9990 chunk 208 optimal weight: 50.0000 overall best weight: 5.5790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 65 HIS b 163 HIS ** b 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 107 GLN h 69 HIS h 310 ASN ** j 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 198 ASN l 155 GLN l 156 GLN q 129 HIS ** u 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** w 87 GLN w 173 GLN w 233 ASN ** w 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 321 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 421 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.154817 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.132782 restraints weight = 77570.414| |-----------------------------------------------------------------------------| r_work (start): 0.3637 rms_B_bonded: 3.17 r_work: 0.3378 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3378 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7890 moved from start: 0.5028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 32717 Z= 0.209 Angle : 0.671 11.326 44264 Z= 0.343 Chirality : 0.044 0.194 4715 Planarity : 0.006 0.066 5773 Dihedral : 6.879 86.522 4490 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 9.88 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.70 % Favored : 96.22 % Rotamer: Outliers : 5.30 % Allowed : 17.90 % Favored : 76.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.02 (0.13), residues: 3785 helix: 0.70 (0.14), residues: 1399 sheet: 0.33 (0.21), residues: 545 loop : -0.55 (0.14), residues: 1841 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP t 101 HIS 0.011 0.001 HIS k 116 PHE 0.021 0.002 PHE n 66 TYR 0.024 0.002 TYR i 245 ARG 0.006 0.001 ARG u 191 Details of bonding type rmsd link_TRANS : bond 0.00151 ( 3) link_TRANS : angle 0.35704 ( 9) hydrogen bonds : bond 0.04247 ( 1304) hydrogen bonds : angle 4.95438 ( 3750) metal coordination : bond 0.00555 ( 3) covalent geometry : bond 0.00491 (32711) covalent geometry : angle 0.67082 (44255) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7570 Ramachandran restraints generated. 3785 Oldfield, 0 Emsley, 3785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7570 Ramachandran restraints generated. 3785 Oldfield, 0 Emsley, 3785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 687 residues out of total 3397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 180 poor density : 507 time to evaluate : 3.640 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: a 141 ASP cc_start: 0.8002 (m-30) cc_final: 0.7776 (t0) REVERT: a 404 ILE cc_start: 0.8775 (OUTLIER) cc_final: 0.8509 (mt) REVERT: b 52 ARG cc_start: 0.8162 (mtt180) cc_final: 0.7726 (ptm160) REVERT: b 154 TYR cc_start: 0.8688 (t80) cc_final: 0.8434 (t80) REVERT: b 184 LEU cc_start: 0.8094 (OUTLIER) cc_final: 0.7795 (pp) REVERT: b 229 ASP cc_start: 0.7841 (m-30) cc_final: 0.7479 (p0) REVERT: b 281 PHE cc_start: 0.1962 (OUTLIER) cc_final: 0.1180 (p90) REVERT: b 356 ARG cc_start: 0.8173 (ttt180) cc_final: 0.7941 (ttp-170) REVERT: c 90 MET cc_start: 0.8218 (mtp) cc_final: 0.7743 (tmm) REVERT: d 83 ILE cc_start: 0.1954 (OUTLIER) cc_final: 0.1615 (mt) REVERT: d 140 LEU cc_start: 0.7531 (OUTLIER) cc_final: 0.7060 (tp) REVERT: e 28 ARG cc_start: 0.8725 (ttt180) cc_final: 0.7191 (mpt180) REVERT: e 74 TYR cc_start: 0.7560 (OUTLIER) cc_final: 0.7128 (m-10) REVERT: e 85 THR cc_start: 0.8773 (m) cc_final: 0.8520 (p) REVERT: e 115 TYR cc_start: 0.7493 (m-80) cc_final: 0.7190 (m-80) REVERT: e 118 GLU cc_start: 0.5406 (pm20) cc_final: 0.5047 (pm20) REVERT: e 122 GLU cc_start: 0.7559 (pp20) cc_final: 0.7255 (tm-30) REVERT: e 127 GLN cc_start: 0.8302 (OUTLIER) cc_final: 0.8006 (mp10) REVERT: e 131 LYS cc_start: 0.8196 (tptt) cc_final: 0.7627 (mttt) REVERT: f 41 ASP cc_start: 0.7137 (t0) cc_final: 0.6549 (t0) REVERT: f 46 LYS cc_start: 0.8566 (ttmt) cc_final: 0.8226 (mttp) REVERT: f 56 ARG cc_start: 0.8307 (mtt180) cc_final: 0.6993 (tpm170) REVERT: f 132 ARG cc_start: 0.8859 (mmt180) cc_final: 0.7239 (mtt180) REVERT: f 134 ARG cc_start: 0.8494 (ttt-90) cc_final: 0.7721 (mmt180) REVERT: f 140 LYS cc_start: 0.8277 (tttt) cc_final: 0.8021 (mptt) REVERT: g 36 ASP cc_start: 0.7683 (m-30) cc_final: 0.7335 (p0) REVERT: g 117 LYS cc_start: 0.8870 (pttt) cc_final: 0.7968 (mmmt) REVERT: h 36 ARG cc_start: 0.6952 (mtt180) cc_final: 0.6009 (mtm180) REVERT: h 233 THR cc_start: 0.8165 (OUTLIER) cc_final: 0.7879 (m) REVERT: h 235 THR cc_start: 0.8014 (p) cc_final: 0.7677 (t) REVERT: i 139 GLU cc_start: 0.8556 (mm-30) cc_final: 0.8270 (mm-30) REVERT: i 140 LYS cc_start: 0.7978 (ttpt) cc_final: 0.7422 (ptmm) REVERT: i 143 ASP cc_start: 0.8482 (t0) cc_final: 0.8023 (m-30) REVERT: i 145 PHE cc_start: 0.7332 (OUTLIER) cc_final: 0.6883 (t80) REVERT: i 209 TYR cc_start: 0.6649 (m-80) cc_final: 0.5990 (m-10) REVERT: i 220 GLN cc_start: 0.6854 (mt0) cc_final: 0.6517 (mt0) REVERT: i 240 ARG cc_start: 0.7120 (tpt170) cc_final: 0.6411 (ptt90) REVERT: i 291 GLU cc_start: 0.6239 (tt0) cc_final: 0.5831 (mm-30) REVERT: j 124 TRP cc_start: 0.4953 (m-10) cc_final: 0.4604 (t-100) REVERT: k 58 ARG cc_start: 0.7903 (ttt180) cc_final: 0.6705 (tpm170) REVERT: k 108 GLN cc_start: 0.7582 (tt0) cc_final: 0.7333 (tp-100) REVERT: k 132 MET cc_start: 0.6625 (tmm) cc_final: 0.6121 (tpp) REVERT: k 151 THR cc_start: 0.6697 (OUTLIER) cc_final: 0.6352 (p) REVERT: m 57 GLN cc_start: 0.6050 (pt0) cc_final: 0.5377 (mp10) REVERT: m 68 GLN cc_start: 0.8149 (mm-40) cc_final: 0.7443 (mp10) REVERT: m 77 GLU cc_start: 0.8241 (pt0) cc_final: 0.7643 (pt0) REVERT: m 90 ILE cc_start: 0.8686 (mp) cc_final: 0.8102 (mm) REVERT: m 125 ARG cc_start: 0.7812 (ptm160) cc_final: 0.7355 (ttm110) REVERT: m 129 ASP cc_start: 0.7937 (m-30) cc_final: 0.7724 (m-30) REVERT: n 46 ARG cc_start: 0.8584 (OUTLIER) cc_final: 0.5418 (mtp-110) REVERT: n 50 LYS cc_start: 0.8668 (ttmt) cc_final: 0.8405 (mtpt) REVERT: n 75 LYS cc_start: 0.7458 (mmtt) cc_final: 0.6914 (tmtt) REVERT: n 92 ILE cc_start: 0.9218 (OUTLIER) cc_final: 0.8794 (mt) REVERT: n 96 ARG cc_start: 0.8557 (mtp180) cc_final: 0.8132 (ttt180) REVERT: n 128 ARG cc_start: 0.7448 (mmt90) cc_final: 0.4897 (mtt180) REVERT: o 48 ASP cc_start: 0.6997 (OUTLIER) cc_final: 0.6431 (p0) REVERT: o 61 LYS cc_start: 0.8382 (mmtt) cc_final: 0.7895 (mtmt) REVERT: p 40 GLU cc_start: 0.5607 (mp0) cc_final: 0.4600 (mp0) REVERT: t 9 ARG cc_start: 0.7592 (OUTLIER) cc_final: 0.5181 (ptt180) REVERT: t 60 ARG cc_start: 0.8452 (mmt90) cc_final: 0.7816 (mmp-170) REVERT: t 98 THR cc_start: 0.8016 (OUTLIER) cc_final: 0.7691 (m) REVERT: u 59 TRP cc_start: 0.7550 (m100) cc_final: 0.5005 (t60) REVERT: u 118 LEU cc_start: 0.8350 (mt) cc_final: 0.8017 (mt) REVERT: u 148 ASP cc_start: 0.8118 (t70) cc_final: 0.7588 (t70) REVERT: u 151 GLN cc_start: 0.8943 (tp40) cc_final: 0.8640 (tp40) REVERT: u 159 GLU cc_start: 0.8200 (pp20) cc_final: 0.7639 (pp20) REVERT: u 186 ARG cc_start: 0.6213 (mtt-85) cc_final: 0.4983 (ptt180) REVERT: v 86 GLU cc_start: 0.8762 (tt0) cc_final: 0.8496 (tt0) REVERT: w 52 THR cc_start: 0.9209 (OUTLIER) cc_final: 0.8908 (p) REVERT: w 59 ARG cc_start: 0.8557 (tmt170) cc_final: 0.8201 (tpt170) REVERT: w 86 MET cc_start: 0.7906 (mmp) cc_final: 0.6826 (mtt) REVERT: w 163 ARG cc_start: 0.6283 (mmp80) cc_final: 0.5787 (ttp80) REVERT: w 216 ARG cc_start: 0.8888 (OUTLIER) cc_final: 0.7499 (mtt180) REVERT: w 271 GLN cc_start: 0.8410 (OUTLIER) cc_final: 0.6580 (tt0) REVERT: x 111 GLU cc_start: 0.8188 (OUTLIER) cc_final: 0.7964 (mm-30) REVERT: x 170 ASN cc_start: 0.8694 (OUTLIER) cc_final: 0.8307 (p0) outliers start: 180 outliers final: 116 residues processed: 639 average time/residue: 0.4374 time to fit residues: 435.5055 Evaluate side-chains 591 residues out of total 3397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 136 poor density : 455 time to evaluate : 3.683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 35 VAL Chi-restraints excluded: chain a residue 117 VAL Chi-restraints excluded: chain a residue 180 ILE Chi-restraints excluded: chain a residue 203 CYS Chi-restraints excluded: chain a residue 248 THR Chi-restraints excluded: chain a residue 270 VAL Chi-restraints excluded: chain a residue 396 VAL Chi-restraints excluded: chain a residue 404 ILE Chi-restraints excluded: chain b residue 32 LEU Chi-restraints excluded: chain b residue 40 ILE Chi-restraints excluded: chain b residue 76 GLU Chi-restraints excluded: chain b residue 127 THR Chi-restraints excluded: chain b residue 184 LEU Chi-restraints excluded: chain b residue 281 PHE Chi-restraints excluded: chain c residue 56 THR Chi-restraints excluded: chain c residue 83 SER Chi-restraints excluded: chain c residue 140 TRP Chi-restraints excluded: chain c residue 177 CYS Chi-restraints excluded: chain c residue 222 VAL Chi-restraints excluded: chain c residue 236 PHE Chi-restraints excluded: chain c residue 256 ASP Chi-restraints excluded: chain c residue 260 VAL Chi-restraints excluded: chain c residue 280 VAL Chi-restraints excluded: chain c residue 285 THR Chi-restraints excluded: chain d residue 83 ILE Chi-restraints excluded: chain d residue 89 ILE Chi-restraints excluded: chain d residue 104 VAL Chi-restraints excluded: chain d residue 118 LEU Chi-restraints excluded: chain d residue 140 LEU Chi-restraints excluded: chain d residue 173 ARG Chi-restraints excluded: chain e residue 19 SER Chi-restraints excluded: chain e residue 39 THR Chi-restraints excluded: chain e residue 49 VAL Chi-restraints excluded: chain e residue 74 TYR Chi-restraints excluded: chain e residue 89 LEU Chi-restraints excluded: chain e residue 120 THR Chi-restraints excluded: chain e residue 127 GLN Chi-restraints excluded: chain f residue 59 VAL Chi-restraints excluded: chain f residue 75 ILE Chi-restraints excluded: chain f residue 108 MET Chi-restraints excluded: chain f residue 109 ILE Chi-restraints excluded: chain g residue 14 VAL Chi-restraints excluded: chain g residue 61 VAL Chi-restraints excluded: chain g residue 62 VAL Chi-restraints excluded: chain g residue 94 VAL Chi-restraints excluded: chain g residue 112 VAL Chi-restraints excluded: chain g residue 113 ILE Chi-restraints excluded: chain g residue 121 THR Chi-restraints excluded: chain g residue 126 ILE Chi-restraints excluded: chain g residue 138 THR Chi-restraints excluded: chain h residue 33 LYS Chi-restraints excluded: chain h residue 45 LEU Chi-restraints excluded: chain h residue 50 LEU Chi-restraints excluded: chain h residue 151 GLU Chi-restraints excluded: chain h residue 215 ILE Chi-restraints excluded: chain h residue 233 THR Chi-restraints excluded: chain h residue 234 ILE Chi-restraints excluded: chain h residue 307 PHE Chi-restraints excluded: chain i residue 66 VAL Chi-restraints excluded: chain i residue 116 VAL Chi-restraints excluded: chain i residue 134 ILE Chi-restraints excluded: chain i residue 145 PHE Chi-restraints excluded: chain i residue 165 THR Chi-restraints excluded: chain i residue 177 ARG Chi-restraints excluded: chain i residue 186 VAL Chi-restraints excluded: chain i residue 196 GLN Chi-restraints excluded: chain i residue 221 THR Chi-restraints excluded: chain i residue 246 VAL Chi-restraints excluded: chain i residue 253 VAL Chi-restraints excluded: chain j residue 60 THR Chi-restraints excluded: chain j residue 84 TYR Chi-restraints excluded: chain j residue 130 HIS Chi-restraints excluded: chain j residue 139 GLU Chi-restraints excluded: chain j residue 240 THR Chi-restraints excluded: chain j residue 255 VAL Chi-restraints excluded: chain j residue 276 LEU Chi-restraints excluded: chain k residue 96 ILE Chi-restraints excluded: chain k residue 151 THR Chi-restraints excluded: chain k residue 154 GLU Chi-restraints excluded: chain k residue 166 PHE Chi-restraints excluded: chain k residue 174 ILE Chi-restraints excluded: chain l residue 39 VAL Chi-restraints excluded: chain l residue 65 HIS Chi-restraints excluded: chain l residue 99 ASP Chi-restraints excluded: chain l residue 135 THR Chi-restraints excluded: chain m residue 83 VAL Chi-restraints excluded: chain m residue 124 VAL Chi-restraints excluded: chain m residue 127 VAL Chi-restraints excluded: chain m residue 133 VAL Chi-restraints excluded: chain n residue 37 THR Chi-restraints excluded: chain n residue 46 ARG Chi-restraints excluded: chain n residue 56 VAL Chi-restraints excluded: chain n residue 66 PHE Chi-restraints excluded: chain n residue 92 ILE Chi-restraints excluded: chain n residue 105 ASP Chi-restraints excluded: chain o residue 48 ASP Chi-restraints excluded: chain o residue 99 LEU Chi-restraints excluded: chain p residue 27 VAL Chi-restraints excluded: chain p residue 50 SER Chi-restraints excluded: chain t residue 9 ARG Chi-restraints excluded: chain t residue 12 ILE Chi-restraints excluded: chain t residue 18 ILE Chi-restraints excluded: chain t residue 32 LYS Chi-restraints excluded: chain t residue 55 THR Chi-restraints excluded: chain t residue 98 THR Chi-restraints excluded: chain t residue 101 TRP Chi-restraints excluded: chain u residue 42 ILE Chi-restraints excluded: chain u residue 77 THR Chi-restraints excluded: chain u residue 104 LEU Chi-restraints excluded: chain u residue 110 ILE Chi-restraints excluded: chain u residue 114 VAL Chi-restraints excluded: chain u residue 153 LEU Chi-restraints excluded: chain w residue 52 THR Chi-restraints excluded: chain w residue 63 VAL Chi-restraints excluded: chain w residue 92 VAL Chi-restraints excluded: chain w residue 97 THR Chi-restraints excluded: chain w residue 166 ILE Chi-restraints excluded: chain w residue 188 VAL Chi-restraints excluded: chain w residue 189 LEU Chi-restraints excluded: chain w residue 205 LEU Chi-restraints excluded: chain w residue 209 GLU Chi-restraints excluded: chain w residue 216 ARG Chi-restraints excluded: chain w residue 271 GLN Chi-restraints excluded: chain w residue 274 ASN Chi-restraints excluded: chain w residue 282 THR Chi-restraints excluded: chain w residue 316 VAL Chi-restraints excluded: chain w residue 345 VAL Chi-restraints excluded: chain w residue 356 THR Chi-restraints excluded: chain w residue 395 LEU Chi-restraints excluded: chain w residue 419 LEU Chi-restraints excluded: chain x residue 54 THR Chi-restraints excluded: chain x residue 56 THR Chi-restraints excluded: chain x residue 104 ILE Chi-restraints excluded: chain x residue 111 GLU Chi-restraints excluded: chain x residue 119 VAL Chi-restraints excluded: chain x residue 170 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 371 random chunks: chunk 175 optimal weight: 8.9990 chunk 265 optimal weight: 8.9990 chunk 96 optimal weight: 9.9990 chunk 204 optimal weight: 30.0000 chunk 296 optimal weight: 9.9990 chunk 328 optimal weight: 10.0000 chunk 283 optimal weight: 2.9990 chunk 155 optimal weight: 4.9990 chunk 336 optimal weight: 3.9990 chunk 98 optimal weight: 1.9990 chunk 206 optimal weight: 0.9980 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 191 ASN ** b 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 274 GLN ** d 158 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 111 HIS g 107 GLN j 179 GLN k 116 HIS k 177 ASN w 71 HIS ** w 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 321 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** x 164 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.156684 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.133980 restraints weight = 76194.566| |-----------------------------------------------------------------------------| r_work (start): 0.3645 rms_B_bonded: 3.00 r_work: 0.3399 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3399 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 moved from start: 0.5324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 32717 Z= 0.137 Angle : 0.603 13.049 44264 Z= 0.309 Chirality : 0.042 0.204 4715 Planarity : 0.005 0.068 5773 Dihedral : 6.511 83.746 4481 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.28 % Favored : 96.64 % Rotamer: Outliers : 4.59 % Allowed : 19.11 % Favored : 76.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.31 (0.13), residues: 3785 helix: 1.00 (0.14), residues: 1413 sheet: 0.45 (0.22), residues: 540 loop : -0.43 (0.14), residues: 1832 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP t 101 HIS 0.022 0.001 HIS d 158 PHE 0.055 0.001 PHE d 169 TYR 0.024 0.001 TYR i 245 ARG 0.011 0.001 ARG d 151 Details of bonding type rmsd link_TRANS : bond 0.00057 ( 3) link_TRANS : angle 0.34179 ( 9) hydrogen bonds : bond 0.03729 ( 1304) hydrogen bonds : angle 4.72709 ( 3750) metal coordination : bond 0.00352 ( 3) covalent geometry : bond 0.00313 (32711) covalent geometry : angle 0.60273 (44255) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7570 Ramachandran restraints generated. 3785 Oldfield, 0 Emsley, 3785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7570 Ramachandran restraints generated. 3785 Oldfield, 0 Emsley, 3785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 672 residues out of total 3397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 156 poor density : 516 time to evaluate : 3.651 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 141 ASP cc_start: 0.7900 (m-30) cc_final: 0.7687 (t0) REVERT: a 263 MET cc_start: 0.8854 (tpp) cc_final: 0.8204 (ttm) REVERT: a 347 THR cc_start: 0.8134 (m) cc_final: 0.7902 (m) REVERT: a 404 ILE cc_start: 0.8715 (OUTLIER) cc_final: 0.8457 (mt) REVERT: b 52 ARG cc_start: 0.8143 (mtt180) cc_final: 0.7627 (ttt180) REVERT: b 184 LEU cc_start: 0.8155 (OUTLIER) cc_final: 0.7886 (pp) REVERT: b 281 PHE cc_start: 0.1878 (OUTLIER) cc_final: 0.1129 (p90) REVERT: c 90 MET cc_start: 0.8042 (mtp) cc_final: 0.7742 (tmm) REVERT: d 83 ILE cc_start: 0.2359 (OUTLIER) cc_final: 0.1929 (mt) REVERT: d 140 LEU cc_start: 0.7476 (OUTLIER) cc_final: 0.7021 (tp) REVERT: d 150 LEU cc_start: 0.5598 (tp) cc_final: 0.4781 (tt) REVERT: e 28 ARG cc_start: 0.8701 (ttt180) cc_final: 0.7163 (mpt180) REVERT: e 67 LYS cc_start: 0.7536 (OUTLIER) cc_final: 0.7285 (mtmm) REVERT: e 71 TYR cc_start: 0.8182 (m-80) cc_final: 0.6471 (t80) REVERT: e 74 TYR cc_start: 0.7764 (OUTLIER) cc_final: 0.6805 (m-10) REVERT: e 85 THR cc_start: 0.8805 (m) cc_final: 0.8541 (p) REVERT: e 115 TYR cc_start: 0.7544 (m-80) cc_final: 0.7102 (m-80) REVERT: e 131 LYS cc_start: 0.8178 (tptt) cc_final: 0.7757 (mptt) REVERT: f 56 ARG cc_start: 0.8395 (mtt180) cc_final: 0.6995 (tpm170) REVERT: f 132 ARG cc_start: 0.8802 (mmt180) cc_final: 0.7242 (mtt180) REVERT: f 134 ARG cc_start: 0.8396 (ttt-90) cc_final: 0.7874 (mpt180) REVERT: g 14 VAL cc_start: 0.8999 (OUTLIER) cc_final: 0.8757 (t) REVERT: g 36 ASP cc_start: 0.7554 (m-30) cc_final: 0.7212 (p0) REVERT: g 117 LYS cc_start: 0.8871 (pttt) cc_final: 0.7953 (mmmt) REVERT: h 36 ARG cc_start: 0.6891 (mtt180) cc_final: 0.5833 (mtm180) REVERT: h 204 GLN cc_start: 0.8439 (OUTLIER) cc_final: 0.8089 (mp-120) REVERT: h 233 THR cc_start: 0.8381 (OUTLIER) cc_final: 0.8087 (m) REVERT: h 234 ILE cc_start: 0.8602 (OUTLIER) cc_final: 0.8160 (tp) REVERT: h 235 THR cc_start: 0.8032 (p) cc_final: 0.7557 (t) REVERT: i 139 GLU cc_start: 0.8578 (mm-30) cc_final: 0.8267 (mm-30) REVERT: i 143 ASP cc_start: 0.8557 (t0) cc_final: 0.8009 (m-30) REVERT: i 145 PHE cc_start: 0.7386 (OUTLIER) cc_final: 0.6819 (t80) REVERT: i 175 ASP cc_start: 0.6384 (m-30) cc_final: 0.5744 (t0) REVERT: i 209 TYR cc_start: 0.6486 (m-80) cc_final: 0.5943 (m-80) REVERT: i 220 GLN cc_start: 0.6833 (mt0) cc_final: 0.6571 (mt0) REVERT: i 240 ARG cc_start: 0.7170 (tpt170) cc_final: 0.6371 (ptt90) REVERT: i 291 GLU cc_start: 0.6142 (tt0) cc_final: 0.5773 (mm-30) REVERT: j 124 TRP cc_start: 0.5035 (m-10) cc_final: 0.4426 (t-100) REVERT: k 58 ARG cc_start: 0.7939 (ttt180) cc_final: 0.6980 (mmp-170) REVERT: k 108 GLN cc_start: 0.7539 (tt0) cc_final: 0.7282 (tp-100) REVERT: k 132 MET cc_start: 0.6628 (tmm) cc_final: 0.6323 (mmm) REVERT: k 151 THR cc_start: 0.6479 (OUTLIER) cc_final: 0.6113 (p) REVERT: k 183 LYS cc_start: 0.6530 (mmtm) cc_final: 0.6327 (mmtp) REVERT: m 57 GLN cc_start: 0.6299 (pt0) cc_final: 0.5314 (mp10) REVERT: m 68 GLN cc_start: 0.8211 (mm-40) cc_final: 0.7440 (mp10) REVERT: m 77 GLU cc_start: 0.8047 (pt0) cc_final: 0.7745 (pt0) REVERT: m 89 ASP cc_start: 0.8440 (m-30) cc_final: 0.7951 (m-30) REVERT: m 90 ILE cc_start: 0.8640 (mp) cc_final: 0.8119 (mm) REVERT: m 91 SER cc_start: 0.8284 (t) cc_final: 0.8068 (p) REVERT: m 125 ARG cc_start: 0.7815 (ptm160) cc_final: 0.7321 (ttm110) REVERT: m 129 ASP cc_start: 0.7971 (m-30) cc_final: 0.7727 (m-30) REVERT: n 46 ARG cc_start: 0.8531 (OUTLIER) cc_final: 0.5354 (mtp-110) REVERT: n 75 LYS cc_start: 0.7447 (mmtt) cc_final: 0.6944 (tmtt) REVERT: n 92 ILE cc_start: 0.9210 (OUTLIER) cc_final: 0.8817 (mt) REVERT: n 96 ARG cc_start: 0.8620 (mtp180) cc_final: 0.8073 (ttt180) REVERT: n 128 ARG cc_start: 0.7232 (mmt90) cc_final: 0.4694 (mtt180) REVERT: o 48 ASP cc_start: 0.7476 (OUTLIER) cc_final: 0.6839 (p0) REVERT: o 61 LYS cc_start: 0.8181 (mmtt) cc_final: 0.7784 (mtmt) REVERT: o 102 GLU cc_start: 0.7519 (mm-30) cc_final: 0.7256 (mm-30) REVERT: p 40 GLU cc_start: 0.5379 (mp0) cc_final: 0.4582 (mp0) REVERT: t 9 ARG cc_start: 0.7501 (OUTLIER) cc_final: 0.5215 (ptt180) REVERT: t 11 ARG cc_start: 0.6354 (tpm170) cc_final: 0.6036 (tpm170) REVERT: t 60 ARG cc_start: 0.8389 (mmt90) cc_final: 0.7767 (mmp-170) REVERT: t 98 THR cc_start: 0.7758 (OUTLIER) cc_final: 0.7467 (m) REVERT: u 59 TRP cc_start: 0.7497 (m100) cc_final: 0.5063 (t60) REVERT: u 118 LEU cc_start: 0.8270 (mt) cc_final: 0.7935 (mt) REVERT: u 148 ASP cc_start: 0.8071 (t70) cc_final: 0.7628 (t70) REVERT: u 159 GLU cc_start: 0.8104 (pp20) cc_final: 0.7576 (pp20) REVERT: u 186 ARG cc_start: 0.5883 (mtt-85) cc_final: 0.4549 (ptt180) REVERT: v 86 GLU cc_start: 0.8765 (tt0) cc_final: 0.8478 (tt0) REVERT: v 128 MET cc_start: 0.5387 (mmm) cc_final: 0.5023 (mmm) REVERT: w 52 THR cc_start: 0.9142 (OUTLIER) cc_final: 0.8882 (p) REVERT: w 59 ARG cc_start: 0.8522 (tmt170) cc_final: 0.8194 (tpt170) REVERT: w 71 HIS cc_start: 0.7781 (OUTLIER) cc_final: 0.7540 (m-70) REVERT: w 86 MET cc_start: 0.7756 (mmp) cc_final: 0.6571 (mtt) REVERT: w 141 CYS cc_start: 0.8015 (m) cc_final: 0.7442 (p) REVERT: w 163 ARG cc_start: 0.6249 (mmp80) cc_final: 0.5737 (ttp80) REVERT: w 179 THR cc_start: 0.8542 (m) cc_final: 0.8250 (p) REVERT: w 271 GLN cc_start: 0.8281 (OUTLIER) cc_final: 0.6628 (tt0) REVERT: x 111 GLU cc_start: 0.8151 (OUTLIER) cc_final: 0.7926 (mm-30) REVERT: x 170 ASN cc_start: 0.8771 (OUTLIER) cc_final: 0.8444 (p0) outliers start: 156 outliers final: 101 residues processed: 630 average time/residue: 0.4342 time to fit residues: 426.1296 Evaluate side-chains 587 residues out of total 3397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 463 time to evaluate : 3.926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 35 VAL Chi-restraints excluded: chain a residue 117 VAL Chi-restraints excluded: chain a residue 167 THR Chi-restraints excluded: chain a residue 268 CYS Chi-restraints excluded: chain a residue 270 VAL Chi-restraints excluded: chain a residue 277 THR Chi-restraints excluded: chain a residue 335 VAL Chi-restraints excluded: chain a residue 396 VAL Chi-restraints excluded: chain a residue 404 ILE Chi-restraints excluded: chain b residue 40 ILE Chi-restraints excluded: chain b residue 127 THR Chi-restraints excluded: chain b residue 184 LEU Chi-restraints excluded: chain b residue 233 VAL Chi-restraints excluded: chain b residue 238 THR Chi-restraints excluded: chain b residue 281 PHE Chi-restraints excluded: chain b residue 316 LEU Chi-restraints excluded: chain c residue 56 THR Chi-restraints excluded: chain c residue 83 SER Chi-restraints excluded: chain c residue 140 TRP Chi-restraints excluded: chain c residue 236 PHE Chi-restraints excluded: chain c residue 256 ASP Chi-restraints excluded: chain c residue 260 VAL Chi-restraints excluded: chain c residue 274 GLN Chi-restraints excluded: chain c residue 280 VAL Chi-restraints excluded: chain c residue 285 THR Chi-restraints excluded: chain d residue 83 ILE Chi-restraints excluded: chain d residue 89 ILE Chi-restraints excluded: chain d residue 140 LEU Chi-restraints excluded: chain d residue 173 ARG Chi-restraints excluded: chain e residue 19 SER Chi-restraints excluded: chain e residue 39 THR Chi-restraints excluded: chain e residue 49 VAL Chi-restraints excluded: chain e residue 67 LYS Chi-restraints excluded: chain e residue 74 TYR Chi-restraints excluded: chain e residue 89 LEU Chi-restraints excluded: chain e residue 127 GLN Chi-restraints excluded: chain f residue 108 MET Chi-restraints excluded: chain f residue 114 LYS Chi-restraints excluded: chain g residue 14 VAL Chi-restraints excluded: chain g residue 62 VAL Chi-restraints excluded: chain g residue 75 VAL Chi-restraints excluded: chain g residue 94 VAL Chi-restraints excluded: chain g residue 112 VAL Chi-restraints excluded: chain g residue 113 ILE Chi-restraints excluded: chain g residue 121 THR Chi-restraints excluded: chain g residue 126 ILE Chi-restraints excluded: chain g residue 138 THR Chi-restraints excluded: chain h residue 33 LYS Chi-restraints excluded: chain h residue 50 LEU Chi-restraints excluded: chain h residue 98 ILE Chi-restraints excluded: chain h residue 151 GLU Chi-restraints excluded: chain h residue 176 GLU Chi-restraints excluded: chain h residue 204 GLN Chi-restraints excluded: chain h residue 233 THR Chi-restraints excluded: chain h residue 234 ILE Chi-restraints excluded: chain i residue 66 VAL Chi-restraints excluded: chain i residue 145 PHE Chi-restraints excluded: chain i residue 162 THR Chi-restraints excluded: chain i residue 177 ARG Chi-restraints excluded: chain i residue 186 VAL Chi-restraints excluded: chain i residue 196 GLN Chi-restraints excluded: chain i residue 221 THR Chi-restraints excluded: chain j residue 60 THR Chi-restraints excluded: chain j residue 84 TYR Chi-restraints excluded: chain j residue 130 HIS Chi-restraints excluded: chain j residue 253 VAL Chi-restraints excluded: chain j residue 276 LEU Chi-restraints excluded: chain k residue 116 HIS Chi-restraints excluded: chain k residue 151 THR Chi-restraints excluded: chain k residue 154 GLU Chi-restraints excluded: chain k residue 166 PHE Chi-restraints excluded: chain k residue 174 ILE Chi-restraints excluded: chain l residue 39 VAL Chi-restraints excluded: chain l residue 99 ASP Chi-restraints excluded: chain l residue 125 GLU Chi-restraints excluded: chain l residue 135 THR Chi-restraints excluded: chain m residue 83 VAL Chi-restraints excluded: chain m residue 124 VAL Chi-restraints excluded: chain m residue 127 VAL Chi-restraints excluded: chain m residue 133 VAL Chi-restraints excluded: chain n residue 46 ARG Chi-restraints excluded: chain n residue 66 PHE Chi-restraints excluded: chain n residue 92 ILE Chi-restraints excluded: chain n residue 105 ASP Chi-restraints excluded: chain o residue 48 ASP Chi-restraints excluded: chain o residue 99 LEU Chi-restraints excluded: chain p residue 27 VAL Chi-restraints excluded: chain p residue 50 SER Chi-restraints excluded: chain p residue 75 ILE Chi-restraints excluded: chain p residue 82 THR Chi-restraints excluded: chain t residue 9 ARG Chi-restraints excluded: chain t residue 12 ILE Chi-restraints excluded: chain t residue 18 ILE Chi-restraints excluded: chain t residue 32 LYS Chi-restraints excluded: chain t residue 98 THR Chi-restraints excluded: chain t residue 101 TRP Chi-restraints excluded: chain u residue 104 LEU Chi-restraints excluded: chain u residue 110 ILE Chi-restraints excluded: chain u residue 114 VAL Chi-restraints excluded: chain u residue 129 SER Chi-restraints excluded: chain v residue 103 LEU Chi-restraints excluded: chain w residue 52 THR Chi-restraints excluded: chain w residue 71 HIS Chi-restraints excluded: chain w residue 92 VAL Chi-restraints excluded: chain w residue 97 THR Chi-restraints excluded: chain w residue 166 ILE Chi-restraints excluded: chain w residue 189 LEU Chi-restraints excluded: chain w residue 205 LEU Chi-restraints excluded: chain w residue 209 GLU Chi-restraints excluded: chain w residue 250 SER Chi-restraints excluded: chain w residue 271 GLN Chi-restraints excluded: chain w residue 282 THR Chi-restraints excluded: chain w residue 316 VAL Chi-restraints excluded: chain w residue 345 VAL Chi-restraints excluded: chain w residue 356 THR Chi-restraints excluded: chain w residue 415 LEU Chi-restraints excluded: chain w residue 419 LEU Chi-restraints excluded: chain x residue 41 ILE Chi-restraints excluded: chain x residue 54 THR Chi-restraints excluded: chain x residue 56 THR Chi-restraints excluded: chain x residue 104 ILE Chi-restraints excluded: chain x residue 111 GLU Chi-restraints excluded: chain x residue 170 ASN Chi-restraints excluded: chain x residue 193 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 371 random chunks: chunk 298 optimal weight: 7.9990 chunk 11 optimal weight: 8.9990 chunk 171 optimal weight: 0.0010 chunk 256 optimal weight: 2.9990 chunk 40 optimal weight: 0.9980 chunk 223 optimal weight: 6.9990 chunk 149 optimal weight: 20.0000 chunk 293 optimal weight: 8.9990 chunk 15 optimal weight: 10.0000 chunk 161 optimal weight: 9.9990 chunk 99 optimal weight: 20.0000 overall best weight: 3.7992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 163 HIS ** b 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 274 GLN g 107 GLN g 135 ASN k 66 GLN k 116 HIS k 177 ASN ** w 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 321 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.158824 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.138177 restraints weight = 76242.655| |-----------------------------------------------------------------------------| r_work (start): 0.3723 rms_B_bonded: 3.29 r_work: 0.3460 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3460 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7851 moved from start: 0.5555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 32717 Z= 0.153 Angle : 0.609 12.746 44264 Z= 0.311 Chirality : 0.042 0.272 4715 Planarity : 0.005 0.071 5773 Dihedral : 6.370 77.203 4476 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.96 % Favored : 95.96 % Rotamer: Outliers : 4.62 % Allowed : 19.87 % Favored : 75.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.37 (0.14), residues: 3785 helix: 1.07 (0.14), residues: 1419 sheet: 0.43 (0.22), residues: 547 loop : -0.41 (0.14), residues: 1819 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP w 66 HIS 0.023 0.001 HIS w 71 PHE 0.053 0.002 PHE d 169 TYR 0.023 0.001 TYR i 245 ARG 0.013 0.001 ARG d 151 Details of bonding type rmsd link_TRANS : bond 0.00086 ( 3) link_TRANS : angle 0.34287 ( 9) hydrogen bonds : bond 0.03730 ( 1304) hydrogen bonds : angle 4.68254 ( 3750) metal coordination : bond 0.00434 ( 3) covalent geometry : bond 0.00358 (32711) covalent geometry : angle 0.60890 (44255) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7570 Ramachandran restraints generated. 3785 Oldfield, 0 Emsley, 3785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7570 Ramachandran restraints generated. 3785 Oldfield, 0 Emsley, 3785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 655 residues out of total 3397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 157 poor density : 498 time to evaluate : 3.900 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 347 THR cc_start: 0.8144 (m) cc_final: 0.7902 (m) REVERT: a 395 LYS cc_start: 0.5014 (mptt) cc_final: 0.4577 (mmtt) REVERT: a 404 ILE cc_start: 0.8861 (OUTLIER) cc_final: 0.8596 (mt) REVERT: b 52 ARG cc_start: 0.8144 (mtt180) cc_final: 0.7644 (ttt90) REVERT: b 184 LEU cc_start: 0.7948 (OUTLIER) cc_final: 0.7690 (pp) REVERT: b 281 PHE cc_start: 0.1897 (OUTLIER) cc_final: 0.1164 (p90) REVERT: c 90 MET cc_start: 0.7954 (mtp) cc_final: 0.7733 (tmm) REVERT: d 83 ILE cc_start: 0.2429 (OUTLIER) cc_final: 0.1985 (mt) REVERT: d 140 LEU cc_start: 0.7499 (OUTLIER) cc_final: 0.7017 (tp) REVERT: d 150 LEU cc_start: 0.6126 (tp) cc_final: 0.5806 (tt) REVERT: e 28 ARG cc_start: 0.8817 (ttt180) cc_final: 0.7189 (mpt180) REVERT: e 67 LYS cc_start: 0.7626 (OUTLIER) cc_final: 0.7359 (mtmm) REVERT: e 71 TYR cc_start: 0.8232 (m-80) cc_final: 0.6489 (t80) REVERT: e 74 TYR cc_start: 0.7918 (OUTLIER) cc_final: 0.6977 (m-10) REVERT: e 115 TYR cc_start: 0.7738 (m-80) cc_final: 0.7237 (m-80) REVERT: e 122 GLU cc_start: 0.7385 (pp20) cc_final: 0.7063 (tm-30) REVERT: e 127 GLN cc_start: 0.8249 (OUTLIER) cc_final: 0.7981 (mp10) REVERT: e 131 LYS cc_start: 0.8175 (tptt) cc_final: 0.7785 (mptt) REVERT: f 56 ARG cc_start: 0.8389 (mtt180) cc_final: 0.7016 (tpm170) REVERT: f 132 ARG cc_start: 0.8893 (mmt180) cc_final: 0.7303 (mtt180) REVERT: f 134 ARG cc_start: 0.8497 (ttt-90) cc_final: 0.7860 (mpt180) REVERT: g 14 VAL cc_start: 0.8853 (OUTLIER) cc_final: 0.8551 (t) REVERT: g 36 ASP cc_start: 0.7548 (m-30) cc_final: 0.7177 (p0) REVERT: g 117 LYS cc_start: 0.8845 (pttt) cc_final: 0.7932 (mmmt) REVERT: h 36 ARG cc_start: 0.6939 (mtt180) cc_final: 0.5743 (mtm180) REVERT: h 52 ARG cc_start: 0.6393 (OUTLIER) cc_final: 0.6081 (ttp-110) REVERT: h 204 GLN cc_start: 0.8412 (OUTLIER) cc_final: 0.8049 (mp-120) REVERT: h 234 ILE cc_start: 0.8579 (OUTLIER) cc_final: 0.8211 (tp) REVERT: h 235 THR cc_start: 0.7730 (p) cc_final: 0.7289 (t) REVERT: i 137 PHE cc_start: 0.7192 (t80) cc_final: 0.6985 (t80) REVERT: i 140 LYS cc_start: 0.7508 (ttpt) cc_final: 0.6899 (ptmm) REVERT: i 143 ASP cc_start: 0.8263 (t0) cc_final: 0.7923 (m-30) REVERT: i 145 PHE cc_start: 0.7437 (OUTLIER) cc_final: 0.6823 (t80) REVERT: i 175 ASP cc_start: 0.6615 (m-30) cc_final: 0.5907 (t0) REVERT: i 209 TYR cc_start: 0.6460 (m-80) cc_final: 0.6040 (m-80) REVERT: i 240 ARG cc_start: 0.7017 (tpt170) cc_final: 0.6378 (ptt90) REVERT: i 291 GLU cc_start: 0.6173 (tt0) cc_final: 0.5760 (mm-30) REVERT: j 124 TRP cc_start: 0.4823 (m-10) cc_final: 0.4383 (t-100) REVERT: k 58 ARG cc_start: 0.7980 (ttt180) cc_final: 0.6939 (mmp-170) REVERT: k 132 MET cc_start: 0.6483 (tmm) cc_final: 0.6230 (mmm) REVERT: k 151 THR cc_start: 0.6408 (OUTLIER) cc_final: 0.6056 (p) REVERT: m 57 GLN cc_start: 0.6487 (pt0) cc_final: 0.5409 (mp10) REVERT: m 68 GLN cc_start: 0.8082 (mm-40) cc_final: 0.7443 (mp10) REVERT: m 77 GLU cc_start: 0.8233 (pt0) cc_final: 0.7806 (pt0) REVERT: m 89 ASP cc_start: 0.8401 (m-30) cc_final: 0.7944 (m-30) REVERT: m 90 ILE cc_start: 0.8724 (mp) cc_final: 0.8232 (mm) REVERT: m 125 ARG cc_start: 0.7766 (ptm160) cc_final: 0.7221 (ttm110) REVERT: m 129 ASP cc_start: 0.7927 (m-30) cc_final: 0.7648 (m-30) REVERT: n 46 ARG cc_start: 0.8534 (OUTLIER) cc_final: 0.5407 (mtp-110) REVERT: n 75 LYS cc_start: 0.7438 (mmtt) cc_final: 0.6902 (tmtt) REVERT: n 92 ILE cc_start: 0.9213 (OUTLIER) cc_final: 0.8815 (mt) REVERT: n 128 ARG cc_start: 0.7427 (mmt90) cc_final: 0.4859 (mtm180) REVERT: o 48 ASP cc_start: 0.7570 (OUTLIER) cc_final: 0.6919 (p0) REVERT: o 61 LYS cc_start: 0.8265 (mmtt) cc_final: 0.7831 (mtmt) REVERT: o 65 ARG cc_start: 0.7986 (OUTLIER) cc_final: 0.7728 (ttm170) REVERT: p 40 GLU cc_start: 0.4771 (mp0) cc_final: 0.4343 (tt0) REVERT: p 85 GLU cc_start: 0.6007 (tt0) cc_final: 0.5169 (mm-30) REVERT: t 9 ARG cc_start: 0.7521 (OUTLIER) cc_final: 0.5122 (ptt180) REVERT: t 60 ARG cc_start: 0.8489 (mmt90) cc_final: 0.7793 (mmp-170) REVERT: t 98 THR cc_start: 0.7793 (OUTLIER) cc_final: 0.7527 (m) REVERT: u 59 TRP cc_start: 0.7530 (m100) cc_final: 0.4995 (t60) REVERT: u 70 ASP cc_start: 0.7762 (t0) cc_final: 0.7549 (t0) REVERT: u 118 LEU cc_start: 0.8474 (mt) cc_final: 0.8139 (mt) REVERT: u 148 ASP cc_start: 0.8040 (t70) cc_final: 0.7769 (t70) REVERT: u 151 GLN cc_start: 0.8871 (tp40) cc_final: 0.8416 (tp40) REVERT: u 186 ARG cc_start: 0.5788 (mtt-85) cc_final: 0.4506 (ptt180) REVERT: u 191 ARG cc_start: 0.7279 (ptm-80) cc_final: 0.6858 (ptp-110) REVERT: v 86 GLU cc_start: 0.8775 (tt0) cc_final: 0.8503 (tt0) REVERT: v 128 MET cc_start: 0.5164 (mmm) cc_final: 0.4308 (mmm) REVERT: w 52 THR cc_start: 0.9187 (OUTLIER) cc_final: 0.8946 (p) REVERT: w 86 MET cc_start: 0.7630 (mmp) cc_final: 0.6546 (mtt) REVERT: w 141 CYS cc_start: 0.7768 (m) cc_final: 0.7297 (p) REVERT: w 163 ARG cc_start: 0.6248 (mmp80) cc_final: 0.5864 (ttp80) REVERT: w 179 THR cc_start: 0.8426 (m) cc_final: 0.8212 (p) REVERT: w 271 GLN cc_start: 0.8309 (OUTLIER) cc_final: 0.6596 (tt0) REVERT: x 99 MET cc_start: 0.8294 (tpp) cc_final: 0.7942 (tpp) REVERT: x 170 ASN cc_start: 0.8777 (OUTLIER) cc_final: 0.8409 (p0) outliers start: 157 outliers final: 106 residues processed: 617 average time/residue: 0.4393 time to fit residues: 422.3258 Evaluate side-chains 598 residues out of total 3397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 129 poor density : 469 time to evaluate : 3.689 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 35 VAL Chi-restraints excluded: chain a residue 64 MET Chi-restraints excluded: chain a residue 117 VAL Chi-restraints excluded: chain a residue 270 VAL Chi-restraints excluded: chain a residue 277 THR Chi-restraints excluded: chain a residue 335 VAL Chi-restraints excluded: chain a residue 396 VAL Chi-restraints excluded: chain a residue 404 ILE Chi-restraints excluded: chain b residue 40 ILE Chi-restraints excluded: chain b residue 127 THR Chi-restraints excluded: chain b residue 163 HIS Chi-restraints excluded: chain b residue 184 LEU Chi-restraints excluded: chain b residue 233 VAL Chi-restraints excluded: chain b residue 238 THR Chi-restraints excluded: chain b residue 281 PHE Chi-restraints excluded: chain b residue 316 LEU Chi-restraints excluded: chain c residue 56 THR Chi-restraints excluded: chain c residue 140 TRP Chi-restraints excluded: chain c residue 177 CYS Chi-restraints excluded: chain c residue 236 PHE Chi-restraints excluded: chain c residue 256 ASP Chi-restraints excluded: chain c residue 260 VAL Chi-restraints excluded: chain c residue 280 VAL Chi-restraints excluded: chain c residue 285 THR Chi-restraints excluded: chain d residue 83 ILE Chi-restraints excluded: chain d residue 89 ILE Chi-restraints excluded: chain d residue 140 LEU Chi-restraints excluded: chain e residue 19 SER Chi-restraints excluded: chain e residue 39 THR Chi-restraints excluded: chain e residue 49 VAL Chi-restraints excluded: chain e residue 60 VAL Chi-restraints excluded: chain e residue 67 LYS Chi-restraints excluded: chain e residue 74 TYR Chi-restraints excluded: chain e residue 127 GLN Chi-restraints excluded: chain f residue 59 VAL Chi-restraints excluded: chain f residue 108 MET Chi-restraints excluded: chain f residue 109 ILE Chi-restraints excluded: chain g residue 14 VAL Chi-restraints excluded: chain g residue 61 VAL Chi-restraints excluded: chain g residue 62 VAL Chi-restraints excluded: chain g residue 75 VAL Chi-restraints excluded: chain g residue 94 VAL Chi-restraints excluded: chain g residue 112 VAL Chi-restraints excluded: chain g residue 113 ILE Chi-restraints excluded: chain g residue 121 THR Chi-restraints excluded: chain g residue 126 ILE Chi-restraints excluded: chain g residue 138 THR Chi-restraints excluded: chain h residue 33 LYS Chi-restraints excluded: chain h residue 45 LEU Chi-restraints excluded: chain h residue 50 LEU Chi-restraints excluded: chain h residue 52 ARG Chi-restraints excluded: chain h residue 98 ILE Chi-restraints excluded: chain h residue 151 GLU Chi-restraints excluded: chain h residue 176 GLU Chi-restraints excluded: chain h residue 204 GLN Chi-restraints excluded: chain h residue 234 ILE Chi-restraints excluded: chain h residue 307 PHE Chi-restraints excluded: chain i residue 66 VAL Chi-restraints excluded: chain i residue 134 ILE Chi-restraints excluded: chain i residue 145 PHE Chi-restraints excluded: chain i residue 177 ARG Chi-restraints excluded: chain i residue 186 VAL Chi-restraints excluded: chain i residue 196 GLN Chi-restraints excluded: chain i residue 221 THR Chi-restraints excluded: chain j residue 60 THR Chi-restraints excluded: chain j residue 84 TYR Chi-restraints excluded: chain j residue 130 HIS Chi-restraints excluded: chain j residue 139 GLU Chi-restraints excluded: chain j residue 276 LEU Chi-restraints excluded: chain k residue 116 HIS Chi-restraints excluded: chain k residue 151 THR Chi-restraints excluded: chain k residue 154 GLU Chi-restraints excluded: chain k residue 166 PHE Chi-restraints excluded: chain k residue 174 ILE Chi-restraints excluded: chain l residue 99 ASP Chi-restraints excluded: chain l residue 125 GLU Chi-restraints excluded: chain l residue 135 THR Chi-restraints excluded: chain m residue 127 VAL Chi-restraints excluded: chain m residue 128 LEU Chi-restraints excluded: chain m residue 133 VAL Chi-restraints excluded: chain n residue 37 THR Chi-restraints excluded: chain n residue 46 ARG Chi-restraints excluded: chain n residue 66 PHE Chi-restraints excluded: chain n residue 92 ILE Chi-restraints excluded: chain n residue 105 ASP Chi-restraints excluded: chain o residue 30 GLN Chi-restraints excluded: chain o residue 48 ASP Chi-restraints excluded: chain o residue 65 ARG Chi-restraints excluded: chain o residue 99 LEU Chi-restraints excluded: chain p residue 27 VAL Chi-restraints excluded: chain p residue 50 SER Chi-restraints excluded: chain p residue 75 ILE Chi-restraints excluded: chain p residue 82 THR Chi-restraints excluded: chain t residue 9 ARG Chi-restraints excluded: chain t residue 12 ILE Chi-restraints excluded: chain t residue 18 ILE Chi-restraints excluded: chain t residue 32 LYS Chi-restraints excluded: chain t residue 55 THR Chi-restraints excluded: chain t residue 98 THR Chi-restraints excluded: chain t residue 101 TRP Chi-restraints excluded: chain u residue 104 LEU Chi-restraints excluded: chain u residue 110 ILE Chi-restraints excluded: chain u residue 114 VAL Chi-restraints excluded: chain u residue 129 SER Chi-restraints excluded: chain v residue 38 ARG Chi-restraints excluded: chain v residue 103 LEU Chi-restraints excluded: chain w residue 52 THR Chi-restraints excluded: chain w residue 92 VAL Chi-restraints excluded: chain w residue 97 THR Chi-restraints excluded: chain w residue 166 ILE Chi-restraints excluded: chain w residue 188 VAL Chi-restraints excluded: chain w residue 189 LEU Chi-restraints excluded: chain w residue 205 LEU Chi-restraints excluded: chain w residue 209 GLU Chi-restraints excluded: chain w residue 250 SER Chi-restraints excluded: chain w residue 271 GLN Chi-restraints excluded: chain w residue 274 ASN Chi-restraints excluded: chain w residue 282 THR Chi-restraints excluded: chain w residue 316 VAL Chi-restraints excluded: chain w residue 345 VAL Chi-restraints excluded: chain w residue 356 THR Chi-restraints excluded: chain w residue 415 LEU Chi-restraints excluded: chain w residue 419 LEU Chi-restraints excluded: chain x residue 41 ILE Chi-restraints excluded: chain x residue 49 ILE Chi-restraints excluded: chain x residue 54 THR Chi-restraints excluded: chain x residue 56 THR Chi-restraints excluded: chain x residue 104 ILE Chi-restraints excluded: chain x residue 170 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 371 random chunks: chunk 339 optimal weight: 20.0000 chunk 139 optimal weight: 2.9990 chunk 316 optimal weight: 10.0000 chunk 281 optimal weight: 5.9990 chunk 209 optimal weight: 8.9990 chunk 91 optimal weight: 5.9990 chunk 313 optimal weight: 8.9990 chunk 341 optimal weight: 6.9990 chunk 323 optimal weight: 10.0000 chunk 335 optimal weight: 2.9990 chunk 40 optimal weight: 0.7980 overall best weight: 3.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 163 HIS ** b 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 88 GLN g 107 GLN j 198 ASN j 252 HIS k 108 GLN k 116 HIS k 158 GLN ** w 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 321 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** x 164 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.139478 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.121850 restraints weight = 87467.295| |-----------------------------------------------------------------------------| r_work (start): 0.3730 rms_B_bonded: 3.57 r_work: 0.3401 rms_B_bonded: 4.45 restraints_weight: 0.5000 r_work (final): 0.3401 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7936 moved from start: 0.5734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 32717 Z= 0.151 Angle : 0.611 12.706 44264 Z= 0.312 Chirality : 0.042 0.237 4715 Planarity : 0.005 0.063 5773 Dihedral : 6.226 72.345 4473 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.86 % Favored : 96.06 % Rotamer: Outliers : 4.45 % Allowed : 20.28 % Favored : 75.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.38 (0.14), residues: 3785 helix: 1.09 (0.14), residues: 1413 sheet: 0.42 (0.22), residues: 551 loop : -0.41 (0.14), residues: 1821 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP t 101 HIS 0.033 0.001 HIS b 163 PHE 0.022 0.002 PHE d 169 TYR 0.023 0.001 TYR i 245 ARG 0.009 0.001 ARG d 151 Details of bonding type rmsd link_TRANS : bond 0.00081 ( 3) link_TRANS : angle 0.33509 ( 9) hydrogen bonds : bond 0.03713 ( 1304) hydrogen bonds : angle 4.65205 ( 3750) metal coordination : bond 0.00337 ( 3) covalent geometry : bond 0.00354 (32711) covalent geometry : angle 0.61090 (44255) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7570 Ramachandran restraints generated. 3785 Oldfield, 0 Emsley, 3785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7570 Ramachandran restraints generated. 3785 Oldfield, 0 Emsley, 3785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 655 residues out of total 3397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 151 poor density : 504 time to evaluate : 3.553 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: a 347 THR cc_start: 0.8101 (m) cc_final: 0.7855 (m) REVERT: a 371 LYS cc_start: 0.8431 (OUTLIER) cc_final: 0.7281 (mmtt) REVERT: a 395 LYS cc_start: 0.5168 (mptt) cc_final: 0.4195 (mmtt) REVERT: a 404 ILE cc_start: 0.8882 (OUTLIER) cc_final: 0.8636 (mt) REVERT: b 27 ARG cc_start: 0.4526 (ptt180) cc_final: 0.3296 (ptt-90) REVERT: b 52 ARG cc_start: 0.8433 (mtt180) cc_final: 0.7688 (ttt90) REVERT: b 281 PHE cc_start: 0.3142 (OUTLIER) cc_final: 0.2042 (p90) REVERT: c 90 MET cc_start: 0.8200 (mtp) cc_final: 0.7819 (tmm) REVERT: d 83 ILE cc_start: 0.2005 (OUTLIER) cc_final: 0.1623 (mt) REVERT: d 140 LEU cc_start: 0.7307 (OUTLIER) cc_final: 0.6756 (tp) REVERT: e 28 ARG cc_start: 0.8741 (ttt180) cc_final: 0.7212 (mpt180) REVERT: e 67 LYS cc_start: 0.7755 (OUTLIER) cc_final: 0.7470 (mtmm) REVERT: e 71 TYR cc_start: 0.8073 (m-80) cc_final: 0.6491 (t80) REVERT: e 74 TYR cc_start: 0.7881 (OUTLIER) cc_final: 0.7012 (m-10) REVERT: e 115 TYR cc_start: 0.7793 (m-80) cc_final: 0.7255 (m-80) REVERT: e 122 GLU cc_start: 0.7679 (pp20) cc_final: 0.7335 (tm-30) REVERT: e 127 GLN cc_start: 0.8378 (OUTLIER) cc_final: 0.8049 (mp10) REVERT: e 131 LYS cc_start: 0.8310 (tptt) cc_final: 0.7768 (mptt) REVERT: f 56 ARG cc_start: 0.8560 (mtt180) cc_final: 0.7003 (tpm170) REVERT: f 114 LYS cc_start: 0.8799 (ttpp) cc_final: 0.8590 (ttpp) REVERT: f 132 ARG cc_start: 0.8879 (mmt180) cc_final: 0.7297 (mtt180) REVERT: f 134 ARG cc_start: 0.8571 (ttt-90) cc_final: 0.7858 (mpt180) REVERT: f 141 ASP cc_start: 0.7914 (t70) cc_final: 0.7522 (t0) REVERT: g 36 ASP cc_start: 0.7717 (m-30) cc_final: 0.7282 (p0) REVERT: g 117 LYS cc_start: 0.8953 (pttt) cc_final: 0.8065 (mmmt) REVERT: h 36 ARG cc_start: 0.7067 (mtt180) cc_final: 0.5946 (mtm180) REVERT: h 204 GLN cc_start: 0.8537 (OUTLIER) cc_final: 0.8181 (mp-120) REVERT: h 234 ILE cc_start: 0.8691 (OUTLIER) cc_final: 0.8210 (tp) REVERT: h 235 THR cc_start: 0.8242 (p) cc_final: 0.7741 (t) REVERT: i 139 GLU cc_start: 0.8168 (mm-30) cc_final: 0.7648 (mm-30) REVERT: i 143 ASP cc_start: 0.8548 (t0) cc_final: 0.8087 (m-30) REVERT: i 145 PHE cc_start: 0.7394 (OUTLIER) cc_final: 0.6688 (t80) REVERT: i 175 ASP cc_start: 0.6623 (m-30) cc_final: 0.5948 (t0) REVERT: i 209 TYR cc_start: 0.6649 (m-80) cc_final: 0.6184 (m-80) REVERT: i 240 ARG cc_start: 0.6918 (tpt170) cc_final: 0.6098 (ptt90) REVERT: i 246 VAL cc_start: 0.7157 (OUTLIER) cc_final: 0.6912 (t) REVERT: i 291 GLU cc_start: 0.5838 (tt0) cc_final: 0.5498 (mm-30) REVERT: j 124 TRP cc_start: 0.5142 (m-10) cc_final: 0.4697 (t60) REVERT: k 58 ARG cc_start: 0.8015 (ttt180) cc_final: 0.6960 (mmp-170) REVERT: k 132 MET cc_start: 0.6652 (tmm) cc_final: 0.6279 (mmm) REVERT: k 151 THR cc_start: 0.6784 (OUTLIER) cc_final: 0.6355 (p) REVERT: l 40 GLU cc_start: 0.6851 (OUTLIER) cc_final: 0.5057 (tp30) REVERT: m 57 GLN cc_start: 0.6598 (pt0) cc_final: 0.5327 (mp10) REVERT: m 68 GLN cc_start: 0.8338 (mm-40) cc_final: 0.7642 (mp10) REVERT: m 89 ASP cc_start: 0.8600 (m-30) cc_final: 0.8177 (m-30) REVERT: m 90 ILE cc_start: 0.8754 (mp) cc_final: 0.8384 (mm) REVERT: m 125 ARG cc_start: 0.8088 (ptm160) cc_final: 0.7436 (ttm110) REVERT: m 129 ASP cc_start: 0.8197 (m-30) cc_final: 0.7875 (m-30) REVERT: n 46 ARG cc_start: 0.8563 (OUTLIER) cc_final: 0.5110 (mtp180) REVERT: n 75 LYS cc_start: 0.7574 (mmtt) cc_final: 0.7005 (tmtt) REVERT: n 92 ILE cc_start: 0.9203 (OUTLIER) cc_final: 0.8827 (mt) REVERT: n 128 ARG cc_start: 0.7478 (mmt90) cc_final: 0.5315 (mtt180) REVERT: o 48 ASP cc_start: 0.7692 (OUTLIER) cc_final: 0.7018 (p0) REVERT: o 61 LYS cc_start: 0.8383 (mmtt) cc_final: 0.7857 (mtmt) REVERT: o 65 ARG cc_start: 0.8172 (OUTLIER) cc_final: 0.7913 (ttm170) REVERT: p 40 GLU cc_start: 0.4961 (mp0) cc_final: 0.4582 (tt0) REVERT: p 85 GLU cc_start: 0.6694 (tt0) cc_final: 0.5711 (mm-30) REVERT: q 128 ARG cc_start: 0.7874 (ttt180) cc_final: 0.7625 (mtt180) REVERT: q 134 LYS cc_start: 0.7489 (mmtt) cc_final: 0.7165 (mmtt) REVERT: t 9 ARG cc_start: 0.7851 (OUTLIER) cc_final: 0.4957 (ptt180) REVERT: t 60 ARG cc_start: 0.8541 (mmt90) cc_final: 0.7805 (mmp-170) REVERT: t 98 THR cc_start: 0.7972 (OUTLIER) cc_final: 0.7725 (m) REVERT: u 59 TRP cc_start: 0.7468 (m100) cc_final: 0.4792 (t60) REVERT: u 70 ASP cc_start: 0.7729 (t0) cc_final: 0.7491 (t0) REVERT: u 118 LEU cc_start: 0.8537 (mt) cc_final: 0.8113 (mt) REVERT: u 148 ASP cc_start: 0.8119 (t70) cc_final: 0.7818 (t70) REVERT: u 186 ARG cc_start: 0.6050 (mtt-85) cc_final: 0.4649 (ptt180) REVERT: v 86 GLU cc_start: 0.8818 (tt0) cc_final: 0.8533 (tt0) REVERT: w 52 THR cc_start: 0.9207 (OUTLIER) cc_final: 0.8984 (p) REVERT: w 86 MET cc_start: 0.7883 (mmp) cc_final: 0.6686 (mtt) REVERT: w 141 CYS cc_start: 0.8206 (m) cc_final: 0.7637 (p) REVERT: w 163 ARG cc_start: 0.6587 (mmp80) cc_final: 0.5904 (ttp80) REVERT: w 179 THR cc_start: 0.8464 (m) cc_final: 0.8237 (p) REVERT: x 99 MET cc_start: 0.8366 (tpp) cc_final: 0.8031 (tpp) REVERT: x 170 ASN cc_start: 0.8865 (OUTLIER) cc_final: 0.8480 (p0) outliers start: 151 outliers final: 112 residues processed: 616 average time/residue: 0.4440 time to fit residues: 422.1730 Evaluate side-chains 608 residues out of total 3397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 134 poor density : 474 time to evaluate : 3.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 35 VAL Chi-restraints excluded: chain a residue 117 VAL Chi-restraints excluded: chain a residue 270 VAL Chi-restraints excluded: chain a residue 277 THR Chi-restraints excluded: chain a residue 335 VAL Chi-restraints excluded: chain a residue 371 LYS Chi-restraints excluded: chain a residue 396 VAL Chi-restraints excluded: chain a residue 404 ILE Chi-restraints excluded: chain b residue 40 ILE Chi-restraints excluded: chain b residue 127 THR Chi-restraints excluded: chain b residue 233 VAL Chi-restraints excluded: chain b residue 238 THR Chi-restraints excluded: chain b residue 281 PHE Chi-restraints excluded: chain b residue 316 LEU Chi-restraints excluded: chain c residue 43 ASP Chi-restraints excluded: chain c residue 56 THR Chi-restraints excluded: chain c residue 140 TRP Chi-restraints excluded: chain c residue 177 CYS Chi-restraints excluded: chain c residue 236 PHE Chi-restraints excluded: chain c residue 256 ASP Chi-restraints excluded: chain c residue 260 VAL Chi-restraints excluded: chain c residue 280 VAL Chi-restraints excluded: chain c residue 285 THR Chi-restraints excluded: chain d residue 83 ILE Chi-restraints excluded: chain d residue 89 ILE Chi-restraints excluded: chain d residue 140 LEU Chi-restraints excluded: chain e residue 19 SER Chi-restraints excluded: chain e residue 39 THR Chi-restraints excluded: chain e residue 49 VAL Chi-restraints excluded: chain e residue 60 VAL Chi-restraints excluded: chain e residue 67 LYS Chi-restraints excluded: chain e residue 74 TYR Chi-restraints excluded: chain e residue 89 LEU Chi-restraints excluded: chain e residue 127 GLN Chi-restraints excluded: chain f residue 59 VAL Chi-restraints excluded: chain f residue 108 MET Chi-restraints excluded: chain f residue 109 ILE Chi-restraints excluded: chain g residue 14 VAL Chi-restraints excluded: chain g residue 61 VAL Chi-restraints excluded: chain g residue 62 VAL Chi-restraints excluded: chain g residue 75 VAL Chi-restraints excluded: chain g residue 94 VAL Chi-restraints excluded: chain g residue 112 VAL Chi-restraints excluded: chain g residue 113 ILE Chi-restraints excluded: chain g residue 121 THR Chi-restraints excluded: chain g residue 126 ILE Chi-restraints excluded: chain g residue 138 THR Chi-restraints excluded: chain h residue 33 LYS Chi-restraints excluded: chain h residue 45 LEU Chi-restraints excluded: chain h residue 50 LEU Chi-restraints excluded: chain h residue 98 ILE Chi-restraints excluded: chain h residue 151 GLU Chi-restraints excluded: chain h residue 176 GLU Chi-restraints excluded: chain h residue 204 GLN Chi-restraints excluded: chain h residue 234 ILE Chi-restraints excluded: chain h residue 307 PHE Chi-restraints excluded: chain i residue 66 VAL Chi-restraints excluded: chain i residue 116 VAL Chi-restraints excluded: chain i residue 145 PHE Chi-restraints excluded: chain i residue 162 THR Chi-restraints excluded: chain i residue 177 ARG Chi-restraints excluded: chain i residue 186 VAL Chi-restraints excluded: chain i residue 196 GLN Chi-restraints excluded: chain i residue 221 THR Chi-restraints excluded: chain i residue 246 VAL Chi-restraints excluded: chain i residue 253 VAL Chi-restraints excluded: chain j residue 60 THR Chi-restraints excluded: chain j residue 84 TYR Chi-restraints excluded: chain j residue 130 HIS Chi-restraints excluded: chain j residue 139 GLU Chi-restraints excluded: chain j residue 198 ASN Chi-restraints excluded: chain j residue 276 LEU Chi-restraints excluded: chain k residue 116 HIS Chi-restraints excluded: chain k residue 123 GLU Chi-restraints excluded: chain k residue 151 THR Chi-restraints excluded: chain k residue 154 GLU Chi-restraints excluded: chain k residue 166 PHE Chi-restraints excluded: chain k residue 174 ILE Chi-restraints excluded: chain l residue 40 GLU Chi-restraints excluded: chain l residue 99 ASP Chi-restraints excluded: chain l residue 125 GLU Chi-restraints excluded: chain l residue 135 THR Chi-restraints excluded: chain m residue 127 VAL Chi-restraints excluded: chain m residue 133 VAL Chi-restraints excluded: chain n residue 37 THR Chi-restraints excluded: chain n residue 46 ARG Chi-restraints excluded: chain n residue 56 VAL Chi-restraints excluded: chain n residue 66 PHE Chi-restraints excluded: chain n residue 92 ILE Chi-restraints excluded: chain n residue 105 ASP Chi-restraints excluded: chain o residue 30 GLN Chi-restraints excluded: chain o residue 48 ASP Chi-restraints excluded: chain o residue 65 ARG Chi-restraints excluded: chain o residue 99 LEU Chi-restraints excluded: chain p residue 27 VAL Chi-restraints excluded: chain p residue 50 SER Chi-restraints excluded: chain p residue 75 ILE Chi-restraints excluded: chain p residue 82 THR Chi-restraints excluded: chain t residue 9 ARG Chi-restraints excluded: chain t residue 12 ILE Chi-restraints excluded: chain t residue 18 ILE Chi-restraints excluded: chain t residue 32 LYS Chi-restraints excluded: chain t residue 55 THR Chi-restraints excluded: chain t residue 98 THR Chi-restraints excluded: chain t residue 101 TRP Chi-restraints excluded: chain u residue 104 LEU Chi-restraints excluded: chain u residue 110 ILE Chi-restraints excluded: chain u residue 114 VAL Chi-restraints excluded: chain u residue 129 SER Chi-restraints excluded: chain v residue 38 ARG Chi-restraints excluded: chain v residue 103 LEU Chi-restraints excluded: chain w residue 52 THR Chi-restraints excluded: chain w residue 92 VAL Chi-restraints excluded: chain w residue 97 THR Chi-restraints excluded: chain w residue 166 ILE Chi-restraints excluded: chain w residue 188 VAL Chi-restraints excluded: chain w residue 189 LEU Chi-restraints excluded: chain w residue 194 LEU Chi-restraints excluded: chain w residue 205 LEU Chi-restraints excluded: chain w residue 209 GLU Chi-restraints excluded: chain w residue 250 SER Chi-restraints excluded: chain w residue 274 ASN Chi-restraints excluded: chain w residue 282 THR Chi-restraints excluded: chain w residue 316 VAL Chi-restraints excluded: chain w residue 345 VAL Chi-restraints excluded: chain w residue 356 THR Chi-restraints excluded: chain w residue 415 LEU Chi-restraints excluded: chain w residue 418 PHE Chi-restraints excluded: chain w residue 419 LEU Chi-restraints excluded: chain x residue 41 ILE Chi-restraints excluded: chain x residue 54 THR Chi-restraints excluded: chain x residue 56 THR Chi-restraints excluded: chain x residue 104 ILE Chi-restraints excluded: chain x residue 170 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 371 random chunks: chunk 228 optimal weight: 1.9990 chunk 2 optimal weight: 0.0040 chunk 275 optimal weight: 20.0000 chunk 133 optimal weight: 9.9990 chunk 264 optimal weight: 0.8980 chunk 66 optimal weight: 9.9990 chunk 360 optimal weight: 5.9990 chunk 159 optimal weight: 5.9990 chunk 51 optimal weight: 9.9990 chunk 355 optimal weight: 9.9990 chunk 34 optimal weight: 5.9990 overall best weight: 2.9798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 163 HIS b 191 ASN b 275 GLN e 88 GLN g 107 GLN j 198 ASN k 116 HIS w 234 GLN ** w 321 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** x 164 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.139883 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.122073 restraints weight = 87900.488| |-----------------------------------------------------------------------------| r_work (start): 0.3738 rms_B_bonded: 3.74 r_work: 0.3448 rms_B_bonded: 4.25 restraints_weight: 0.5000 r_work (final): 0.3448 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7858 moved from start: 0.5897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 32717 Z= 0.137 Angle : 0.606 12.776 44264 Z= 0.310 Chirality : 0.042 0.236 4715 Planarity : 0.005 0.061 5773 Dihedral : 6.079 68.532 4470 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.94 % Favored : 95.98 % Rotamer: Outliers : 4.62 % Allowed : 20.34 % Favored : 75.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.43 (0.14), residues: 3785 helix: 1.17 (0.14), residues: 1404 sheet: 0.45 (0.22), residues: 551 loop : -0.40 (0.14), residues: 1830 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP t 101 HIS 0.023 0.001 HIS k 116 PHE 0.024 0.001 PHE h 184 TYR 0.023 0.001 TYR i 245 ARG 0.008 0.000 ARG m 123 Details of bonding type rmsd link_TRANS : bond 0.00070 ( 3) link_TRANS : angle 0.34207 ( 9) hydrogen bonds : bond 0.03619 ( 1304) hydrogen bonds : angle 4.60981 ( 3750) metal coordination : bond 0.00281 ( 3) covalent geometry : bond 0.00318 (32711) covalent geometry : angle 0.60635 (44255) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7570 Ramachandran restraints generated. 3785 Oldfield, 0 Emsley, 3785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7570 Ramachandran restraints generated. 3785 Oldfield, 0 Emsley, 3785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 658 residues out of total 3397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 157 poor density : 501 time to evaluate : 3.769 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 347 THR cc_start: 0.8131 (m) cc_final: 0.7836 (m) REVERT: a 371 LYS cc_start: 0.8320 (OUTLIER) cc_final: 0.7277 (mmtt) REVERT: a 395 LYS cc_start: 0.5176 (mptt) cc_final: 0.4178 (mmtt) REVERT: b 27 ARG cc_start: 0.4593 (ptt180) cc_final: 0.3114 (ptt-90) REVERT: b 52 ARG cc_start: 0.8170 (mtt180) cc_final: 0.7823 (ttt90) REVERT: b 227 GLU cc_start: 0.8054 (tp30) cc_final: 0.7514 (tp30) REVERT: b 281 PHE cc_start: 0.2953 (OUTLIER) cc_final: 0.1975 (p90) REVERT: c 90 MET cc_start: 0.8155 (mtp) cc_final: 0.7770 (tmm) REVERT: d 83 ILE cc_start: 0.2098 (OUTLIER) cc_final: 0.1725 (mt) REVERT: d 140 LEU cc_start: 0.7351 (OUTLIER) cc_final: 0.6702 (tp) REVERT: e 28 ARG cc_start: 0.8705 (ttt180) cc_final: 0.7194 (mpt180) REVERT: e 67 LYS cc_start: 0.7706 (OUTLIER) cc_final: 0.7423 (mtmm) REVERT: e 71 TYR cc_start: 0.8083 (m-80) cc_final: 0.6505 (t80) REVERT: e 74 TYR cc_start: 0.7716 (OUTLIER) cc_final: 0.6973 (m-10) REVERT: e 115 TYR cc_start: 0.7483 (m-80) cc_final: 0.6943 (m-80) REVERT: e 122 GLU cc_start: 0.7398 (pp20) cc_final: 0.7131 (tm-30) REVERT: e 127 GLN cc_start: 0.8349 (OUTLIER) cc_final: 0.8017 (mp10) REVERT: e 131 LYS cc_start: 0.8225 (tptt) cc_final: 0.7780 (mptt) REVERT: f 56 ARG cc_start: 0.8580 (mtt180) cc_final: 0.6898 (tpm170) REVERT: f 114 LYS cc_start: 0.8666 (ttpp) cc_final: 0.8460 (ttpp) REVERT: f 132 ARG cc_start: 0.8884 (mmt180) cc_final: 0.7288 (mtt180) REVERT: f 134 ARG cc_start: 0.8497 (ttt-90) cc_final: 0.7820 (mpt180) REVERT: f 141 ASP cc_start: 0.7994 (t70) cc_final: 0.7640 (t0) REVERT: g 117 LYS cc_start: 0.8898 (pttt) cc_final: 0.8076 (mmmt) REVERT: g 122 ASP cc_start: 0.7619 (m-30) cc_final: 0.7203 (m-30) REVERT: g 144 ARG cc_start: 0.7613 (mmt90) cc_final: 0.6661 (mtp180) REVERT: h 36 ARG cc_start: 0.7019 (mtt180) cc_final: 0.5777 (mtm180) REVERT: h 204 GLN cc_start: 0.8424 (OUTLIER) cc_final: 0.8043 (mp-120) REVERT: h 234 ILE cc_start: 0.8640 (OUTLIER) cc_final: 0.8189 (tp) REVERT: h 235 THR cc_start: 0.8135 (p) cc_final: 0.7657 (t) REVERT: h 283 GLU cc_start: 0.7894 (tp30) cc_final: 0.7620 (tp30) REVERT: i 139 GLU cc_start: 0.8155 (mm-30) cc_final: 0.7640 (mm-30) REVERT: i 140 LYS cc_start: 0.7567 (ttpt) cc_final: 0.6937 (ptmm) REVERT: i 143 ASP cc_start: 0.8517 (t0) cc_final: 0.8074 (m-30) REVERT: i 145 PHE cc_start: 0.7338 (OUTLIER) cc_final: 0.6656 (t80) REVERT: i 175 ASP cc_start: 0.6462 (m-30) cc_final: 0.5904 (t0) REVERT: i 209 TYR cc_start: 0.6578 (m-80) cc_final: 0.5976 (m-80) REVERT: i 240 ARG cc_start: 0.6890 (tpt170) cc_final: 0.6129 (ptt90) REVERT: j 72 ASP cc_start: 0.7229 (m-30) cc_final: 0.6994 (t70) REVERT: j 198 ASN cc_start: 0.3775 (OUTLIER) cc_final: 0.3465 (p0) REVERT: k 58 ARG cc_start: 0.8101 (ttt180) cc_final: 0.7021 (mmp-170) REVERT: k 132 MET cc_start: 0.6307 (tmm) cc_final: 0.6104 (mmm) REVERT: k 151 THR cc_start: 0.6766 (OUTLIER) cc_final: 0.6325 (p) REVERT: l 40 GLU cc_start: 0.6791 (OUTLIER) cc_final: 0.4965 (tp30) REVERT: m 57 GLN cc_start: 0.6562 (pt0) cc_final: 0.5476 (mp10) REVERT: m 68 GLN cc_start: 0.8000 (mm-40) cc_final: 0.7532 (mp10) REVERT: m 77 GLU cc_start: 0.8064 (pt0) cc_final: 0.7630 (pt0) REVERT: m 89 ASP cc_start: 0.8528 (m-30) cc_final: 0.8147 (m-30) REVERT: m 90 ILE cc_start: 0.8630 (mp) cc_final: 0.8225 (mm) REVERT: m 125 ARG cc_start: 0.7921 (ptm160) cc_final: 0.7351 (ttm110) REVERT: m 129 ASP cc_start: 0.8202 (m-30) cc_final: 0.7910 (m-30) REVERT: m 136 GLN cc_start: 0.8653 (mt0) cc_final: 0.8447 (mt0) REVERT: m 138 ARG cc_start: 0.5917 (OUTLIER) cc_final: 0.5457 (ptt-90) REVERT: n 46 ARG cc_start: 0.8549 (OUTLIER) cc_final: 0.5086 (mtp180) REVERT: n 75 LYS cc_start: 0.7770 (mmtt) cc_final: 0.7087 (tmtt) REVERT: n 92 ILE cc_start: 0.9201 (OUTLIER) cc_final: 0.8818 (mt) REVERT: n 128 ARG cc_start: 0.7273 (mmt90) cc_final: 0.5444 (mtt180) REVERT: o 48 ASP cc_start: 0.7622 (OUTLIER) cc_final: 0.6953 (p0) REVERT: o 61 LYS cc_start: 0.8284 (mmtt) cc_final: 0.7840 (mtmt) REVERT: p 40 GLU cc_start: 0.4785 (mp0) cc_final: 0.4278 (tt0) REVERT: q 134 LYS cc_start: 0.7547 (mmtt) cc_final: 0.7283 (mmtt) REVERT: t 9 ARG cc_start: 0.7587 (OUTLIER) cc_final: 0.4902 (ptt180) REVERT: t 60 ARG cc_start: 0.8390 (mmt90) cc_final: 0.7745 (mmp-170) REVERT: t 98 THR cc_start: 0.7886 (OUTLIER) cc_final: 0.7618 (m) REVERT: t 100 LYS cc_start: 0.7750 (tppt) cc_final: 0.7058 (tptp) REVERT: u 118 LEU cc_start: 0.8644 (mt) cc_final: 0.8305 (mt) REVERT: u 151 GLN cc_start: 0.8740 (tp40) cc_final: 0.8355 (tp40) REVERT: u 159 GLU cc_start: 0.8012 (pp20) cc_final: 0.7556 (pp20) REVERT: u 186 ARG cc_start: 0.6298 (mtt-85) cc_final: 0.4842 (ptt180) REVERT: v 86 GLU cc_start: 0.8748 (tt0) cc_final: 0.8489 (tt0) REVERT: v 128 MET cc_start: 0.5277 (mmm) cc_final: 0.4332 (mmm) REVERT: w 52 THR cc_start: 0.9182 (OUTLIER) cc_final: 0.8974 (p) REVERT: w 86 MET cc_start: 0.7710 (mmp) cc_final: 0.6456 (mtt) REVERT: w 141 CYS cc_start: 0.8122 (m) cc_final: 0.7482 (p) REVERT: w 163 ARG cc_start: 0.6281 (mmp80) cc_final: 0.5891 (ttp80) REVERT: w 179 THR cc_start: 0.8548 (m) cc_final: 0.8289 (p) REVERT: w 216 ARG cc_start: 0.8888 (OUTLIER) cc_final: 0.7631 (mtt-85) REVERT: x 99 MET cc_start: 0.8293 (tpp) cc_final: 0.7923 (tpp) REVERT: x 170 ASN cc_start: 0.8862 (OUTLIER) cc_final: 0.8520 (p0) outliers start: 157 outliers final: 116 residues processed: 617 average time/residue: 0.4372 time to fit residues: 417.8627 Evaluate side-chains 619 residues out of total 3397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 138 poor density : 481 time to evaluate : 3.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 35 VAL Chi-restraints excluded: chain a residue 117 VAL Chi-restraints excluded: chain a residue 270 VAL Chi-restraints excluded: chain a residue 277 THR Chi-restraints excluded: chain a residue 335 VAL Chi-restraints excluded: chain a residue 371 LYS Chi-restraints excluded: chain a residue 396 VAL Chi-restraints excluded: chain b residue 40 ILE Chi-restraints excluded: chain b residue 127 THR Chi-restraints excluded: chain b residue 163 HIS Chi-restraints excluded: chain b residue 233 VAL Chi-restraints excluded: chain b residue 238 THR Chi-restraints excluded: chain b residue 281 PHE Chi-restraints excluded: chain b residue 316 LEU Chi-restraints excluded: chain c residue 43 ASP Chi-restraints excluded: chain c residue 56 THR Chi-restraints excluded: chain c residue 140 TRP Chi-restraints excluded: chain c residue 177 CYS Chi-restraints excluded: chain c residue 236 PHE Chi-restraints excluded: chain c residue 256 ASP Chi-restraints excluded: chain c residue 260 VAL Chi-restraints excluded: chain c residue 280 VAL Chi-restraints excluded: chain c residue 285 THR Chi-restraints excluded: chain d residue 83 ILE Chi-restraints excluded: chain d residue 89 ILE Chi-restraints excluded: chain d residue 140 LEU Chi-restraints excluded: chain d residue 150 LEU Chi-restraints excluded: chain e residue 19 SER Chi-restraints excluded: chain e residue 39 THR Chi-restraints excluded: chain e residue 49 VAL Chi-restraints excluded: chain e residue 60 VAL Chi-restraints excluded: chain e residue 67 LYS Chi-restraints excluded: chain e residue 74 TYR Chi-restraints excluded: chain e residue 89 LEU Chi-restraints excluded: chain e residue 127 GLN Chi-restraints excluded: chain f residue 59 VAL Chi-restraints excluded: chain f residue 108 MET Chi-restraints excluded: chain f residue 109 ILE Chi-restraints excluded: chain g residue 14 VAL Chi-restraints excluded: chain g residue 61 VAL Chi-restraints excluded: chain g residue 62 VAL Chi-restraints excluded: chain g residue 75 VAL Chi-restraints excluded: chain g residue 94 VAL Chi-restraints excluded: chain g residue 112 VAL Chi-restraints excluded: chain g residue 113 ILE Chi-restraints excluded: chain g residue 121 THR Chi-restraints excluded: chain g residue 126 ILE Chi-restraints excluded: chain g residue 138 THR Chi-restraints excluded: chain h residue 33 LYS Chi-restraints excluded: chain h residue 45 LEU Chi-restraints excluded: chain h residue 98 ILE Chi-restraints excluded: chain h residue 151 GLU Chi-restraints excluded: chain h residue 176 GLU Chi-restraints excluded: chain h residue 204 GLN Chi-restraints excluded: chain h residue 234 ILE Chi-restraints excluded: chain i residue 66 VAL Chi-restraints excluded: chain i residue 116 VAL Chi-restraints excluded: chain i residue 144 ILE Chi-restraints excluded: chain i residue 145 PHE Chi-restraints excluded: chain i residue 172 MET Chi-restraints excluded: chain i residue 186 VAL Chi-restraints excluded: chain i residue 196 GLN Chi-restraints excluded: chain i residue 221 THR Chi-restraints excluded: chain i residue 253 VAL Chi-restraints excluded: chain i residue 258 SER Chi-restraints excluded: chain j residue 60 THR Chi-restraints excluded: chain j residue 84 TYR Chi-restraints excluded: chain j residue 130 HIS Chi-restraints excluded: chain j residue 139 GLU Chi-restraints excluded: chain j residue 198 ASN Chi-restraints excluded: chain j residue 240 THR Chi-restraints excluded: chain j residue 276 LEU Chi-restraints excluded: chain k residue 116 HIS Chi-restraints excluded: chain k residue 123 GLU Chi-restraints excluded: chain k residue 151 THR Chi-restraints excluded: chain k residue 154 GLU Chi-restraints excluded: chain k residue 166 PHE Chi-restraints excluded: chain k residue 174 ILE Chi-restraints excluded: chain l residue 40 GLU Chi-restraints excluded: chain l residue 99 ASP Chi-restraints excluded: chain l residue 107 MET Chi-restraints excluded: chain l residue 125 GLU Chi-restraints excluded: chain l residue 135 THR Chi-restraints excluded: chain m residue 67 LEU Chi-restraints excluded: chain m residue 127 VAL Chi-restraints excluded: chain m residue 128 LEU Chi-restraints excluded: chain m residue 133 VAL Chi-restraints excluded: chain m residue 138 ARG Chi-restraints excluded: chain n residue 37 THR Chi-restraints excluded: chain n residue 46 ARG Chi-restraints excluded: chain n residue 56 VAL Chi-restraints excluded: chain n residue 66 PHE Chi-restraints excluded: chain n residue 92 ILE Chi-restraints excluded: chain n residue 105 ASP Chi-restraints excluded: chain o residue 30 GLN Chi-restraints excluded: chain o residue 48 ASP Chi-restraints excluded: chain o residue 99 LEU Chi-restraints excluded: chain p residue 27 VAL Chi-restraints excluded: chain p residue 50 SER Chi-restraints excluded: chain p residue 75 ILE Chi-restraints excluded: chain p residue 82 THR Chi-restraints excluded: chain t residue 9 ARG Chi-restraints excluded: chain t residue 12 ILE Chi-restraints excluded: chain t residue 18 ILE Chi-restraints excluded: chain t residue 32 LYS Chi-restraints excluded: chain t residue 55 THR Chi-restraints excluded: chain t residue 98 THR Chi-restraints excluded: chain t residue 101 TRP Chi-restraints excluded: chain u residue 104 LEU Chi-restraints excluded: chain u residue 110 ILE Chi-restraints excluded: chain u residue 129 SER Chi-restraints excluded: chain v residue 38 ARG Chi-restraints excluded: chain v residue 103 LEU Chi-restraints excluded: chain w residue 52 THR Chi-restraints excluded: chain w residue 92 VAL Chi-restraints excluded: chain w residue 97 THR Chi-restraints excluded: chain w residue 166 ILE Chi-restraints excluded: chain w residue 178 LEU Chi-restraints excluded: chain w residue 188 VAL Chi-restraints excluded: chain w residue 189 LEU Chi-restraints excluded: chain w residue 194 LEU Chi-restraints excluded: chain w residue 205 LEU Chi-restraints excluded: chain w residue 216 ARG Chi-restraints excluded: chain w residue 250 SER Chi-restraints excluded: chain w residue 274 ASN Chi-restraints excluded: chain w residue 282 THR Chi-restraints excluded: chain w residue 316 VAL Chi-restraints excluded: chain w residue 345 VAL Chi-restraints excluded: chain w residue 356 THR Chi-restraints excluded: chain w residue 415 LEU Chi-restraints excluded: chain w residue 418 PHE Chi-restraints excluded: chain w residue 419 LEU Chi-restraints excluded: chain x residue 41 ILE Chi-restraints excluded: chain x residue 54 THR Chi-restraints excluded: chain x residue 56 THR Chi-restraints excluded: chain x residue 104 ILE Chi-restraints excluded: chain x residue 119 VAL Chi-restraints excluded: chain x residue 170 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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-5687/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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-5687/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-5687/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-5687/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-5687/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-5687/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-5687/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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-5687/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-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 71.8799 > 50: distance: 0 - 1: 10.287 distance: 0 - 6: 48.124 distance: 1 - 2: 41.468 distance: 1 - 4: 39.952 distance: 2 - 3: 39.509 distance: 2 - 7: 30.303 distance: 4 - 5: 64.002 distance: 5 - 6: 67.512 distance: 8 - 9: 39.484 distance: 8 - 11: 62.817 distance: 9 - 10: 46.167 distance: 9 - 14: 56.897 distance: 11 - 12: 14.775 distance: 11 - 13: 44.586 distance: 14 - 15: 55.596 distance: 15 - 16: 41.188 distance: 15 - 18: 55.402 distance: 16 - 17: 39.599 distance: 16 - 19: 17.464 distance: 19 - 20: 27.274 distance: 20 - 21: 46.930 distance: 20 - 23: 16.089 distance: 21 - 22: 68.124 distance: 23 - 24: 11.876 distance: 24 - 25: 59.813 distance: 25 - 26: 7.109 distance: 26 - 27: 11.722 distance: 27 - 28: 16.916 distance: 27 - 29: 30.299 distance: 30 - 31: 9.123 distance: 31 - 32: 51.089 distance: 31 - 34: 51.534 distance: 32 - 33: 60.504 distance: 32 - 42: 46.304 distance: 35 - 36: 40.427 distance: 35 - 37: 39.009 distance: 38 - 40: 55.897 distance: 39 - 40: 57.153 distance: 40 - 41: 39.701 distance: 42 - 43: 40.946 distance: 42 - 48: 42.523 distance: 43 - 44: 13.986 distance: 43 - 46: 39.359 distance: 44 - 45: 40.237 distance: 44 - 49: 13.991 distance: 46 - 47: 49.839 distance: 49 - 50: 56.697 distance: 49 - 55: 55.943 distance: 50 - 51: 44.056 distance: 50 - 53: 19.496 distance: 51 - 52: 24.205 distance: 51 - 56: 44.526 distance: 53 - 54: 33.833 distance: 54 - 55: 26.905 distance: 56 - 57: 38.775 distance: 57 - 60: 58.429 distance: 58 - 59: 40.115 distance: 58 - 64: 56.191 distance: 60 - 61: 48.804 distance: 60 - 62: 48.974 distance: 61 - 63: 12.670 distance: 64 - 65: 43.645 distance: 65 - 66: 36.197 distance: 65 - 68: 26.785 distance: 66 - 67: 58.232 distance: 66 - 71: 29.397 distance: 68 - 69: 19.067