Starting phenix.real_space_refine on Fri Dec 27 15:14:25 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7zyj_15025/12_2024/7zyj_15025.cif Found real_map, /net/cci-nas-00/data/ceres_data/7zyj_15025/12_2024/7zyj_15025.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7zyj_15025/12_2024/7zyj_15025.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7zyj_15025/12_2024/7zyj_15025.map" model { file = "/net/cci-nas-00/data/ceres_data/7zyj_15025/12_2024/7zyj_15025.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7zyj_15025/12_2024/7zyj_15025.cif" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.069 sd= 0.611 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: 4 Type Number sf(0) Gaussians S 326 5.16 5 C 30950 2.51 5 N 8488 2.21 5 O 9470 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 61 residue(s): 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 49234 Number of models: 1 Model: "" Number of chains: 30 Chain: "A" Number of atoms: 1861 Number of conformers: 1 Conformer: "" Number of residues, atoms: 245, 1861 Classifications: {'peptide': 245} Link IDs: {'PTRANS': 12, 'TRANS': 232} Chain: "B" Number of atoms: 1753 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1753 Classifications: {'peptide': 229} Link IDs: {'PTRANS': 8, 'TRANS': 220} Chain: "C" Number of atoms: 2155 Number of conformers: 1 Conformer: "" Number of residues, atoms: 272, 2155 Classifications: {'peptide': 272} Link IDs: {'PTRANS': 11, 'TRANS': 260} Chain: "D" Number of atoms: 1882 Number of conformers: 1 Conformer: "" Number of residues, atoms: 240, 1882 Classifications: {'peptide': 240} Link IDs: {'PTRANS': 4, 'TRANS': 235} Chain: "E" Number of atoms: 1802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1802 Classifications: {'peptide': 235} Link IDs: {'PTRANS': 10, 'TRANS': 224} Chain: "F" Number of atoms: 1869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 238, 1869 Classifications: {'peptide': 238} Link IDs: {'PTRANS': 8, 'TRANS': 229} Chain: "G" Number of atoms: 1741 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1741 Classifications: {'peptide': 230} Link IDs: {'PTRANS': 7, 'TRANS': 222} Chain: "H" Number of atoms: 1709 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1709 Classifications: {'peptide': 229} Link IDs: {'PTRANS': 8, 'TRANS': 220} Chain: "I" Number of atoms: 1659 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1659 Classifications: {'peptide': 219} Link IDs: {'PTRANS': 10, 'TRANS': 208} Chain: "J" Number of atoms: 1557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1557 Classifications: {'peptide': 204} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 196} Chain: "K" Number of atoms: 1612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1612 Classifications: {'peptide': 206} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 200} Chain: "L" Number of atoms: 1577 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1577 Classifications: {'peptide': 202} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 2, 'TRANS': 199} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "M" Number of atoms: 1702 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1702 Classifications: {'peptide': 214} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 205} Chain: "N" Number of atoms: 1712 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1712 Classifications: {'peptide': 218} Link IDs: {'PTRANS': 7, 'TRANS': 210} Chain: "a" Number of atoms: 1861 Number of conformers: 1 Conformer: "" Number of residues, atoms: 245, 1861 Classifications: {'peptide': 245} Link IDs: {'PTRANS': 12, 'TRANS': 232} Chain: "b" Number of atoms: 1753 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1753 Classifications: {'peptide': 229} Link IDs: {'PTRANS': 8, 'TRANS': 220} Chain: "c" Number of atoms: 2155 Number of conformers: 1 Conformer: "" Number of residues, atoms: 272, 2155 Classifications: {'peptide': 272} Link IDs: {'PTRANS': 11, 'TRANS': 260} Chain: "d" Number of atoms: 1882 Number of conformers: 1 Conformer: "" Number of residues, atoms: 240, 1882 Classifications: {'peptide': 240} Link IDs: {'PTRANS': 4, 'TRANS': 235} Chain: "e" Number of atoms: 1802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1802 Classifications: {'peptide': 235} Link IDs: {'PTRANS': 10, 'TRANS': 224} Chain: "f" Number of atoms: 1869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 238, 1869 Classifications: {'peptide': 238} Link IDs: {'PTRANS': 8, 'TRANS': 229} Chain: "g" Number of atoms: 1741 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1741 Classifications: {'peptide': 230} Link IDs: {'PTRANS': 7, 'TRANS': 222} Chain: "h" Number of atoms: 1709 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1709 Classifications: {'peptide': 229} Link IDs: {'PTRANS': 8, 'TRANS': 220} Chain: "i" Number of atoms: 1659 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1659 Classifications: {'peptide': 219} Link IDs: {'PTRANS': 10, 'TRANS': 208} Chain: "j" Number of atoms: 1557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1557 Classifications: {'peptide': 204} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 196} Chain: "k" Number of atoms: 1612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1612 Classifications: {'peptide': 206} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 200} Chain: "l" Number of atoms: 1577 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1577 Classifications: {'peptide': 202} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 2, 'TRANS': 199} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "m" Number of atoms: 1702 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1702 Classifications: {'peptide': 214} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 205} Chain: "n" Number of atoms: 1712 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1712 Classifications: {'peptide': 218} Link IDs: {'PTRANS': 7, 'TRANS': 210} Chain: "L" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 26 Unusual residues: {'KFC': 1} Classifications: {'undetermined': 1} Chain: "l" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 26 Unusual residues: {'KFC': 1} Classifications: {'undetermined': 1} Time building chain proxies: 21.65, per 1000 atoms: 0.44 Number of scatterers: 49234 At special positions: 0 Unit cell: (136.74, 190.06, 132.44, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 326 16.00 O 9470 8.00 N 8488 7.00 C 30950 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 9.03 Conformation dependent library (CDL) restraints added in 4.7 seconds 12612 Ramachandran restraints generated. 6306 Oldfield, 0 Emsley, 6306 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 11716 Finding SS restraints... Secondary structure from input PDB file: 175 helices and 70 sheets defined 39.1% alpha, 22.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.00 Creating SS restraints... Processing helix chain 'A' and resid 19 through 31 removed outlier: 3.586A pdb=" N VAL A 29 " --> pdb=" O ALA A 25 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N THR A 30 " --> pdb=" O PHE A 26 " (cutoff:3.500A) Processing helix chain 'A' and resid 80 through 103 removed outlier: 3.571A pdb=" N TYR A 98 " --> pdb=" O GLU A 94 " (cutoff:3.500A) Processing helix chain 'A' and resid 107 through 123 removed outlier: 3.767A pdb=" N ARG A 122 " --> pdb=" O LYS A 118 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N THR A 123 " --> pdb=" O ALA A 119 " (cutoff:3.500A) Processing helix chain 'A' and resid 173 through 186 removed outlier: 3.501A pdb=" N ALA A 177 " --> pdb=" O LYS A 173 " (cutoff:3.500A) Processing helix chain 'A' and resid 189 through 193 Processing helix chain 'A' and resid 194 through 211 Processing helix chain 'A' and resid 235 through 247 Processing helix chain 'B' and resid 17 through 28 Processing helix chain 'B' and resid 77 through 100 removed outlier: 3.820A pdb=" N VAL B 83 " --> pdb=" O PRO B 79 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N LEU B 84 " --> pdb=" O ASP B 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 104 through 122 removed outlier: 3.652A pdb=" N ILE B 115 " --> pdb=" O LYS B 111 " (cutoff:3.500A) Processing helix chain 'B' and resid 164 through 176 removed outlier: 3.614A pdb=" N LYS B 174 " --> pdb=" O ALA B 170 " (cutoff:3.500A) Processing helix chain 'B' and resid 181 through 197 removed outlier: 3.631A pdb=" N GLY B 196 " --> pdb=" O THR B 192 " (cutoff:3.500A) Processing helix chain 'B' and resid 220 through 229 Processing helix chain 'C' and resid 2 through 6 Processing helix chain 'C' and resid 18 through 30 removed outlier: 3.708A pdb=" N GLN C 30 " --> pdb=" O GLU C 26 " (cutoff:3.500A) Processing helix chain 'C' and resid 85 through 108 removed outlier: 3.790A pdb=" N ALA C 91 " --> pdb=" O SER C 87 " (cutoff:3.500A) Processing helix chain 'C' and resid 112 through 127 removed outlier: 3.637A pdb=" N GLU C 123 " --> pdb=" O ILE C 119 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N TYR C 127 " --> pdb=" O GLU C 123 " (cutoff:3.500A) Processing helix chain 'C' and resid 173 through 184 Processing helix chain 'C' and resid 190 through 206 removed outlier: 3.633A pdb=" N LYS C 204 " --> pdb=" O ARG C 200 " (cutoff:3.500A) Processing helix chain 'C' and resid 230 through 234 removed outlier: 3.655A pdb=" N LEU C 233 " --> pdb=" O ASP C 230 " (cutoff:3.500A) Processing helix chain 'C' and resid 250 through 270 removed outlier: 3.565A pdb=" N LYS C 255 " --> pdb=" O ARG C 251 " (cutoff:3.500A) Proline residue: C 256 - end of helix Processing helix chain 'D' and resid 16 through 28 Processing helix chain 'D' and resid 76 through 98 Processing helix chain 'D' and resid 103 through 119 Processing helix chain 'D' and resid 164 through 174 removed outlier: 4.102A pdb=" N LYS D 174 " --> pdb=" O GLU D 170 " (cutoff:3.500A) Processing helix chain 'D' and resid 181 through 194 Processing helix chain 'D' and resid 218 through 241 removed outlier: 3.563A pdb=" N GLU D 228 " --> pdb=" O LYS D 224 " (cutoff:3.500A) Processing helix chain 'E' and resid 121 through 132 removed outlier: 3.545A pdb=" N ILE E 131 " --> pdb=" O ALA E 127 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LYS E 132 " --> pdb=" O VAL E 128 " (cutoff:3.500A) Processing helix chain 'E' and resid 160 through 165 removed outlier: 3.886A pdb=" N SER E 165 " --> pdb=" O SER E 162 " (cutoff:3.500A) Processing helix chain 'E' and resid 181 through 204 removed outlier: 4.182A pdb=" N ILE E 187 " --> pdb=" O ALA E 183 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEU E 188 " --> pdb=" O ASP E 184 " (cutoff:3.500A) Processing helix chain 'E' and resid 208 through 222 removed outlier: 4.006A pdb=" N GLN E 222 " --> pdb=" O ASP E 218 " (cutoff:3.500A) Processing helix chain 'E' and resid 273 through 283 removed outlier: 3.613A pdb=" N ALA E 277 " --> pdb=" O GLY E 273 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N GLU E 283 " --> pdb=" O SER E 279 " (cutoff:3.500A) Processing helix chain 'E' and resid 290 through 306 Processing helix chain 'E' and resid 331 through 340 Processing helix chain 'F' and resid 183 through 194 Processing helix chain 'F' and resid 242 through 265 Processing helix chain 'F' and resid 269 through 283 Processing helix chain 'F' and resid 329 through 341 removed outlier: 4.387A pdb=" N SER F 333 " --> pdb=" O ARG F 329 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N ARG F 339 " --> pdb=" O THR F 335 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N HIS F 340 " --> pdb=" O TYR F 336 " (cutoff:3.500A) Processing helix chain 'F' and resid 342 through 344 No H-bonds generated for 'chain 'F' and resid 342 through 344' Processing helix chain 'F' and resid 348 through 362 Processing helix chain 'F' and resid 371 through 375 removed outlier: 3.778A pdb=" N THR F 375 " --> pdb=" O VAL F 372 " (cutoff:3.500A) Processing helix chain 'F' and resid 394 through 399 Processing helix chain 'G' and resid 6 through 10 removed outlier: 4.288A pdb=" N ASP G 9 " --> pdb=" O SER G 6 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N GLN G 10 " --> pdb=" O GLY G 7 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 6 through 10' Processing helix chain 'G' and resid 21 through 33 Processing helix chain 'G' and resid 81 through 103 Processing helix chain 'G' and resid 108 through 122 Processing helix chain 'G' and resid 123 through 125 No H-bonds generated for 'chain 'G' and resid 123 through 125' Processing helix chain 'G' and resid 168 through 177 removed outlier: 3.565A pdb=" N ALA G 172 " --> pdb=" O ALA G 168 " (cutoff:3.500A) Processing helix chain 'G' and resid 185 through 201 removed outlier: 4.078A pdb=" N GLY G 191 " --> pdb=" O ASP G 187 " (cutoff:3.500A) Processing helix chain 'G' and resid 219 through 221 No H-bonds generated for 'chain 'G' and resid 219 through 221' Processing helix chain 'G' and resid 228 through 232 removed outlier: 4.192A pdb=" N VAL G 232 " --> pdb=" O ALA G 229 " (cutoff:3.500A) Processing helix chain 'H' and resid 102 through 125 removed outlier: 3.517A pdb=" N THR H 122 " --> pdb=" O GLY H 118 " (cutoff:3.500A) Processing helix chain 'H' and resid 129 through 144 removed outlier: 3.658A pdb=" N ALA H 133 " --> pdb=" O ASN H 129 " (cutoff:3.500A) Processing helix chain 'H' and resid 183 through 188 removed outlier: 3.802A pdb=" N ILE H 187 " --> pdb=" O SER H 184 " (cutoff:3.500A) Processing helix chain 'H' and resid 189 through 197 Processing helix chain 'H' and resid 202 through 221 removed outlier: 3.830A pdb=" N ARG H 220 " --> pdb=" O HIS H 216 " (cutoff:3.500A) Processing helix chain 'H' and resid 244 through 248 Processing helix chain 'H' and resid 255 through 259 Processing helix chain 'I' and resid 77 through 100 Processing helix chain 'I' and resid 104 through 119 removed outlier: 3.673A pdb=" N TYR I 119 " --> pdb=" O HIS I 115 " (cutoff:3.500A) Processing helix chain 'I' and resid 159 through 171 removed outlier: 3.659A pdb=" N GLN I 166 " --> pdb=" O ALA I 162 " (cutoff:3.500A) Processing helix chain 'I' and resid 176 through 195 Processing helix chain 'J' and resid 56 through 78 Processing helix chain 'J' and resid 83 through 98 removed outlier: 3.836A pdb=" N ALA J 98 " --> pdb=" O MET J 94 " (cutoff:3.500A) Processing helix chain 'J' and resid 142 through 154 Processing helix chain 'J' and resid 159 through 177 removed outlier: 3.734A pdb=" N ARG J 177 " --> pdb=" O SER J 173 " (cutoff:3.500A) Processing helix chain 'K' and resid 50 through 72 Processing helix chain 'K' and resid 78 through 94 Processing helix chain 'K' and resid 146 through 158 removed outlier: 3.555A pdb=" N LEU K 153 " --> pdb=" O PHE K 149 " (cutoff:3.500A) Processing helix chain 'K' and resid 163 through 182 Processing helix chain 'L' and resid 147 through 170 Processing helix chain 'L' and resid 174 through 189 Processing helix chain 'L' and resid 230 through 242 removed outlier: 4.073A pdb=" N GLY L 236 " --> pdb=" O ILE L 232 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N VAL L 237 " --> pdb=" O TYR L 233 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N THR L 240 " --> pdb=" O GLY L 236 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N GLY L 241 " --> pdb=" O VAL L 237 " (cutoff:3.500A) Processing helix chain 'L' and resid 247 through 266 removed outlier: 3.737A pdb=" N ARG L 265 " --> pdb=" O HIS L 261 " (cutoff:3.500A) Processing helix chain 'L' and resid 291 through 299 Processing helix chain 'M' and resid 182 through 204 Processing helix chain 'M' and resid 210 through 225 removed outlier: 3.574A pdb=" N ARG M 225 " --> pdb=" O MET M 221 " (cutoff:3.500A) Processing helix chain 'M' and resid 267 through 281 Proline residue: M 273 - end of helix Processing helix chain 'M' and resid 293 through 310 Processing helix chain 'N' and resid 53 through 74 Processing helix chain 'N' and resid 80 through 98 Processing helix chain 'N' and resid 136 through 139 Processing helix chain 'N' and resid 141 through 152 removed outlier: 4.315A pdb=" N LEU N 145 " --> pdb=" O ILE N 141 " (cutoff:3.500A) Processing helix chain 'N' and resid 158 through 177 Processing helix chain 'N' and resid 208 through 211 Processing helix chain 'N' and resid 212 through 217 Processing helix chain 'a' and resid 19 through 31 removed outlier: 3.584A pdb=" N VAL a 29 " --> pdb=" O ALA a 25 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N THR a 30 " --> pdb=" O PHE a 26 " (cutoff:3.500A) Processing helix chain 'a' and resid 80 through 103 removed outlier: 3.709A pdb=" N TYR a 98 " --> pdb=" O GLU a 94 " (cutoff:3.500A) Processing helix chain 'a' and resid 107 through 123 removed outlier: 3.768A pdb=" N ARG a 122 " --> pdb=" O LYS a 118 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N THR a 123 " --> pdb=" O ALA a 119 " (cutoff:3.500A) Processing helix chain 'a' and resid 173 through 186 removed outlier: 3.501A pdb=" N ALA a 177 " --> pdb=" O LYS a 173 " (cutoff:3.500A) Processing helix chain 'a' and resid 189 through 193 Processing helix chain 'a' and resid 194 through 211 Processing helix chain 'a' and resid 235 through 247 Processing helix chain 'b' and resid 17 through 28 Processing helix chain 'b' and resid 77 through 100 removed outlier: 3.822A pdb=" N VAL b 83 " --> pdb=" O PRO b 79 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N LEU b 84 " --> pdb=" O ASP b 80 " (cutoff:3.500A) Processing helix chain 'b' and resid 104 through 122 removed outlier: 3.654A pdb=" N ILE b 115 " --> pdb=" O LYS b 111 " (cutoff:3.500A) Processing helix chain 'b' and resid 164 through 176 removed outlier: 3.569A pdb=" N LYS b 174 " --> pdb=" O ALA b 170 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ARG b 175 " --> pdb=" O PHE b 171 " (cutoff:3.500A) Processing helix chain 'b' and resid 181 through 197 removed outlier: 3.639A pdb=" N GLY b 196 " --> pdb=" O THR b 192 " (cutoff:3.500A) Processing helix chain 'b' and resid 220 through 229 Processing helix chain 'b' and resid 230 through 231 No H-bonds generated for 'chain 'b' and resid 230 through 231' Processing helix chain 'c' and resid 2 through 6 Processing helix chain 'c' and resid 18 through 30 removed outlier: 3.724A pdb=" N GLN c 30 " --> pdb=" O GLU c 26 " (cutoff:3.500A) Processing helix chain 'c' and resid 85 through 108 removed outlier: 3.790A pdb=" N ALA c 91 " --> pdb=" O SER c 87 " (cutoff:3.500A) Processing helix chain 'c' and resid 112 through 127 removed outlier: 3.620A pdb=" N GLU c 123 " --> pdb=" O ILE c 119 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N TYR c 127 " --> pdb=" O GLU c 123 " (cutoff:3.500A) Processing helix chain 'c' and resid 173 through 184 Processing helix chain 'c' and resid 190 through 206 removed outlier: 3.565A pdb=" N LYS c 204 " --> pdb=" O ARG c 200 " (cutoff:3.500A) Processing helix chain 'c' and resid 212 through 214 No H-bonds generated for 'chain 'c' and resid 212 through 214' Processing helix chain 'c' and resid 230 through 234 removed outlier: 3.588A pdb=" N LEU c 233 " --> pdb=" O ASP c 230 " (cutoff:3.500A) Processing helix chain 'c' and resid 250 through 270 removed outlier: 3.561A pdb=" N LYS c 255 " --> pdb=" O ARG c 251 " (cutoff:3.500A) Proline residue: c 256 - end of helix removed outlier: 3.616A pdb=" N ARG c 260 " --> pdb=" O PRO c 256 " (cutoff:3.500A) Processing helix chain 'c' and resid 271 through 273 No H-bonds generated for 'chain 'c' and resid 271 through 273' Processing helix chain 'd' and resid 16 through 28 Processing helix chain 'd' and resid 76 through 98 Processing helix chain 'd' and resid 103 through 119 Processing helix chain 'd' and resid 164 through 174 removed outlier: 4.091A pdb=" N LYS d 174 " --> pdb=" O GLU d 170 " (cutoff:3.500A) Processing helix chain 'd' and resid 181 through 194 Processing helix chain 'd' and resid 218 through 241 removed outlier: 3.611A pdb=" N GLU d 228 " --> pdb=" O LYS d 224 " (cutoff:3.500A) Processing helix chain 'e' and resid 121 through 133 removed outlier: 3.545A pdb=" N ILE e 131 " --> pdb=" O ALA e 127 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LYS e 132 " --> pdb=" O VAL e 128 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LEU e 133 " --> pdb=" O GLU e 129 " (cutoff:3.500A) Processing helix chain 'e' and resid 160 through 165 removed outlier: 3.855A pdb=" N SER e 165 " --> pdb=" O SER e 162 " (cutoff:3.500A) Processing helix chain 'e' and resid 181 through 204 removed outlier: 4.160A pdb=" N ILE e 187 " --> pdb=" O ALA e 183 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LEU e 188 " --> pdb=" O ASP e 184 " (cutoff:3.500A) Processing helix chain 'e' and resid 208 through 222 removed outlier: 4.032A pdb=" N GLN e 222 " --> pdb=" O ASP e 218 " (cutoff:3.500A) Processing helix chain 'e' and resid 273 through 283 removed outlier: 3.600A pdb=" N ALA e 277 " --> pdb=" O GLY e 273 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N GLU e 283 " --> pdb=" O SER e 279 " (cutoff:3.500A) Processing helix chain 'e' and resid 290 through 305 Processing helix chain 'e' and resid 331 through 340 Processing helix chain 'f' and resid 183 through 195 Processing helix chain 'f' and resid 242 through 265 Processing helix chain 'f' and resid 269 through 283 Processing helix chain 'f' and resid 329 through 341 removed outlier: 4.373A pdb=" N SER f 333 " --> pdb=" O ARG f 329 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N ARG f 339 " --> pdb=" O THR f 335 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N HIS f 340 " --> pdb=" O TYR f 336 " (cutoff:3.500A) Processing helix chain 'f' and resid 342 through 344 No H-bonds generated for 'chain 'f' and resid 342 through 344' Processing helix chain 'f' and resid 348 through 362 Processing helix chain 'f' and resid 371 through 375 removed outlier: 3.509A pdb=" N ASN f 374 " --> pdb=" O ASN f 371 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N THR f 375 " --> pdb=" O VAL f 372 " (cutoff:3.500A) No H-bonds generated for 'chain 'f' and resid 371 through 375' Processing helix chain 'f' and resid 394 through 399 Processing helix chain 'g' and resid 6 through 10 removed outlier: 4.296A pdb=" N ASP g 9 " --> pdb=" O SER g 6 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N GLN g 10 " --> pdb=" O GLY g 7 " (cutoff:3.500A) No H-bonds generated for 'chain 'g' and resid 6 through 10' Processing helix chain 'g' and resid 21 through 33 Processing helix chain 'g' and resid 81 through 103 Processing helix chain 'g' and resid 108 through 122 Processing helix chain 'g' and resid 123 through 125 No H-bonds generated for 'chain 'g' and resid 123 through 125' Processing helix chain 'g' and resid 168 through 177 removed outlier: 3.619A pdb=" N ALA g 172 " --> pdb=" O ALA g 168 " (cutoff:3.500A) Processing helix chain 'g' and resid 185 through 201 removed outlier: 4.077A pdb=" N GLY g 191 " --> pdb=" O ASP g 187 " (cutoff:3.500A) Processing helix chain 'g' and resid 219 through 221 No H-bonds generated for 'chain 'g' and resid 219 through 221' Processing helix chain 'g' and resid 228 through 232 removed outlier: 4.193A pdb=" N VAL g 232 " --> pdb=" O ALA g 229 " (cutoff:3.500A) Processing helix chain 'h' and resid 102 through 125 removed outlier: 3.516A pdb=" N THR h 122 " --> pdb=" O GLY h 118 " (cutoff:3.500A) Processing helix chain 'h' and resid 129 through 144 removed outlier: 3.658A pdb=" N ALA h 133 " --> pdb=" O ASN h 129 " (cutoff:3.500A) Processing helix chain 'h' and resid 183 through 188 removed outlier: 3.802A pdb=" N ILE h 187 " --> pdb=" O SER h 184 " (cutoff:3.500A) Processing helix chain 'h' and resid 189 through 197 Processing helix chain 'h' and resid 202 through 221 removed outlier: 3.830A pdb=" N ARG h 220 " --> pdb=" O HIS h 216 " (cutoff:3.500A) Processing helix chain 'h' and resid 244 through 248 Processing helix chain 'h' and resid 255 through 259 Processing helix chain 'i' and resid 77 through 100 Processing helix chain 'i' and resid 104 through 119 removed outlier: 3.666A pdb=" N TYR i 119 " --> pdb=" O HIS i 115 " (cutoff:3.500A) Processing helix chain 'i' and resid 159 through 171 removed outlier: 3.659A pdb=" N GLN i 166 " --> pdb=" O ALA i 162 " (cutoff:3.500A) Processing helix chain 'i' and resid 176 through 195 Processing helix chain 'j' and resid 56 through 78 Processing helix chain 'j' and resid 83 through 98 removed outlier: 3.837A pdb=" N ALA j 98 " --> pdb=" O MET j 94 " (cutoff:3.500A) Processing helix chain 'j' and resid 142 through 154 Processing helix chain 'j' and resid 159 through 177 removed outlier: 3.737A pdb=" N ARG j 177 " --> pdb=" O SER j 173 " (cutoff:3.500A) Processing helix chain 'k' and resid 50 through 72 Processing helix chain 'k' and resid 78 through 94 Processing helix chain 'k' and resid 146 through 158 removed outlier: 3.554A pdb=" N LEU k 153 " --> pdb=" O PHE k 149 " (cutoff:3.500A) Processing helix chain 'k' and resid 163 through 182 Processing helix chain 'l' and resid 147 through 170 Processing helix chain 'l' and resid 174 through 189 Processing helix chain 'l' and resid 230 through 242 removed outlier: 4.075A pdb=" N GLY l 236 " --> pdb=" O ILE l 232 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N VAL l 237 " --> pdb=" O TYR l 233 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N THR l 240 " --> pdb=" O GLY l 236 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N GLY l 241 " --> pdb=" O VAL l 237 " (cutoff:3.500A) Processing helix chain 'l' and resid 247 through 266 removed outlier: 3.738A pdb=" N ARG l 265 " --> pdb=" O HIS l 261 " (cutoff:3.500A) Processing helix chain 'l' and resid 291 through 299 Processing helix chain 'm' and resid 182 through 204 Processing helix chain 'm' and resid 210 through 225 removed outlier: 3.574A pdb=" N ARG m 225 " --> pdb=" O MET m 221 " (cutoff:3.500A) Processing helix chain 'm' and resid 267 through 281 Proline residue: m 273 - end of helix Processing helix chain 'm' and resid 293 through 310 Processing helix chain 'n' and resid 53 through 74 Processing helix chain 'n' and resid 80 through 98 Processing helix chain 'n' and resid 136 through 139 Processing helix chain 'n' and resid 141 through 152 removed outlier: 4.317A pdb=" N LEU n 145 " --> pdb=" O ILE n 141 " (cutoff:3.500A) Processing helix chain 'n' and resid 158 through 177 Processing helix chain 'n' and resid 208 through 211 Processing helix chain 'n' and resid 212 through 217 Processing sheet with id=AA1, first strand: chain 'A' and resid 167 through 171 removed outlier: 5.777A pdb=" N LEU A 35 " --> pdb=" O GLN A 50 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 66 through 70 removed outlier: 6.496A pdb=" N ILE A 73 " --> pdb=" O VAL A 69 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 158 through 161 removed outlier: 3.657A pdb=" N GLN B 207 " --> pdb=" O ALA B 46 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 63 through 67 removed outlier: 6.500A pdb=" N VAL B 70 " --> pdb=" O LEU B 66 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 167 through 170 Processing sheet with id=AA6, first strand: chain 'C' and resid 71 through 75 removed outlier: 6.343A pdb=" N ILE C 78 " --> pdb=" O ILE C 74 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N PHE C 140 " --> pdb=" O THR C 156 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLY C 144 " --> pdb=" O GLN C 152 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 158 through 161 Processing sheet with id=AA8, first strand: chain 'D' and resid 63 through 66 removed outlier: 6.446A pdb=" N ILE D 69 " --> pdb=" O VAL D 65 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ASN D 137 " --> pdb=" O LYS D 141 " (cutoff:3.500A) removed outlier: 5.247A pdb=" N LYS D 141 " --> pdb=" O ASN D 137 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 137 through 142 removed outlier: 3.510A pdb=" N ALA E 149 " --> pdb=" O LEU E 138 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 167 through 171 removed outlier: 6.391A pdb=" N ILE E 174 " --> pdb=" O VAL E 170 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N LEU E 253 " --> pdb=" O TYR E 265 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 323 through 326 Processing sheet with id=AB3, first strand: chain 'F' and resid 228 through 232 removed outlier: 6.322A pdb=" N VAL F 235 " --> pdb=" O ILE F 231 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'G' and resid 162 through 165 removed outlier: 4.273A pdb=" N LEU G 208 " --> pdb=" O HIS G 54 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'G' and resid 67 through 69 removed outlier: 3.549A pdb=" N ALA G 142 " --> pdb=" O GLY G 145 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'H' and resid 179 through 182 Processing sheet with id=AB7, first strand: chain 'H' and resid 74 through 76 removed outlier: 6.434A pdb=" N SER H 76 " --> pdb=" O VAL H 80 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N VAL H 80 " --> pdb=" O SER H 76 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'H' and resid 88 through 90 removed outlier: 4.035A pdb=" N VAL H 165 " --> pdb=" O LEU H 177 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'I' and resid 153 through 157 removed outlier: 3.999A pdb=" N GLY I 40 " --> pdb=" O TYR I 37 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N VAL I 202 " --> pdb=" O GLY I 217 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N GLY I 217 " --> pdb=" O VAL I 202 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'I' and resid 49 through 50 Processing sheet with id=AC2, first strand: chain 'I' and resid 63 through 65 Processing sheet with id=AC3, first strand: chain 'I' and resid 240 through 247 removed outlier: 3.952A pdb=" N LYS I 242 " --> pdb=" O LEU J 199 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N LYS J 194 " --> pdb=" O THR J 191 " (cutoff:3.500A) removed outlier: 5.808A pdb=" N SER J 10 " --> pdb=" O ASP J 25 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'J' and resid 28 through 30 removed outlier: 6.917A pdb=" N LEU J 28 " --> pdb=" O ILE J 35 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'J' and resid 42 through 44 Processing sheet with id=AC6, first strand: chain 'K' and resid 140 through 143 removed outlier: 4.183A pdb=" N VAL K 191 " --> pdb=" O ILE K 202 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'K' and resid 22 through 24 removed outlier: 6.779A pdb=" N ASN K 22 " --> pdb=" O ILE K 29 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'K' and resid 36 through 40 removed outlier: 6.490A pdb=" N GLN K 43 " --> pdb=" O LEU K 39 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'L' and resid 224 through 228 removed outlier: 6.529A pdb=" N HIS L 277 " --> pdb=" O LYS L 285 " (cutoff:3.500A) removed outlier: 5.558A pdb=" N LYS L 285 " --> pdb=" O HIS L 277 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N HIS L 279 " --> pdb=" O TRP L 283 " (cutoff:3.500A) removed outlier: 5.044A pdb=" N TRP L 283 " --> pdb=" O HIS L 279 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'L' and resid 119 through 120 Processing sheet with id=AD2, first strand: chain 'L' and resid 133 through 135 removed outlier: 4.517A pdb=" N MET L 199 " --> pdb=" O THR L 143 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'M' and resid 261 through 265 removed outlier: 5.111A pdb=" N THR M 135 " --> pdb=" O ASP M 150 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'M' and resid 153 through 154 Processing sheet with id=AD5, first strand: chain 'M' and resid 168 through 172 removed outlier: 6.533A pdb=" N THR M 175 " --> pdb=" O LEU M 171 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'N' and resid 29 through 32 removed outlier: 6.773A pdb=" N LEU N 24 " --> pdb=" O LYS N 31 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'N' and resid 29 through 32 removed outlier: 6.773A pdb=" N LEU N 24 " --> pdb=" O LYS N 31 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'N' and resid 132 through 135 Processing sheet with id=AD9, first strand: chain 'a' and resid 167 through 171 removed outlier: 5.836A pdb=" N LEU a 35 " --> pdb=" O GLN a 50 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'a' and resid 66 through 70 removed outlier: 6.493A pdb=" N ILE a 73 " --> pdb=" O VAL a 69 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'b' and resid 158 through 161 removed outlier: 3.674A pdb=" N GLN b 207 " --> pdb=" O ALA b 46 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'b' and resid 63 through 67 removed outlier: 6.503A pdb=" N VAL b 70 " --> pdb=" O LEU b 66 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'c' and resid 167 through 170 Processing sheet with id=AE5, first strand: chain 'c' and resid 71 through 75 removed outlier: 6.342A pdb=" N ILE c 78 " --> pdb=" O ILE c 74 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N PHE c 140 " --> pdb=" O THR c 156 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLY c 144 " --> pdb=" O GLN c 152 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'd' and resid 158 through 161 removed outlier: 3.508A pdb=" N VAL d 208 " --> pdb=" O ARG d 215 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'd' and resid 63 through 66 removed outlier: 6.440A pdb=" N ILE d 69 " --> pdb=" O VAL d 65 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ASN d 137 " --> pdb=" O LYS d 141 " (cutoff:3.500A) removed outlier: 5.263A pdb=" N LYS d 141 " --> pdb=" O ASN d 137 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'e' and resid 137 through 142 Processing sheet with id=AE9, first strand: chain 'e' and resid 167 through 171 removed outlier: 6.388A pdb=" N ILE e 174 " --> pdb=" O VAL e 170 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N LEU e 253 " --> pdb=" O TYR e 265 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'f' and resid 323 through 326 Processing sheet with id=AF2, first strand: chain 'f' and resid 228 through 232 removed outlier: 6.333A pdb=" N VAL f 235 " --> pdb=" O ILE f 231 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'g' and resid 162 through 165 removed outlier: 4.275A pdb=" N LEU g 208 " --> pdb=" O HIS g 54 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'g' and resid 67 through 69 removed outlier: 3.549A pdb=" N ALA g 142 " --> pdb=" O GLY g 145 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'h' and resid 179 through 182 Processing sheet with id=AF6, first strand: chain 'h' and resid 74 through 76 removed outlier: 6.430A pdb=" N SER h 76 " --> pdb=" O VAL h 80 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N VAL h 80 " --> pdb=" O SER h 76 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'h' and resid 88 through 90 removed outlier: 4.035A pdb=" N VAL h 165 " --> pdb=" O LEU h 177 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'i' and resid 153 through 157 removed outlier: 3.999A pdb=" N GLY i 40 " --> pdb=" O TYR i 37 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N VAL i 202 " --> pdb=" O GLY i 217 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N GLY i 217 " --> pdb=" O VAL i 202 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'i' and resid 49 through 50 Processing sheet with id=AG1, first strand: chain 'i' and resid 63 through 65 Processing sheet with id=AG2, first strand: chain 'i' and resid 240 through 247 removed outlier: 3.952A pdb=" N LYS i 242 " --> pdb=" O LEU j 199 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N LYS j 194 " --> pdb=" O THR j 191 " (cutoff:3.500A) removed outlier: 5.797A pdb=" N SER j 10 " --> pdb=" O ASP j 25 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'j' and resid 28 through 30 removed outlier: 6.918A pdb=" N LEU j 28 " --> pdb=" O ILE j 35 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'j' and resid 42 through 44 Processing sheet with id=AG5, first strand: chain 'k' and resid 140 through 143 removed outlier: 4.183A pdb=" N VAL k 191 " --> pdb=" O ILE k 202 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'k' and resid 22 through 24 removed outlier: 6.779A pdb=" N ASN k 22 " --> pdb=" O ILE k 29 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'k' and resid 36 through 40 removed outlier: 6.463A pdb=" N GLN k 43 " --> pdb=" O LEU k 39 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'l' and resid 224 through 228 removed outlier: 6.531A pdb=" N HIS l 277 " --> pdb=" O LYS l 285 " (cutoff:3.500A) removed outlier: 5.557A pdb=" N LYS l 285 " --> pdb=" O HIS l 277 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N HIS l 279 " --> pdb=" O TRP l 283 " (cutoff:3.500A) removed outlier: 5.044A pdb=" N TRP l 283 " --> pdb=" O HIS l 279 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'l' and resid 119 through 120 Processing sheet with id=AH1, first strand: chain 'l' and resid 133 through 135 removed outlier: 4.515A pdb=" N MET l 199 " --> pdb=" O THR l 143 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'm' and resid 261 through 265 removed outlier: 5.113A pdb=" N THR m 135 " --> pdb=" O ASP m 150 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'm' and resid 153 through 154 Processing sheet with id=AH4, first strand: chain 'm' and resid 168 through 172 removed outlier: 6.531A pdb=" N THR m 175 " --> pdb=" O LEU m 171 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'n' and resid 29 through 32 removed outlier: 6.777A pdb=" N LEU n 24 " --> pdb=" O LYS n 31 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'n' and resid 29 through 32 removed outlier: 6.777A pdb=" N LEU n 24 " --> pdb=" O LYS n 31 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'n' and resid 132 through 135 2767 hydrogen bonds defined for protein. 7872 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: 17.49 Time building geometry restraints manager: 10.61 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.13 - 1.27: 8338 1.27 - 1.40: 12278 1.40 - 1.54: 28161 1.54 - 1.67: 883 1.67 - 1.81: 512 Bond restraints: 50172 Sorted by residual: bond pdb=" C PRO l 300 " pdb=" O PRO l 300 " ideal model delta sigma weight residual 1.233 1.130 0.103 9.90e-03 1.02e+04 1.09e+02 bond pdb=" C PRO l 300 " pdb=" N SER l 301 " ideal model delta sigma weight residual 1.329 1.387 -0.058 1.40e-02 5.10e+03 1.73e+01 bond pdb=" N ILE k 27 " pdb=" CA ILE k 27 " ideal model delta sigma weight residual 1.459 1.490 -0.032 1.24e-02 6.50e+03 6.46e+00 bond pdb=" C16 KFC l 901 " pdb=" N14 KFC l 901 " ideal model delta sigma weight residual 1.400 1.354 0.046 2.00e-02 2.50e+03 5.31e+00 bond pdb=" C16 KFC L 901 " pdb=" N14 KFC L 901 " ideal model delta sigma weight residual 1.400 1.354 0.046 2.00e-02 2.50e+03 5.20e+00 ... (remaining 50167 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.92: 67583 2.92 - 5.84: 267 5.84 - 8.76: 17 8.76 - 11.68: 2 11.68 - 14.60: 1 Bond angle restraints: 67870 Sorted by residual: angle pdb=" O PRO l 300 " pdb=" C PRO l 300 " pdb=" N SER l 301 " ideal model delta sigma weight residual 122.78 108.18 14.60 1.40e+00 5.10e-01 1.09e+02 angle pdb=" CA PRO l 300 " pdb=" C PRO l 300 " pdb=" N SER l 301 " ideal model delta sigma weight residual 115.14 106.66 8.48 1.38e+00 5.25e-01 3.77e+01 angle pdb=" C VAL B 212 " pdb=" N GLU B 213 " pdb=" CA GLU B 213 " ideal model delta sigma weight residual 121.54 129.35 -7.81 1.91e+00 2.74e-01 1.67e+01 angle pdb=" C PRO l 300 " pdb=" N SER l 301 " pdb=" CA SER l 301 " ideal model delta sigma weight residual 121.70 114.46 7.24 1.80e+00 3.09e-01 1.62e+01 angle pdb=" C SER G 151 " pdb=" N ASP G 152 " pdb=" CA ASP G 152 " ideal model delta sigma weight residual 120.69 132.18 -11.49 2.95e+00 1.15e-01 1.52e+01 ... (remaining 67865 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 27738 17.96 - 35.93: 1954 35.93 - 53.89: 299 53.89 - 71.86: 100 71.86 - 89.82: 49 Dihedral angle restraints: 30140 sinusoidal: 11792 harmonic: 18348 Sorted by residual: dihedral pdb=" CA TYR K 25 " pdb=" C TYR K 25 " pdb=" N TYR K 26 " pdb=" CA TYR K 26 " ideal model delta harmonic sigma weight residual 180.00 150.02 29.98 0 5.00e+00 4.00e-02 3.60e+01 dihedral pdb=" CA VAL b 212 " pdb=" C VAL b 212 " pdb=" N GLU b 213 " pdb=" CA GLU b 213 " ideal model delta harmonic sigma weight residual 180.00 154.97 25.03 0 5.00e+00 4.00e-02 2.51e+01 dihedral pdb=" CA LYS d 47 " pdb=" C LYS d 47 " pdb=" N LYS d 48 " pdb=" CA LYS d 48 " ideal model delta harmonic sigma weight residual 180.00 -155.28 -24.72 0 5.00e+00 4.00e-02 2.44e+01 ... (remaining 30137 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 5624 0.043 - 0.086: 1385 0.086 - 0.129: 518 0.129 - 0.173: 21 0.173 - 0.216: 2 Chirality restraints: 7550 Sorted by residual: chirality pdb=" CB VAL N 124 " pdb=" CA VAL N 124 " pdb=" CG1 VAL N 124 " pdb=" CG2 VAL N 124 " both_signs ideal model delta sigma weight residual False -2.63 -2.41 -0.22 2.00e-01 2.50e+01 1.16e+00 chirality pdb=" CB VAL n 124 " pdb=" CA VAL n 124 " pdb=" CG1 VAL n 124 " pdb=" CG2 VAL n 124 " both_signs ideal model delta sigma weight residual False -2.63 -2.42 -0.21 2.00e-01 2.50e+01 1.14e+00 chirality pdb=" CA PHE k 189 " pdb=" N PHE k 189 " pdb=" C PHE k 189 " pdb=" CB PHE k 189 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 6.95e-01 ... (remaining 7547 not shown) Planarity restraints: 8800 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PRO l 300 " 0.084 2.00e-02 2.50e+03 1.64e-01 2.69e+02 pdb=" C PRO l 300 " -0.283 2.00e-02 2.50e+03 pdb=" O PRO l 300 " 0.122 2.00e-02 2.50e+03 pdb=" N SER l 301 " 0.077 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR l 298 " 0.021 2.00e-02 2.50e+03 4.40e-02 1.93e+01 pdb=" C TYR l 298 " -0.076 2.00e-02 2.50e+03 pdb=" O TYR l 298 " 0.029 2.00e-02 2.50e+03 pdb=" N PHE l 299 " 0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE K 190 " 0.012 2.00e-02 2.50e+03 2.35e-02 5.54e+00 pdb=" C PHE K 190 " -0.041 2.00e-02 2.50e+03 pdb=" O PHE K 190 " 0.015 2.00e-02 2.50e+03 pdb=" N VAL K 191 " 0.014 2.00e-02 2.50e+03 ... (remaining 8797 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 1282 2.71 - 3.25: 47861 3.25 - 3.80: 82306 3.80 - 4.35: 108978 4.35 - 4.90: 182392 Nonbonded interactions: 422819 Sorted by model distance: nonbonded pdb=" OG SER D 11 " pdb=" OD1 ASP D 13 " model vdw 2.158 3.040 nonbonded pdb=" OG SER d 11 " pdb=" OD1 ASP d 13 " model vdw 2.160 3.040 nonbonded pdb=" NH1 ARG E 287 " pdb=" O GLU F 220 " model vdw 2.182 3.120 nonbonded pdb=" O GLU C 259 " pdb=" NE2 GLN C 263 " model vdw 2.182 3.120 nonbonded pdb=" O TYR a 100 " pdb=" NH1 ARG i 114 " model vdw 2.186 3.120 ... (remaining 422814 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 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'a' } ncs_group { reference = chain 'B' selection = chain 'b' } ncs_group { reference = chain 'C' selection = chain 'c' } ncs_group { reference = chain 'D' selection = chain 'd' } ncs_group { reference = chain 'E' selection = chain 'e' } ncs_group { reference = chain 'F' selection = chain 'f' } ncs_group { reference = chain 'G' selection = chain 'g' } ncs_group { reference = chain 'H' selection = chain 'h' } ncs_group { reference = chain 'I' selection = chain 'i' } ncs_group { reference = chain 'J' selection = chain 'j' } ncs_group { reference = chain 'K' selection = chain 'k' } ncs_group { reference = chain 'L' selection = chain 'l' } ncs_group { reference = chain 'M' selection = chain 'm' } ncs_group { reference = chain 'N' selection = chain 'n' } 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: 1.540 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: 0.040 Extract box with map and model: 1.390 Check model and map are aligned: 0.270 Set scattering table: 0.330 Process input model: 82.700 Find NCS groups from input model: 3.100 Set up NCS constraints: 0.300 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:10.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 100.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 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 : 0.003 0.103 50172 Z= 0.163 Angle : 0.545 14.601 67870 Z= 0.313 Chirality : 0.042 0.216 7550 Planarity : 0.004 0.164 8800 Dihedral : 13.262 89.822 18424 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 0.06 % Allowed : 0.15 % Favored : 99.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.56 (0.10), residues: 6306 helix: 1.71 (0.11), residues: 2292 sheet: 0.31 (0.13), residues: 1496 loop : -0.82 (0.12), residues: 2518 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP L 154 HIS 0.007 0.001 HIS i 115 PHE 0.020 0.001 PHE l 299 TYR 0.032 0.001 TYR k 25 ARG 0.008 0.000 ARG M 186 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12612 Ramachandran restraints generated. 6306 Oldfield, 0 Emsley, 6306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12612 Ramachandran restraints generated. 6306 Oldfield, 0 Emsley, 6306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 813 residues out of total 5242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 810 time to evaluate : 4.224 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: b 183 GLU cc_start: 0.8026 (pm20) cc_final: 0.7705 (pm20) outliers start: 3 outliers final: 0 residues processed: 812 average time/residue: 1.5102 time to fit residues: 1488.2283 Evaluate side-chains 594 residues out of total 5242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 594 time to evaluate : 4.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 622 random chunks: chunk 525 optimal weight: 4.9990 chunk 471 optimal weight: 8.9990 chunk 261 optimal weight: 5.9990 chunk 161 optimal weight: 4.9990 chunk 318 optimal weight: 10.0000 chunk 251 optimal weight: 10.0000 chunk 487 optimal weight: 5.9990 chunk 188 optimal weight: 0.9980 chunk 296 optimal weight: 2.9990 chunk 362 optimal weight: 5.9990 chunk 564 optimal weight: 3.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 263 GLN D 210 GLN E 262 HIS E 328 HIS F 225 GLN F 272 GLN F 286 GLN F 308 HIS F 331 GLN I 201 GLN K 165 GLN M 163 HIS M 170 GLN a 89 GLN d 210 GLN e 262 HIS f 272 GLN f 286 GLN f 308 HIS i 201 GLN k 125 GLN k 165 GLN m 163 HIS m 170 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8357 moved from start: 0.1451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 50172 Z= 0.282 Angle : 0.554 11.180 67870 Z= 0.299 Chirality : 0.044 0.169 7550 Planarity : 0.004 0.060 8800 Dihedral : 4.509 28.894 7020 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 1.51 % Allowed : 7.96 % Favored : 90.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.91 (0.11), residues: 6306 helix: 2.18 (0.11), residues: 2322 sheet: 0.36 (0.13), residues: 1528 loop : -0.76 (0.12), residues: 2456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP L 165 HIS 0.010 0.001 HIS E 262 PHE 0.021 0.001 PHE B 171 TYR 0.028 0.001 TYR H 218 ARG 0.011 0.000 ARG N 195 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12612 Ramachandran restraints generated. 6306 Oldfield, 0 Emsley, 6306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12612 Ramachandran restraints generated. 6306 Oldfield, 0 Emsley, 6306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 710 residues out of total 5242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 631 time to evaluate : 4.179 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 181 GLU cc_start: 0.6834 (tm-30) cc_final: 0.6371 (tm-30) REVERT: C 62 GLN cc_start: 0.7451 (mt0) cc_final: 0.6966 (mt0) REVERT: C 265 ARG cc_start: 0.8805 (OUTLIER) cc_final: 0.8249 (tpt90) REVERT: D 205 GLU cc_start: 0.7645 (OUTLIER) cc_final: 0.7215 (tp30) REVERT: L 281 LYS cc_start: 0.7987 (OUTLIER) cc_final: 0.7724 (mtpp) REVERT: c 62 GLN cc_start: 0.7469 (mt0) cc_final: 0.6996 (mt0) REVERT: c 265 ARG cc_start: 0.8792 (OUTLIER) cc_final: 0.8448 (tpt90) REVERT: f 311 GLN cc_start: 0.8439 (OUTLIER) cc_final: 0.7975 (tt0) REVERT: l 281 LYS cc_start: 0.7985 (OUTLIER) cc_final: 0.7721 (mtpp) outliers start: 79 outliers final: 20 residues processed: 659 average time/residue: 1.4751 time to fit residues: 1185.5676 Evaluate side-chains 615 residues out of total 5242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 589 time to evaluate : 4.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 THR Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain C residue 71 MET Chi-restraints excluded: chain C residue 265 ARG Chi-restraints excluded: chain D residue 205 GLU Chi-restraints excluded: chain F residue 277 ILE Chi-restraints excluded: chain F residue 312 THR Chi-restraints excluded: chain I residue 211 LYS Chi-restraints excluded: chain J residue 25 ASP Chi-restraints excluded: chain L residue 137 ASN Chi-restraints excluded: chain L residue 252 CYS Chi-restraints excluded: chain L residue 281 LYS Chi-restraints excluded: chain M residue 198 LYS Chi-restraints excluded: chain a residue 214 VAL Chi-restraints excluded: chain c residue 71 MET Chi-restraints excluded: chain c residue 78 ILE Chi-restraints excluded: chain c residue 265 ARG Chi-restraints excluded: chain d residue 236 GLU Chi-restraints excluded: chain f residue 277 ILE Chi-restraints excluded: chain f residue 311 GLN Chi-restraints excluded: chain f residue 312 THR Chi-restraints excluded: chain i residue 66 MET Chi-restraints excluded: chain i residue 211 LYS Chi-restraints excluded: chain l residue 137 ASN Chi-restraints excluded: chain l residue 252 CYS Chi-restraints excluded: chain l residue 281 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 622 random chunks: chunk 313 optimal weight: 3.9990 chunk 175 optimal weight: 7.9990 chunk 470 optimal weight: 9.9990 chunk 384 optimal weight: 9.9990 chunk 155 optimal weight: 10.0000 chunk 565 optimal weight: 10.0000 chunk 611 optimal weight: 5.9990 chunk 503 optimal weight: 9.9990 chunk 561 optimal weight: 5.9990 chunk 192 optimal weight: 9.9990 chunk 453 optimal weight: 7.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 262 HIS F 286 GLN G 147 GLN ** a 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 187 HIS d 54 GLN e 262 HIS f 286 GLN g 147 GLN ** h 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8421 moved from start: 0.1871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.073 50172 Z= 0.447 Angle : 0.595 11.285 67870 Z= 0.320 Chirality : 0.046 0.196 7550 Planarity : 0.004 0.060 8800 Dihedral : 4.653 27.897 7020 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 1.58 % Allowed : 10.21 % Favored : 88.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.91 (0.10), residues: 6306 helix: 2.17 (0.11), residues: 2342 sheet: 0.33 (0.12), residues: 1542 loop : -0.77 (0.12), residues: 2422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP h 245 HIS 0.006 0.001 HIS i 91 PHE 0.015 0.001 PHE B 171 TYR 0.031 0.001 TYR h 218 ARG 0.014 0.001 ARG e 287 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12612 Ramachandran restraints generated. 6306 Oldfield, 0 Emsley, 6306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12612 Ramachandran restraints generated. 6306 Oldfield, 0 Emsley, 6306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 678 residues out of total 5242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 595 time to evaluate : 4.215 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: B 77 MET cc_start: 0.8224 (OUTLIER) cc_final: 0.7900 (mtt) REVERT: B 181 GLU cc_start: 0.6859 (tm-30) cc_final: 0.6483 (tm-30) REVERT: C 265 ARG cc_start: 0.8765 (OUTLIER) cc_final: 0.8192 (tpt90) REVERT: F 311 GLN cc_start: 0.8488 (OUTLIER) cc_final: 0.8039 (tt0) REVERT: b 77 MET cc_start: 0.8231 (OUTLIER) cc_final: 0.7907 (mtt) REVERT: b 187 HIS cc_start: 0.8243 (t-90) cc_final: 0.8024 (t70) REVERT: c 265 ARG cc_start: 0.8801 (OUTLIER) cc_final: 0.8291 (tpt90) REVERT: e 255 GLN cc_start: 0.8850 (OUTLIER) cc_final: 0.8033 (tt0) REVERT: f 311 GLN cc_start: 0.8469 (OUTLIER) cc_final: 0.8011 (tt0) outliers start: 83 outliers final: 33 residues processed: 634 average time/residue: 1.4591 time to fit residues: 1132.7222 Evaluate side-chains 588 residues out of total 5242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 548 time to evaluate : 4.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 THR Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 145 GLN Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain B residue 77 MET Chi-restraints excluded: chain B residue 211 VAL Chi-restraints excluded: chain C residue 78 ILE Chi-restraints excluded: chain C residue 265 ARG Chi-restraints excluded: chain C residue 266 GLU Chi-restraints excluded: chain D residue 203 ASN Chi-restraints excluded: chain F residue 277 ILE Chi-restraints excluded: chain F residue 311 GLN Chi-restraints excluded: chain F residue 312 THR Chi-restraints excluded: chain G residue 157 VAL Chi-restraints excluded: chain I residue 211 LYS Chi-restraints excluded: chain K residue 1 MET Chi-restraints excluded: chain L residue 137 ASN Chi-restraints excluded: chain L residue 196 MET Chi-restraints excluded: chain L residue 252 CYS Chi-restraints excluded: chain M residue 198 LYS Chi-restraints excluded: chain N residue 124 VAL Chi-restraints excluded: chain a residue 145 GLN Chi-restraints excluded: chain a residue 214 VAL Chi-restraints excluded: chain b residue 77 MET Chi-restraints excluded: chain b residue 211 VAL Chi-restraints excluded: chain c residue 78 ILE Chi-restraints excluded: chain c residue 265 ARG Chi-restraints excluded: chain d residue 236 GLU Chi-restraints excluded: chain e residue 255 GLN Chi-restraints excluded: chain f residue 277 ILE Chi-restraints excluded: chain f residue 311 GLN Chi-restraints excluded: chain f residue 312 THR Chi-restraints excluded: chain g residue 157 VAL Chi-restraints excluded: chain i residue 66 MET Chi-restraints excluded: chain i residue 211 LYS Chi-restraints excluded: chain k residue 1 MET Chi-restraints excluded: chain l residue 137 ASN Chi-restraints excluded: chain l residue 196 MET Chi-restraints excluded: chain l residue 252 CYS Chi-restraints excluded: chain n residue 124 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 622 random chunks: chunk 559 optimal weight: 3.9990 chunk 425 optimal weight: 9.9990 chunk 293 optimal weight: 7.9990 chunk 62 optimal weight: 1.9990 chunk 270 optimal weight: 6.9990 chunk 379 optimal weight: 2.9990 chunk 567 optimal weight: 9.9990 chunk 601 optimal weight: 8.9990 chunk 296 optimal weight: 1.9990 chunk 538 optimal weight: 9.9990 chunk 162 optimal weight: 4.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 205 ASN E 222 GLN E 262 HIS F 286 GLN M 280 ASN a 207 GLN b 205 ASN e 262 HIS f 286 GLN m 280 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8378 moved from start: 0.1947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 50172 Z= 0.249 Angle : 0.526 8.889 67870 Z= 0.285 Chirality : 0.043 0.181 7550 Planarity : 0.004 0.057 8800 Dihedral : 4.455 29.194 7020 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 1.34 % Allowed : 11.43 % Favored : 87.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.08 (0.11), residues: 6306 helix: 2.36 (0.11), residues: 2338 sheet: 0.37 (0.13), residues: 1538 loop : -0.68 (0.12), residues: 2430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP l 154 HIS 0.005 0.001 HIS D 187 PHE 0.021 0.001 PHE B 171 TYR 0.022 0.001 TYR H 218 ARG 0.008 0.000 ARG b 225 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12612 Ramachandran restraints generated. 6306 Oldfield, 0 Emsley, 6306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12612 Ramachandran restraints generated. 6306 Oldfield, 0 Emsley, 6306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 680 residues out of total 5242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 610 time to evaluate : 4.185 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 175 ARG cc_start: 0.8388 (ttm110) cc_final: 0.8095 (ttm110) REVERT: C 221 MET cc_start: 0.8913 (OUTLIER) cc_final: 0.7891 (tpp) REVERT: C 265 ARG cc_start: 0.8742 (OUTLIER) cc_final: 0.8099 (tpt90) REVERT: c 221 MET cc_start: 0.8926 (OUTLIER) cc_final: 0.7857 (tpp) REVERT: c 265 ARG cc_start: 0.8823 (OUTLIER) cc_final: 0.8292 (tpt90) outliers start: 70 outliers final: 29 residues processed: 644 average time/residue: 1.4696 time to fit residues: 1156.4819 Evaluate side-chains 591 residues out of total 5242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 558 time to evaluate : 4.128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 THR Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 145 GLN Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 211 VAL Chi-restraints excluded: chain C residue 78 ILE Chi-restraints excluded: chain C residue 221 MET Chi-restraints excluded: chain C residue 265 ARG Chi-restraints excluded: chain D residue 203 ASN Chi-restraints excluded: chain F residue 277 ILE Chi-restraints excluded: chain F residue 312 THR Chi-restraints excluded: chain I residue 211 LYS Chi-restraints excluded: chain K residue 1 MET Chi-restraints excluded: chain L residue 137 ASN Chi-restraints excluded: chain L residue 252 CYS Chi-restraints excluded: chain M residue 198 LYS Chi-restraints excluded: chain M residue 224 HIS Chi-restraints excluded: chain M residue 329 VAL Chi-restraints excluded: chain a residue 48 VAL Chi-restraints excluded: chain a residue 145 GLN Chi-restraints excluded: chain a residue 214 VAL Chi-restraints excluded: chain b residue 211 VAL Chi-restraints excluded: chain c residue 78 ILE Chi-restraints excluded: chain c residue 221 MET Chi-restraints excluded: chain c residue 265 ARG Chi-restraints excluded: chain d residue 236 GLU Chi-restraints excluded: chain f residue 277 ILE Chi-restraints excluded: chain i residue 211 LYS Chi-restraints excluded: chain l residue 137 ASN Chi-restraints excluded: chain l residue 252 CYS Chi-restraints excluded: chain m residue 224 HIS Chi-restraints excluded: chain m residue 329 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 622 random chunks: chunk 500 optimal weight: 10.0000 chunk 341 optimal weight: 6.9990 chunk 8 optimal weight: 7.9990 chunk 447 optimal weight: 9.9990 chunk 248 optimal weight: 0.9980 chunk 513 optimal weight: 1.9990 chunk 415 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 307 optimal weight: 8.9990 chunk 539 optimal weight: 6.9990 chunk 151 optimal weight: 8.9990 overall best weight: 4.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 205 ASN E 262 HIS F 286 GLN G 33 ASN H 121 GLN ** L 291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 280 ASN b 205 ASN e 262 HIS f 286 GLN g 33 ASN h 121 GLN ** l 291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** m 280 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8408 moved from start: 0.2083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 50172 Z= 0.360 Angle : 0.561 8.314 67870 Z= 0.303 Chirality : 0.045 0.182 7550 Planarity : 0.004 0.052 8800 Dihedral : 4.546 28.960 7020 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 1.43 % Allowed : 11.85 % Favored : 86.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.06 (0.11), residues: 6306 helix: 2.31 (0.11), residues: 2348 sheet: 0.41 (0.13), residues: 1548 loop : -0.69 (0.12), residues: 2410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP l 165 HIS 0.005 0.001 HIS D 187 PHE 0.012 0.001 PHE l 260 TYR 0.025 0.001 TYR H 218 ARG 0.009 0.000 ARG b 225 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12612 Ramachandran restraints generated. 6306 Oldfield, 0 Emsley, 6306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12612 Ramachandran restraints generated. 6306 Oldfield, 0 Emsley, 6306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 664 residues out of total 5242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 589 time to evaluate : 4.288 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 77 MET cc_start: 0.8138 (OUTLIER) cc_final: 0.7868 (mtt) REVERT: B 175 ARG cc_start: 0.8431 (OUTLIER) cc_final: 0.8072 (ttm110) REVERT: B 217 GLU cc_start: 0.8261 (pp20) cc_final: 0.7985 (pp20) REVERT: C 265 ARG cc_start: 0.8737 (OUTLIER) cc_final: 0.8221 (tpt90) REVERT: b 77 MET cc_start: 0.8150 (OUTLIER) cc_final: 0.7880 (mtt) REVERT: c 265 ARG cc_start: 0.8823 (OUTLIER) cc_final: 0.8252 (tpt90) outliers start: 75 outliers final: 35 residues processed: 627 average time/residue: 1.4516 time to fit residues: 1113.4969 Evaluate side-chains 581 residues out of total 5242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 541 time to evaluate : 4.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 THR Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 145 GLN Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain B residue 77 MET Chi-restraints excluded: chain B residue 175 ARG Chi-restraints excluded: chain B residue 211 VAL Chi-restraints excluded: chain C residue 78 ILE Chi-restraints excluded: chain C residue 265 ARG Chi-restraints excluded: chain F residue 277 ILE Chi-restraints excluded: chain F residue 312 THR Chi-restraints excluded: chain G residue 157 VAL Chi-restraints excluded: chain G residue 200 VAL Chi-restraints excluded: chain I residue 211 LYS Chi-restraints excluded: chain I residue 241 LEU Chi-restraints excluded: chain K residue 1 MET Chi-restraints excluded: chain L residue 137 ASN Chi-restraints excluded: chain L residue 196 MET Chi-restraints excluded: chain L residue 252 CYS Chi-restraints excluded: chain M residue 198 LYS Chi-restraints excluded: chain M residue 329 VAL Chi-restraints excluded: chain a residue 48 VAL Chi-restraints excluded: chain a residue 145 GLN Chi-restraints excluded: chain a residue 214 VAL Chi-restraints excluded: chain b residue 77 MET Chi-restraints excluded: chain b residue 211 VAL Chi-restraints excluded: chain c residue 78 ILE Chi-restraints excluded: chain c residue 265 ARG Chi-restraints excluded: chain d residue 236 GLU Chi-restraints excluded: chain e residue 304 GLN Chi-restraints excluded: chain f residue 277 ILE Chi-restraints excluded: chain g residue 157 VAL Chi-restraints excluded: chain g residue 200 VAL Chi-restraints excluded: chain i residue 211 LYS Chi-restraints excluded: chain i residue 241 LEU Chi-restraints excluded: chain k residue 1 MET Chi-restraints excluded: chain l residue 137 ASN Chi-restraints excluded: chain l residue 196 MET Chi-restraints excluded: chain l residue 252 CYS Chi-restraints excluded: chain m residue 329 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 622 random chunks: chunk 202 optimal weight: 7.9990 chunk 541 optimal weight: 0.9990 chunk 118 optimal weight: 10.0000 chunk 352 optimal weight: 5.9990 chunk 148 optimal weight: 10.0000 chunk 601 optimal weight: 8.9990 chunk 499 optimal weight: 4.9990 chunk 278 optimal weight: 10.0000 chunk 50 optimal weight: 20.0000 chunk 199 optimal weight: 7.9990 chunk 315 optimal weight: 3.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 205 ASN E 262 HIS F 286 GLN G 33 ASN H 121 GLN ** L 291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 280 ASN b 205 ASN e 262 HIS f 286 GLN g 33 ASN h 121 GLN ** l 291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** m 280 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8408 moved from start: 0.2146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 50172 Z= 0.347 Angle : 0.563 8.369 67870 Z= 0.303 Chirality : 0.044 0.180 7550 Planarity : 0.004 0.048 8800 Dihedral : 4.542 28.951 7020 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 1.28 % Allowed : 12.79 % Favored : 85.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.10 (0.11), residues: 6306 helix: 2.34 (0.11), residues: 2344 sheet: 0.43 (0.13), residues: 1546 loop : -0.67 (0.12), residues: 2416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP h 245 HIS 0.005 0.001 HIS i 91 PHE 0.014 0.001 PHE B 171 TYR 0.024 0.001 TYR h 218 ARG 0.009 0.000 ARG b 225 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12612 Ramachandran restraints generated. 6306 Oldfield, 0 Emsley, 6306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12612 Ramachandran restraints generated. 6306 Oldfield, 0 Emsley, 6306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 658 residues out of total 5242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 591 time to evaluate : 4.306 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 77 MET cc_start: 0.8136 (OUTLIER) cc_final: 0.7864 (mtt) REVERT: B 82 ARG cc_start: 0.8059 (OUTLIER) cc_final: 0.7493 (mmm-85) REVERT: B 175 ARG cc_start: 0.8405 (OUTLIER) cc_final: 0.8075 (ttm110) REVERT: B 181 GLU cc_start: 0.6741 (tm-30) cc_final: 0.6147 (tm-30) REVERT: C 265 ARG cc_start: 0.8759 (OUTLIER) cc_final: 0.8252 (tpt90) REVERT: b 77 MET cc_start: 0.8145 (OUTLIER) cc_final: 0.7873 (mtt) REVERT: c 265 ARG cc_start: 0.8809 (OUTLIER) cc_final: 0.8223 (tpt90) outliers start: 67 outliers final: 43 residues processed: 626 average time/residue: 1.4821 time to fit residues: 1131.4688 Evaluate side-chains 585 residues out of total 5242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 536 time to evaluate : 4.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 THR Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 145 GLN Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain B residue 77 MET Chi-restraints excluded: chain B residue 82 ARG Chi-restraints excluded: chain B residue 175 ARG Chi-restraints excluded: chain B residue 211 VAL Chi-restraints excluded: chain C residue 78 ILE Chi-restraints excluded: chain C residue 265 ARG Chi-restraints excluded: chain E residue 289 MET Chi-restraints excluded: chain F residue 277 ILE Chi-restraints excluded: chain F residue 312 THR Chi-restraints excluded: chain G residue 157 VAL Chi-restraints excluded: chain G residue 200 VAL Chi-restraints excluded: chain I residue 54 ILE Chi-restraints excluded: chain I residue 211 LYS Chi-restraints excluded: chain I residue 241 LEU Chi-restraints excluded: chain J residue 124 THR Chi-restraints excluded: chain K residue 1 MET Chi-restraints excluded: chain K residue 97 ARG Chi-restraints excluded: chain L residue 137 ASN Chi-restraints excluded: chain L residue 252 CYS Chi-restraints excluded: chain M residue 198 LYS Chi-restraints excluded: chain M residue 329 VAL Chi-restraints excluded: chain N residue 124 VAL Chi-restraints excluded: chain a residue 48 VAL Chi-restraints excluded: chain a residue 145 GLN Chi-restraints excluded: chain a residue 214 VAL Chi-restraints excluded: chain b residue 77 MET Chi-restraints excluded: chain b residue 211 VAL Chi-restraints excluded: chain c residue 78 ILE Chi-restraints excluded: chain c residue 265 ARG Chi-restraints excluded: chain d residue 236 GLU Chi-restraints excluded: chain e residue 289 MET Chi-restraints excluded: chain f residue 277 ILE Chi-restraints excluded: chain g residue 157 VAL Chi-restraints excluded: chain g residue 200 VAL Chi-restraints excluded: chain i residue 54 ILE Chi-restraints excluded: chain i residue 211 LYS Chi-restraints excluded: chain i residue 241 LEU Chi-restraints excluded: chain j residue 124 THR Chi-restraints excluded: chain k residue 1 MET Chi-restraints excluded: chain k residue 97 ARG Chi-restraints excluded: chain l residue 137 ASN Chi-restraints excluded: chain l residue 252 CYS Chi-restraints excluded: chain m residue 329 VAL Chi-restraints excluded: chain n residue 124 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 622 random chunks: chunk 580 optimal weight: 9.9990 chunk 67 optimal weight: 5.9990 chunk 342 optimal weight: 8.9990 chunk 439 optimal weight: 10.0000 chunk 340 optimal weight: 0.9980 chunk 506 optimal weight: 2.9990 chunk 336 optimal weight: 5.9990 chunk 599 optimal weight: 10.0000 chunk 375 optimal weight: 8.9990 chunk 365 optimal weight: 8.9990 chunk 276 optimal weight: 2.9990 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 205 ASN E 222 GLN E 262 HIS F 286 GLN G 33 ASN H 121 GLN ** L 291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 280 ASN ** b 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 205 ASN e 262 HIS f 286 GLN g 33 ASN h 121 GLN ** l 291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** m 280 ASN m 282 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8393 moved from start: 0.2192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 50172 Z= 0.287 Angle : 0.552 9.599 67870 Z= 0.297 Chirality : 0.044 0.175 7550 Planarity : 0.004 0.047 8800 Dihedral : 4.492 29.322 7020 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 1.30 % Allowed : 13.28 % Favored : 85.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.16 (0.11), residues: 6306 helix: 2.40 (0.11), residues: 2348 sheet: 0.44 (0.13), residues: 1548 loop : -0.63 (0.12), residues: 2410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP L 154 HIS 0.004 0.001 HIS D 187 PHE 0.011 0.001 PHE K 24 TYR 0.022 0.001 TYR h 218 ARG 0.010 0.000 ARG B 225 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12612 Ramachandran restraints generated. 6306 Oldfield, 0 Emsley, 6306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12612 Ramachandran restraints generated. 6306 Oldfield, 0 Emsley, 6306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 661 residues out of total 5242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 593 time to evaluate : 4.237 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 77 MET cc_start: 0.8085 (OUTLIER) cc_final: 0.7818 (mtt) REVERT: B 175 ARG cc_start: 0.8434 (OUTLIER) cc_final: 0.8140 (ttm110) REVERT: B 181 GLU cc_start: 0.6636 (tm-30) cc_final: 0.6089 (tm-30) REVERT: B 217 GLU cc_start: 0.8258 (pp20) cc_final: 0.8051 (pp20) REVERT: E 324 ASP cc_start: 0.7771 (t0) cc_final: 0.7313 (t0) REVERT: b 77 MET cc_start: 0.8096 (OUTLIER) cc_final: 0.7825 (mtt) REVERT: b 82 ARG cc_start: 0.8032 (OUTLIER) cc_final: 0.7457 (mmm-85) REVERT: b 181 GLU cc_start: 0.6860 (tm-30) cc_final: 0.5440 (tm-30) REVERT: b 217 GLU cc_start: 0.8373 (pp20) cc_final: 0.7866 (pp20) REVERT: c 265 ARG cc_start: 0.8823 (OUTLIER) cc_final: 0.8229 (tpt90) REVERT: e 324 ASP cc_start: 0.7971 (t0) cc_final: 0.7482 (t0) outliers start: 68 outliers final: 39 residues processed: 633 average time/residue: 1.4882 time to fit residues: 1156.1889 Evaluate side-chains 602 residues out of total 5242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 558 time to evaluate : 4.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 THR Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 145 GLN Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain B residue 77 MET Chi-restraints excluded: chain B residue 175 ARG Chi-restraints excluded: chain B residue 211 VAL Chi-restraints excluded: chain C residue 78 ILE Chi-restraints excluded: chain F residue 277 ILE Chi-restraints excluded: chain F residue 312 THR Chi-restraints excluded: chain G residue 157 VAL Chi-restraints excluded: chain G residue 200 VAL Chi-restraints excluded: chain G residue 231 MET Chi-restraints excluded: chain I residue 241 LEU Chi-restraints excluded: chain J residue 124 THR Chi-restraints excluded: chain K residue 1 MET Chi-restraints excluded: chain K residue 97 ARG Chi-restraints excluded: chain L residue 137 ASN Chi-restraints excluded: chain L residue 252 CYS Chi-restraints excluded: chain M residue 198 LYS Chi-restraints excluded: chain M residue 224 HIS Chi-restraints excluded: chain M residue 329 VAL Chi-restraints excluded: chain N residue 124 VAL Chi-restraints excluded: chain a residue 48 VAL Chi-restraints excluded: chain a residue 145 GLN Chi-restraints excluded: chain a residue 214 VAL Chi-restraints excluded: chain b residue 77 MET Chi-restraints excluded: chain b residue 82 ARG Chi-restraints excluded: chain b residue 211 VAL Chi-restraints excluded: chain c residue 78 ILE Chi-restraints excluded: chain c residue 265 ARG Chi-restraints excluded: chain f residue 277 ILE Chi-restraints excluded: chain g residue 157 VAL Chi-restraints excluded: chain g residue 200 VAL Chi-restraints excluded: chain i residue 241 LEU Chi-restraints excluded: chain j residue 124 THR Chi-restraints excluded: chain k residue 1 MET Chi-restraints excluded: chain k residue 97 ARG Chi-restraints excluded: chain l residue 137 ASN Chi-restraints excluded: chain l residue 252 CYS Chi-restraints excluded: chain m residue 224 HIS Chi-restraints excluded: chain m residue 329 VAL Chi-restraints excluded: chain n residue 124 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 622 random chunks: chunk 370 optimal weight: 0.5980 chunk 239 optimal weight: 8.9990 chunk 358 optimal weight: 0.9990 chunk 180 optimal weight: 3.9990 chunk 117 optimal weight: 0.0980 chunk 116 optimal weight: 8.9990 chunk 381 optimal weight: 4.9990 chunk 408 optimal weight: 9.9990 chunk 296 optimal weight: 8.9990 chunk 55 optimal weight: 3.9990 chunk 471 optimal weight: 5.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 205 ASN E 262 HIS F 286 GLN G 33 ASN H 121 GLN I 201 GLN L 291 GLN M 280 ASN a 207 GLN ** b 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 205 ASN e 262 HIS f 286 GLN g 33 ASN h 121 GLN i 201 GLN l 291 GLN m 280 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8356 moved from start: 0.2245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 50172 Z= 0.189 Angle : 0.539 8.959 67870 Z= 0.289 Chirality : 0.043 0.179 7550 Planarity : 0.004 0.046 8800 Dihedral : 4.360 29.985 7020 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 0.99 % Allowed : 14.31 % Favored : 84.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.28 (0.11), residues: 6306 helix: 2.53 (0.11), residues: 2336 sheet: 0.50 (0.13), residues: 1544 loop : -0.59 (0.12), residues: 2426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP l 154 HIS 0.004 0.001 HIS D 187 PHE 0.014 0.001 PHE B 171 TYR 0.018 0.001 TYR H 218 ARG 0.009 0.000 ARG f 404 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12612 Ramachandran restraints generated. 6306 Oldfield, 0 Emsley, 6306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12612 Ramachandran restraints generated. 6306 Oldfield, 0 Emsley, 6306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 679 residues out of total 5242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 627 time to evaluate : 4.604 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: B 82 ARG cc_start: 0.7954 (OUTLIER) cc_final: 0.7384 (mmm-85) REVERT: B 175 ARG cc_start: 0.8422 (OUTLIER) cc_final: 0.8122 (ttm110) REVERT: B 217 GLU cc_start: 0.8179 (pp20) cc_final: 0.7823 (pp20) REVERT: b 82 ARG cc_start: 0.7946 (OUTLIER) cc_final: 0.7407 (mmm-85) REVERT: b 181 GLU cc_start: 0.6724 (tm-30) cc_final: 0.6366 (tm-30) REVERT: b 183 GLU cc_start: 0.7971 (pm20) cc_final: 0.7753 (pm20) REVERT: b 217 GLU cc_start: 0.8239 (pp20) cc_final: 0.7884 (pp20) outliers start: 52 outliers final: 31 residues processed: 652 average time/residue: 1.4694 time to fit residues: 1179.2978 Evaluate side-chains 600 residues out of total 5242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 566 time to evaluate : 4.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 THR Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 49 THR Chi-restraints excluded: chain A residue 145 GLN Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain B residue 82 ARG Chi-restraints excluded: chain B residue 175 ARG Chi-restraints excluded: chain B residue 211 VAL Chi-restraints excluded: chain C residue 56 PHE Chi-restraints excluded: chain C residue 78 ILE Chi-restraints excluded: chain C residue 234 ASP Chi-restraints excluded: chain F residue 312 THR Chi-restraints excluded: chain G residue 231 MET Chi-restraints excluded: chain I residue 241 LEU Chi-restraints excluded: chain J residue 124 THR Chi-restraints excluded: chain L residue 137 ASN Chi-restraints excluded: chain L residue 252 CYS Chi-restraints excluded: chain M residue 198 LYS Chi-restraints excluded: chain M residue 224 HIS Chi-restraints excluded: chain N residue 124 VAL Chi-restraints excluded: chain a residue 47 VAL Chi-restraints excluded: chain a residue 48 VAL Chi-restraints excluded: chain a residue 145 GLN Chi-restraints excluded: chain a residue 214 VAL Chi-restraints excluded: chain b residue 82 ARG Chi-restraints excluded: chain b residue 211 VAL Chi-restraints excluded: chain c residue 78 ILE Chi-restraints excluded: chain e residue 324 ASP Chi-restraints excluded: chain i residue 241 LEU Chi-restraints excluded: chain j residue 124 THR Chi-restraints excluded: chain l residue 137 ASN Chi-restraints excluded: chain l residue 252 CYS Chi-restraints excluded: chain m residue 224 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 622 random chunks: chunk 545 optimal weight: 0.8980 chunk 574 optimal weight: 5.9990 chunk 524 optimal weight: 0.9990 chunk 558 optimal weight: 10.0000 chunk 336 optimal weight: 2.9990 chunk 243 optimal weight: 9.9990 chunk 438 optimal weight: 10.0000 chunk 171 optimal weight: 9.9990 chunk 504 optimal weight: 8.9990 chunk 528 optimal weight: 10.0000 chunk 556 optimal weight: 2.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 205 ASN E 262 HIS G 33 ASN H 121 GLN ** H 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 291 GLN M 280 ASN N 94 GLN ** b 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 205 ASN e 262 HIS g 33 ASN h 121 GLN ** h 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 291 GLN m 280 ASN n 94 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8370 moved from start: 0.2277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 50172 Z= 0.234 Angle : 0.562 9.675 67870 Z= 0.300 Chirality : 0.044 0.196 7550 Planarity : 0.004 0.053 8800 Dihedral : 4.385 29.897 7020 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 1.01 % Allowed : 14.90 % Favored : 84.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.28 (0.11), residues: 6306 helix: 2.54 (0.11), residues: 2332 sheet: 0.51 (0.13), residues: 1548 loop : -0.60 (0.12), residues: 2426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP l 154 HIS 0.004 0.001 HIS D 187 PHE 0.011 0.001 PHE K 24 TYR 0.020 0.001 TYR H 218 ARG 0.012 0.000 ARG f 404 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12612 Ramachandran restraints generated. 6306 Oldfield, 0 Emsley, 6306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12612 Ramachandran restraints generated. 6306 Oldfield, 0 Emsley, 6306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 645 residues out of total 5242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 592 time to evaluate : 4.190 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 82 ARG cc_start: 0.7961 (OUTLIER) cc_final: 0.7394 (mmm-85) REVERT: B 217 GLU cc_start: 0.8196 (pp20) cc_final: 0.7817 (pp20) REVERT: E 300 ASP cc_start: 0.7887 (m-30) cc_final: 0.7555 (m-30) REVERT: E 324 ASP cc_start: 0.8139 (t0) cc_final: 0.7670 (t0) REVERT: I 194 ASN cc_start: 0.8323 (m-40) cc_final: 0.8104 (m110) REVERT: b 82 ARG cc_start: 0.7951 (OUTLIER) cc_final: 0.7390 (mmm-85) REVERT: b 217 GLU cc_start: 0.8233 (pp20) cc_final: 0.7669 (pp20) REVERT: d 171 TYR cc_start: 0.8591 (t80) cc_final: 0.8352 (t80) REVERT: e 329 MET cc_start: 0.8264 (OUTLIER) cc_final: 0.7541 (mmm) outliers start: 53 outliers final: 32 residues processed: 617 average time/residue: 1.4437 time to fit residues: 1090.4344 Evaluate side-chains 599 residues out of total 5242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 564 time to evaluate : 4.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 THR Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 49 THR Chi-restraints excluded: chain A residue 145 GLN Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain B residue 82 ARG Chi-restraints excluded: chain B residue 211 VAL Chi-restraints excluded: chain C residue 56 PHE Chi-restraints excluded: chain C residue 78 ILE Chi-restraints excluded: chain F residue 312 THR Chi-restraints excluded: chain G residue 157 VAL Chi-restraints excluded: chain G residue 231 MET Chi-restraints excluded: chain I residue 241 LEU Chi-restraints excluded: chain J residue 124 THR Chi-restraints excluded: chain L residue 137 ASN Chi-restraints excluded: chain L residue 252 CYS Chi-restraints excluded: chain M residue 198 LYS Chi-restraints excluded: chain M residue 224 HIS Chi-restraints excluded: chain M residue 329 VAL Chi-restraints excluded: chain a residue 47 VAL Chi-restraints excluded: chain a residue 48 VAL Chi-restraints excluded: chain a residue 145 GLN Chi-restraints excluded: chain a residue 214 VAL Chi-restraints excluded: chain b residue 82 ARG Chi-restraints excluded: chain b residue 211 VAL Chi-restraints excluded: chain c residue 78 ILE Chi-restraints excluded: chain e residue 324 ASP Chi-restraints excluded: chain e residue 329 MET Chi-restraints excluded: chain i residue 241 LEU Chi-restraints excluded: chain j residue 124 THR Chi-restraints excluded: chain l residue 137 ASN Chi-restraints excluded: chain l residue 252 CYS Chi-restraints excluded: chain m residue 224 HIS Chi-restraints excluded: chain m residue 329 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 622 random chunks: chunk 366 optimal weight: 7.9990 chunk 590 optimal weight: 7.9990 chunk 360 optimal weight: 0.9990 chunk 280 optimal weight: 6.9990 chunk 410 optimal weight: 0.1980 chunk 619 optimal weight: 5.9990 chunk 570 optimal weight: 5.9990 chunk 493 optimal weight: 0.0010 chunk 51 optimal weight: 5.9990 chunk 381 optimal weight: 4.9990 chunk 302 optimal weight: 0.0170 overall best weight: 1.2428 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 89 GLN ** B 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 262 HIS F 286 GLN G 33 ASN H 121 GLN ** H 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 291 GLN M 280 ASN ** b 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 205 ASN e 262 HIS f 286 GLN g 33 ASN h 121 GLN ** h 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 291 GLN m 280 ASN m 282 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8328 moved from start: 0.2381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 50172 Z= 0.165 Angle : 0.557 12.312 67870 Z= 0.296 Chirality : 0.043 0.218 7550 Planarity : 0.004 0.072 8800 Dihedral : 4.288 29.428 7020 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 0.80 % Allowed : 14.94 % Favored : 84.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.34 (0.11), residues: 6306 helix: 2.62 (0.11), residues: 2332 sheet: 0.51 (0.13), residues: 1544 loop : -0.58 (0.12), residues: 2430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP l 154 HIS 0.004 0.000 HIS D 187 PHE 0.032 0.001 PHE B 171 TYR 0.018 0.001 TYR h 218 ARG 0.013 0.000 ARG f 404 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12612 Ramachandran restraints generated. 6306 Oldfield, 0 Emsley, 6306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12612 Ramachandran restraints generated. 6306 Oldfield, 0 Emsley, 6306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 656 residues out of total 5242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 614 time to evaluate : 4.352 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 82 ARG cc_start: 0.7887 (OUTLIER) cc_final: 0.7313 (mmm-85) REVERT: B 217 GLU cc_start: 0.8093 (pp20) cc_final: 0.7791 (pp20) REVERT: D 171 TYR cc_start: 0.8515 (t80) cc_final: 0.8253 (t80) REVERT: E 300 ASP cc_start: 0.7813 (m-30) cc_final: 0.7509 (m-30) REVERT: M 312 ASP cc_start: 0.7127 (t0) cc_final: 0.6705 (t0) REVERT: b 82 ARG cc_start: 0.7885 (OUTLIER) cc_final: 0.7333 (mmm-85) REVERT: d 171 TYR cc_start: 0.8557 (t80) cc_final: 0.8325 (t80) REVERT: m 312 ASP cc_start: 0.7130 (t0) cc_final: 0.6714 (t0) outliers start: 42 outliers final: 29 residues processed: 637 average time/residue: 1.4360 time to fit residues: 1122.4962 Evaluate side-chains 615 residues out of total 5242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 584 time to evaluate : 4.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 THR Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 49 THR Chi-restraints excluded: chain A residue 145 GLN Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain B residue 82 ARG Chi-restraints excluded: chain B residue 211 VAL Chi-restraints excluded: chain C residue 78 ILE Chi-restraints excluded: chain D residue 203 ASN Chi-restraints excluded: chain E residue 324 ASP Chi-restraints excluded: chain G residue 200 VAL Chi-restraints excluded: chain I residue 241 LEU Chi-restraints excluded: chain L residue 137 ASN Chi-restraints excluded: chain L residue 252 CYS Chi-restraints excluded: chain M residue 198 LYS Chi-restraints excluded: chain M residue 224 HIS Chi-restraints excluded: chain M residue 329 VAL Chi-restraints excluded: chain a residue 47 VAL Chi-restraints excluded: chain a residue 48 VAL Chi-restraints excluded: chain a residue 145 GLN Chi-restraints excluded: chain a residue 214 VAL Chi-restraints excluded: chain b residue 82 ARG Chi-restraints excluded: chain b residue 211 VAL Chi-restraints excluded: chain c residue 78 ILE Chi-restraints excluded: chain g residue 200 VAL Chi-restraints excluded: chain i residue 241 LEU Chi-restraints excluded: chain l residue 137 ASN Chi-restraints excluded: chain l residue 252 CYS Chi-restraints excluded: chain m residue 224 HIS Chi-restraints excluded: chain m residue 329 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 622 random chunks: chunk 391 optimal weight: 10.0000 chunk 525 optimal weight: 3.9990 chunk 151 optimal weight: 10.0000 chunk 454 optimal weight: 7.9990 chunk 72 optimal weight: 6.9990 chunk 137 optimal weight: 9.9990 chunk 494 optimal weight: 9.9990 chunk 206 optimal weight: 7.9990 chunk 507 optimal weight: 9.9990 chunk 62 optimal weight: 0.0270 chunk 91 optimal weight: 9.9990 overall best weight: 5.4046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 262 HIS G 33 ASN H 121 GLN ** H 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 282 GLN N 94 GLN ** b 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 205 ASN e 262 HIS g 33 ASN h 121 GLN ** h 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** m 282 GLN n 94 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.069090 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2590 r_free = 0.2590 target = 0.050633 restraints weight = 112305.996| |-----------------------------------------------------------------------------| r_work (start): 0.2582 rms_B_bonded: 2.75 r_work: 0.2444 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2312 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.2312 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9124 moved from start: 0.2371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 50172 Z= 0.387 Angle : 0.621 15.699 67870 Z= 0.330 Chirality : 0.046 0.263 7550 Planarity : 0.004 0.055 8800 Dihedral : 4.563 28.787 7020 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 0.88 % Allowed : 15.08 % Favored : 84.05 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.19 (0.11), residues: 6306 helix: 2.42 (0.11), residues: 2346 sheet: 0.49 (0.13), residues: 1538 loop : -0.65 (0.12), residues: 2422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP l 165 HIS 0.004 0.001 HIS i 91 PHE 0.018 0.001 PHE B 171 TYR 0.025 0.001 TYR H 218 ARG 0.013 0.000 ARG f 404 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 16268.03 seconds wall clock time: 282 minutes 38.02 seconds (16958.02 seconds total)