Starting phenix.real_space_refine on Fri Aug 7 00:32:45 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8x5d_38066/08_2026/8x5d_38066.cif Found real_map, /net/cci-nas-00/data/ceres_data/8x5d_38066/08_2026/8x5d_38066.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8x5d_38066/08_2026/8x5d_38066.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8x5d_38066/08_2026/8x5d_38066.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8x5d_38066/08_2026/8x5d_38066.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8x5d_38066/08_2026/8x5d_38066.map" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.050 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 47 5.49 5 S 44 5.16 5 C 11470 2.51 5 N 3285 2.21 5 O 3631 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 104 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 18477 Number of models: 1 Model: "" Number of chains: 13 Chain: "K" Number of atoms: 1815 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 235, 1807 Classifications: {'peptide': 235} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 226} Conformer: "B" Number of residues, atoms: 235, 1807 Classifications: {'peptide': 235} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 226} bond proxies already assigned to first conformer: 1825 Chain: "G" Number of atoms: 573 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 573 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 4, 'TRANS': 72} Chain breaks: 4 Chain: "N" Number of atoms: 2943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 2943 Classifications: {'peptide': 370} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 346} Chain breaks: 1 Chain: "L" Number of atoms: 1814 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 235, 1806 Classifications: {'peptide': 235} Link IDs: {'PTRANS': 8, 'TRANS': 226} Conformer: "B" Number of residues, atoms: 235, 1806 Classifications: {'peptide': 235} Link IDs: {'PTRANS': 8, 'TRANS': 226} bond proxies already assigned to first conformer: 1824 Chain: "O" Number of atoms: 996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 996 Classifications: {'RNA': 47} Modifications used: {'rna2p_pur': 8, 'rna2p_pyr': 14, 'rna3p_pur': 15, 'rna3p_pyr': 10} Link IDs: {'rna2p': 21, 'rna3p': 25} Chain: "J" Number of atoms: 1815 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 235, 1807 Classifications: {'peptide': 235} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 226} Conformer: "B" Number of residues, atoms: 235, 1807 Classifications: {'peptide': 235} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 226} bond proxies already assigned to first conformer: 1825 Chain: "I" Number of atoms: 1815 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 235, 1807 Classifications: {'peptide': 235} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 226} Conformer: "B" Number of residues, atoms: 235, 1807 Classifications: {'peptide': 235} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 226} bond proxies already assigned to first conformer: 1825 Chain: "H" Number of atoms: 1815 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 235, 1807 Classifications: {'peptide': 235} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 226} Conformer: "B" Number of residues, atoms: 235, 1807 Classifications: {'peptide': 235} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 226} bond proxies already assigned to first conformer: 1825 Chain: "F" Number of atoms: 1006 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 1006 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 3, 'TRANS': 120} Chain: "E" Number of atoms: 1020 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 1020 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 3, 'TRANS': 122} Chain: "D" Number of atoms: 1014 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 1014 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 3, 'TRANS': 121} Chain: "C" Number of atoms: 1006 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 1006 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 3, 'TRANS': 120} Chain: "B" Number of atoms: 845 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 845 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 2, 'TRANS': 101} Chain breaks: 1 Time building chain proxies: 5.54, per 1000 atoms: 0.30 Number of scatterers: 18477 At special positions: 0 Unit cell: (94.05, 94.905, 213.75, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 44 16.00 P 47 15.00 O 3631 8.00 N 3285 7.00 C 11470 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: 1.42 Conformation dependent library (CDL) restraints added in 1.0 seconds 4388 Ramachandran restraints generated. 2194 Oldfield, 0 Emsley, 2194 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4106 Finding SS restraints... Secondary structure from input PDB file: 77 helices and 25 sheets defined 37.2% alpha, 15.3% beta 0 base pairs and 16 stacking pairs defined. Time for finding SS restraints: 1.89 Creating SS restraints... Processing helix chain 'K' and resid 50 through 69 removed outlier: 3.697A pdb=" N LEU K 54 " --> pdb=" O PRO K 50 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N VAL K 58 " --> pdb=" O LEU K 54 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N THR K 60 " --> pdb=" O GLY K 56 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLN K 65 " --> pdb=" O LEU K 61 " (cutoff:3.500A) Processing helix chain 'K' and resid 108 through 115 Processing helix chain 'K' and resid 173 through 193 removed outlier: 3.941A pdb=" N ILE K 178 " --> pdb=" O SER K 174 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ALA K 183 " --> pdb=" O GLU K 179 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N LEU K 191 " --> pdb=" O GLY K 187 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N GLU K 192 " --> pdb=" O LEU K 188 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LEU K 193 " --> pdb=" O LYS K 189 " (cutoff:3.500A) Processing helix chain 'K' and resid 199 through 203 Processing helix chain 'K' and resid 225 through 234 removed outlier: 3.593A pdb=" N GLU K 232 " --> pdb=" O LYS K 228 " (cutoff:3.500A) Processing helix chain 'G' and resid 51 through 56 removed outlier: 3.939A pdb=" N LYS G 55 " --> pdb=" O THR G 52 " (cutoff:3.500A) Processing helix chain 'N' and resid 44 through 49 removed outlier: 3.704A pdb=" N ASP N 49 " --> pdb=" O LEU N 45 " (cutoff:3.500A) Processing helix chain 'N' and resid 54 through 63 Processing helix chain 'N' and resid 73 through 79 removed outlier: 4.277A pdb=" N TRP N 77 " --> pdb=" O PRO N 73 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N GLU N 79 " --> pdb=" O LYS N 75 " (cutoff:3.500A) Processing helix chain 'N' and resid 137 through 156 removed outlier: 3.852A pdb=" N VAL N 141 " --> pdb=" O PRO N 137 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLY N 143 " --> pdb=" O SER N 139 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N SER N 147 " --> pdb=" O GLY N 143 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N LEU N 150 " --> pdb=" O ARG N 146 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LEU N 153 " --> pdb=" O TYR N 149 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N VAL N 154 " --> pdb=" O LEU N 150 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N LYS N 156 " --> pdb=" O SER N 152 " (cutoff:3.500A) Processing helix chain 'N' and resid 168 through 184 removed outlier: 3.525A pdb=" N TYR N 175 " --> pdb=" O GLU N 171 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N GLY N 176 " --> pdb=" O HIS N 172 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLU N 177 " --> pdb=" O ARG N 173 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ARG N 178 " --> pdb=" O GLN N 174 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N GLU N 180 " --> pdb=" O GLY N 176 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N ARG N 181 " --> pdb=" O GLU N 177 " (cutoff:3.500A) Processing helix chain 'N' and resid 196 through 203 removed outlier: 3.536A pdb=" N ASP N 200 " --> pdb=" O ALA N 197 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N LEU N 201 " --> pdb=" O VAL N 198 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N PHE N 202 " --> pdb=" O ASN N 199 " (cutoff:3.500A) Processing helix chain 'N' and resid 264 through 273 removed outlier: 4.111A pdb=" N GLU N 268 " --> pdb=" O TRP N 264 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N ARG N 269 " --> pdb=" O ARG N 265 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N THR N 273 " --> pdb=" O ARG N 269 " (cutoff:3.500A) Processing helix chain 'N' and resid 273 through 286 removed outlier: 3.693A pdb=" N ALA N 284 " --> pdb=" O SER N 280 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N TYR N 286 " --> pdb=" O ASN N 282 " (cutoff:3.500A) Processing helix chain 'N' and resid 286 through 291 removed outlier: 3.549A pdb=" N ARG N 290 " --> pdb=" O TYR N 286 " (cutoff:3.500A) Processing helix chain 'N' and resid 312 through 316 removed outlier: 3.873A pdb=" N THR N 316 " --> pdb=" O ARG N 313 " (cutoff:3.500A) Processing helix chain 'N' and resid 322 through 329 removed outlier: 3.901A pdb=" N LYS N 326 " --> pdb=" O ASP N 322 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N VAL N 327 " --> pdb=" O ASP N 323 " (cutoff:3.500A) Processing helix chain 'L' and resid 51 through 70 removed outlier: 3.572A pdb=" N VAL L 58 " --> pdb=" O LEU L 54 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ARG L 64 " --> pdb=" O THR L 60 " (cutoff:3.500A) Processing helix chain 'L' and resid 83 through 88 removed outlier: 4.069A pdb=" N LEU L 87 " --> pdb=" O HIS L 83 " (cutoff:3.500A) Processing helix chain 'L' and resid 108 through 115 removed outlier: 3.637A pdb=" N ARG L 115 " --> pdb=" O ASP L 111 " (cutoff:3.500A) Processing helix chain 'L' and resid 173 through 190 removed outlier: 3.774A pdb=" N ILE L 178 " --> pdb=" O SER L 174 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLU L 179 " --> pdb=" O ASP L 175 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ALA L 183 " --> pdb=" O GLU L 179 " (cutoff:3.500A) Processing helix chain 'L' and resid 225 through 230 Processing helix chain 'J' and resid 51 through 69 removed outlier: 3.660A pdb=" N LYS J 57 " --> pdb=" O SER J 53 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N THR J 60 " --> pdb=" O GLY J 56 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLN J 65 " --> pdb=" O LEU J 61 " (cutoff:3.500A) Processing helix chain 'J' and resid 81 through 86 Processing helix chain 'J' and resid 108 through 115 removed outlier: 3.610A pdb=" N GLU J 113 " --> pdb=" O LYS J 109 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ARG J 115 " --> pdb=" O ASP J 111 " (cutoff:3.500A) Processing helix chain 'J' and resid 177 through 185 removed outlier: 3.693A pdb=" N ALA J 183 " --> pdb=" O GLU J 179 " (cutoff:3.500A) Processing helix chain 'J' and resid 186 through 193 removed outlier: 3.556A pdb=" N LEU J 190 " --> pdb=" O ARG J 186 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU J 191 " --> pdb=" O GLY J 187 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLU J 192 " --> pdb=" O LEU J 188 " (cutoff:3.500A) Processing helix chain 'J' and resid 222 through 233 removed outlier: 3.609A pdb=" N LEU J 226 " --> pdb=" O ASP J 222 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N GLU J 227 " --> pdb=" O GLY J 223 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N LYS J 228 " --> pdb=" O SER J 224 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N HIS J 231 " --> pdb=" O GLU J 227 " (cutoff:3.500A) Processing helix chain 'I' and resid 50 through 70 removed outlier: 3.712A pdb=" N LEU I 54 " --> pdb=" O PRO I 50 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N LYS I 57 " --> pdb=" O SER I 53 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N THR I 70 " --> pdb=" O TYR I 66 " (cutoff:3.500A) Processing helix chain 'I' and resid 76 through 80 removed outlier: 3.812A pdb=" N ASP I 80 " --> pdb=" O PRO I 77 " (cutoff:3.500A) Processing helix chain 'I' and resid 109 through 114 removed outlier: 3.571A pdb=" N ALA I 114 " --> pdb=" O ASP I 110 " (cutoff:3.500A) Processing helix chain 'I' and resid 177 through 191 removed outlier: 3.555A pdb=" N ALA I 183 " --> pdb=" O GLU I 179 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N LYS I 189 " --> pdb=" O ALA I 185 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LEU I 191 " --> pdb=" O GLY I 187 " (cutoff:3.500A) Processing helix chain 'I' and resid 225 through 230 Processing helix chain 'I' and resid 232 through 236 removed outlier: 3.539A pdb=" N ALA I 235 " --> pdb=" O GLU I 232 " (cutoff:3.500A) Processing helix chain 'H' and resid 50 through 70 removed outlier: 3.647A pdb=" N LEU H 54 " --> pdb=" O PRO H 50 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LYS H 57 " --> pdb=" O SER H 53 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLN H 65 " --> pdb=" O LEU H 61 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N THR H 70 " --> pdb=" O TYR H 66 " (cutoff:3.500A) Processing helix chain 'H' and resid 76 through 80 Processing helix chain 'H' and resid 81 through 88 removed outlier: 3.567A pdb=" N LEU H 87 " --> pdb=" O HIS H 83 " (cutoff:3.500A) Processing helix chain 'H' and resid 108 through 113 Processing helix chain 'H' and resid 114 through 116 No H-bonds generated for 'chain 'H' and resid 114 through 116' Processing helix chain 'H' and resid 180 through 194 removed outlier: 3.646A pdb=" N ILE H 184 " --> pdb=" O ASP H 180 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LYS H 189 " --> pdb=" O ALA H 185 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N LEU H 191 " --> pdb=" O GLY H 187 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N GLU H 192 " --> pdb=" O LEU H 188 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LEU H 193 " --> pdb=" O LYS H 189 " (cutoff:3.500A) Processing helix chain 'H' and resid 225 through 233 removed outlier: 4.147A pdb=" N HIS H 231 " --> pdb=" O GLU H 227 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LEU H 233 " --> pdb=" O LEU H 229 " (cutoff:3.500A) Processing helix chain 'F' and resid 7 through 18 removed outlier: 3.929A pdb=" N GLN F 11 " --> pdb=" O ASP F 7 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLU F 13 " --> pdb=" O VAL F 9 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N GLN F 14 " --> pdb=" O LYS F 10 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N VAL F 15 " --> pdb=" O GLN F 11 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N ILE F 16 " --> pdb=" O ALA F 12 " (cutoff:3.500A) Processing helix chain 'F' and resid 33 through 50 removed outlier: 3.864A pdb=" N LEU F 39 " --> pdb=" O VAL F 35 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N GLN F 42 " --> pdb=" O SER F 38 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N ASP F 45 " --> pdb=" O ALA F 41 " (cutoff:3.500A) Processing helix chain 'F' and resid 57 through 73 removed outlier: 4.563A pdb=" N VAL F 63 " --> pdb=" O LEU F 59 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N VAL F 68 " --> pdb=" O GLN F 64 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N VAL F 71 " --> pdb=" O ARG F 67 " (cutoff:3.500A) Processing helix chain 'F' and resid 77 through 88 removed outlier: 3.612A pdb=" N ARG F 81 " --> pdb=" O GLU F 77 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N VAL F 82 " --> pdb=" O LYS F 78 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N PHE F 83 " --> pdb=" O ALA F 79 " (cutoff:3.500A) Processing helix chain 'F' and resid 88 through 96 removed outlier: 4.140A pdb=" N ALA F 94 " --> pdb=" O LEU F 90 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N GLN F 95 " --> pdb=" O ASP F 91 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ILE F 96 " --> pdb=" O GLU F 92 " (cutoff:3.500A) Processing helix chain 'F' and resid 99 through 111 removed outlier: 3.766A pdb=" N LEU F 103 " --> pdb=" O SER F 99 " (cutoff:3.500A) Processing helix chain 'F' and resid 114 through 120 removed outlier: 3.822A pdb=" N LYS F 118 " --> pdb=" O VAL F 114 " (cutoff:3.500A) Processing helix chain 'E' and resid 7 through 18 removed outlier: 3.658A pdb=" N GLN E 11 " --> pdb=" O ASP E 7 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLN E 14 " --> pdb=" O LYS E 10 " (cutoff:3.500A) Processing helix chain 'E' and resid 30 through 32 No H-bonds generated for 'chain 'E' and resid 30 through 32' Processing helix chain 'E' and resid 33 through 48 removed outlier: 3.978A pdb=" N LEU E 39 " --> pdb=" O VAL E 35 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N GLN E 42 " --> pdb=" O SER E 38 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLU E 46 " --> pdb=" O GLN E 42 " (cutoff:3.500A) Processing helix chain 'E' and resid 62 through 76 removed outlier: 4.132A pdb=" N VAL E 71 " --> pdb=" O ARG E 67 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ARG E 76 " --> pdb=" O TYR E 72 " (cutoff:3.500A) Processing helix chain 'E' and resid 77 through 88 removed outlier: 3.521A pdb=" N VAL E 82 " --> pdb=" O LYS E 78 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N PHE E 83 " --> pdb=" O ALA E 79 " (cutoff:3.500A) Processing helix chain 'E' and resid 88 through 95 removed outlier: 3.630A pdb=" N GLU E 92 " --> pdb=" O GLY E 88 " (cutoff:3.500A) Processing helix chain 'E' and resid 103 through 120 removed outlier: 3.578A pdb=" N ALA E 112 " --> pdb=" O HIS E 108 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LEU E 113 " --> pdb=" O TYR E 109 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N VAL E 114 " --> pdb=" O MET E 110 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N PHE E 119 " --> pdb=" O ALA E 115 " (cutoff:3.500A) Processing helix chain 'D' and resid 12 through 17 removed outlier: 3.981A pdb=" N ILE D 16 " --> pdb=" O ALA D 12 " (cutoff:3.500A) Processing helix chain 'D' and resid 33 through 38 Processing helix chain 'D' and resid 38 through 48 removed outlier: 3.814A pdb=" N GLN D 42 " --> pdb=" O SER D 38 " (cutoff:3.500A) Processing helix chain 'D' and resid 60 through 76 removed outlier: 3.856A pdb=" N GLN D 64 " --> pdb=" O ARG D 60 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N TYR D 65 " --> pdb=" O ASP D 61 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LEU D 66 " --> pdb=" O LYS D 62 " (cutoff:3.500A) Processing helix chain 'D' and resid 77 through 88 removed outlier: 3.742A pdb=" N ARG D 86 " --> pdb=" O VAL D 82 " (cutoff:3.500A) Processing helix chain 'D' and resid 99 through 120 removed outlier: 3.646A pdb=" N PHE D 106 " --> pdb=" O ARG D 102 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LEU D 113 " --> pdb=" O TYR D 109 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N TYR D 116 " --> pdb=" O ALA D 112 " (cutoff:3.500A) Processing helix chain 'C' and resid 7 through 18 removed outlier: 3.560A pdb=" N GLN C 11 " --> pdb=" O ASP C 7 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ILE C 16 " --> pdb=" O ALA C 12 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 32 Processing helix chain 'C' and resid 33 through 48 removed outlier: 3.651A pdb=" N ALA C 41 " --> pdb=" O LEU C 37 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N GLU C 46 " --> pdb=" O GLN C 42 " (cutoff:3.500A) Processing helix chain 'C' and resid 56 through 77 removed outlier: 3.690A pdb=" N ASP C 61 " --> pdb=" O PRO C 57 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N LYS C 62 " --> pdb=" O ALA C 58 " (cutoff:3.500A) Processing helix chain 'C' and resid 77 through 87 removed outlier: 3.601A pdb=" N VAL C 82 " --> pdb=" O LYS C 78 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N PHE C 83 " --> pdb=" O ALA C 79 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N GLU C 85 " --> pdb=" O ARG C 81 " (cutoff:3.500A) Processing helix chain 'C' and resid 89 through 94 removed outlier: 3.971A pdb=" N ALA C 94 " --> pdb=" O LEU C 90 " (cutoff:3.500A) Processing helix chain 'C' and resid 99 through 120 removed outlier: 3.612A pdb=" N LEU C 103 " --> pdb=" O SER C 99 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ALA C 112 " --> pdb=" O HIS C 108 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N VAL C 114 " --> pdb=" O MET C 110 " (cutoff:3.500A) Processing helix chain 'B' and resid 8 through 13 removed outlier: 3.711A pdb=" N ALA B 12 " --> pdb=" O TYR B 8 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N GLU B 13 " --> pdb=" O VAL B 9 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 8 through 13' Processing helix chain 'B' and resid 31 through 36 removed outlier: 3.616A pdb=" N VAL B 35 " --> pdb=" O THR B 31 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N LEU B 36 " --> pdb=" O GLN B 32 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 31 through 36' Processing helix chain 'B' and resid 37 through 45 removed outlier: 3.618A pdb=" N GLN B 42 " --> pdb=" O SER B 38 " (cutoff:3.500A) removed outlier: 4.790A pdb=" N LEU B 43 " --> pdb=" O LEU B 39 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ASP B 45 " --> pdb=" O ALA B 41 " (cutoff:3.500A) Processing helix chain 'B' and resid 65 through 77 removed outlier: 3.598A pdb=" N ARG B 69 " --> pdb=" O TYR B 65 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N VAL B 71 " --> pdb=" O ARG B 67 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N TYR B 72 " --> pdb=" O VAL B 68 " (cutoff:3.500A) Processing helix chain 'B' and resid 78 through 80 No H-bonds generated for 'chain 'B' and resid 78 through 80' Processing helix chain 'B' and resid 81 through 86 removed outlier: 3.522A pdb=" N ARG B 86 " --> pdb=" O VAL B 82 " (cutoff:3.500A) Processing helix chain 'B' and resid 88 through 93 removed outlier: 3.651A pdb=" N GLU B 92 " --> pdb=" O GLY B 88 " (cutoff:3.500A) Processing helix chain 'B' and resid 102 through 106 Processing helix chain 'B' and resid 108 through 116 removed outlier: 3.723A pdb=" N ALA B 112 " --> pdb=" O HIS B 108 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N VAL B 114 " --> pdb=" O MET B 110 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N TYR B 116 " --> pdb=" O ALA B 112 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'K' and resid 207 through 219 removed outlier: 5.744A pdb=" N PHE K 209 " --> pdb=" O THR K 15 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N THR K 15 " --> pdb=" O PHE K 209 " (cutoff:3.500A) removed outlier: 5.472A pdb=" N ASN K 211 " --> pdb=" O THR K 13 " (cutoff:3.500A) removed outlier: 4.982A pdb=" N THR K 13 " --> pdb=" O ASN K 211 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N LYS K 7 " --> pdb=" O ALA K 217 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ALA K 6 " --> pdb=" O VAL K 158 " (cutoff:3.500A) removed outlier: 6.008A pdb=" N SER K 153 " --> pdb=" O ARG K 102 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N ARG K 102 " --> pdb=" O SER K 153 " (cutoff:3.500A) removed outlier: 7.752A pdb=" N GLY J 203 " --> pdb=" O LEU K 99 " (cutoff:3.500A) removed outlier: 7.469A pdb=" N PHE K 101 " --> pdb=" O GLY J 203 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'K' and resid 48 through 49 Processing sheet with id=AA3, first strand: chain 'K' and resid 121 through 129 Processing sheet with id=AA4, first strand: chain 'G' and resid 121 through 128 removed outlier: 3.545A pdb=" N GLU G 122 " --> pdb=" O ARG G 143 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLU G 126 " --> pdb=" O ARG G 139 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'N' and resid 5 through 7 Processing sheet with id=AA6, first strand: chain 'N' and resid 247 through 250 removed outlier: 3.502A pdb=" N VAL N 304 " --> pdb=" O CYS N 367 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'N' and resid 21 through 27 removed outlier: 5.205A pdb=" N GLU N 24 " --> pdb=" O ALA N 125 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'N' and resid 32 through 34 removed outlier: 3.657A pdb=" N HIS N 32 " --> pdb=" O TYR N 39 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'N' and resid 220 through 221 removed outlier: 3.615A pdb=" N ARG N 239 " --> pdb=" O CYS N 221 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'N' and resid 224 through 226 removed outlier: 3.517A pdb=" N MET N 226 " --> pdb=" O LEU N 352 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'L' and resid 99 through 100 Processing sheet with id=AB3, first strand: chain 'L' and resid 99 through 100 removed outlier: 6.523A pdb=" N GLU L 9 " --> pdb=" O ALA L 214 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N ALA L 214 " --> pdb=" O GLU L 9 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N THR L 11 " --> pdb=" O LEU L 212 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N LEU L 212 " --> pdb=" O THR L 11 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'L' and resid 48 through 49 Processing sheet with id=AB5, first strand: chain 'L' and resid 121 through 128 removed outlier: 3.648A pdb=" N ASN L 137 " --> pdb=" O ALA L 128 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'J' and resid 149 through 150 removed outlier: 6.731A pdb=" N LYS J 7 " --> pdb=" O ALA J 217 " (cutoff:3.500A) removed outlier: 4.977A pdb=" N THR J 13 " --> pdb=" O ASN J 211 " (cutoff:3.500A) removed outlier: 5.658A pdb=" N ASN J 211 " --> pdb=" O THR J 13 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N THR J 15 " --> pdb=" O PHE J 209 " (cutoff:3.500A) removed outlier: 5.535A pdb=" N PHE J 209 " --> pdb=" O THR J 15 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'J' and resid 149 through 150 removed outlier: 6.342A pdb=" N SER J 153 " --> pdb=" O ARG J 102 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N ARG J 102 " --> pdb=" O SER J 153 " (cutoff:3.500A) removed outlier: 7.765A pdb=" N GLY I 203 " --> pdb=" O LEU J 99 " (cutoff:3.500A) removed outlier: 7.185A pdb=" N PHE J 101 " --> pdb=" O GLY I 203 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'J' and resid 48 through 49 Processing sheet with id=AB9, first strand: chain 'J' and resid 121 through 126 Processing sheet with id=AC1, first strand: chain 'I' and resid 207 through 218 removed outlier: 4.050A pdb=" N LEU I 212 " --> pdb=" O THR I 11 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N THR I 11 " --> pdb=" O LEU I 212 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N ALA I 214 " --> pdb=" O GLU I 9 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N GLU I 9 " --> pdb=" O ALA I 214 " (cutoff:3.500A) removed outlier: 5.075A pdb=" N ALA I 216 " --> pdb=" O LYS I 7 " (cutoff:3.500A) removed outlier: 7.172A pdb=" N LYS I 7 " --> pdb=" O ALA I 216 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ALA I 6 " --> pdb=" O VAL I 158 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N SER I 153 " --> pdb=" O ARG I 102 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ARG I 102 " --> pdb=" O SER I 153 " (cutoff:3.500A) removed outlier: 7.855A pdb=" N GLY H 203 " --> pdb=" O LEU I 99 " (cutoff:3.500A) removed outlier: 7.435A pdb=" N PHE I 101 " --> pdb=" O GLY H 203 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'I' and resid 48 through 49 Processing sheet with id=AC3, first strand: chain 'I' and resid 121 through 129 Processing sheet with id=AC4, first strand: chain 'H' and resid 99 through 101 removed outlier: 3.592A pdb=" N VAL H 158 " --> pdb=" O ALA H 6 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'H' and resid 99 through 101 removed outlier: 3.592A pdb=" N VAL H 158 " --> pdb=" O ALA H 6 " (cutoff:3.500A) removed outlier: 4.860A pdb=" N THR H 13 " --> pdb=" O ASN H 211 " (cutoff:3.500A) removed outlier: 5.666A pdb=" N ASN H 211 " --> pdb=" O THR H 13 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N THR H 15 " --> pdb=" O PHE H 209 " (cutoff:3.500A) removed outlier: 5.598A pdb=" N PHE H 209 " --> pdb=" O THR H 15 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'H' and resid 48 through 49 Processing sheet with id=AC7, first strand: chain 'H' and resid 121 through 129 removed outlier: 3.589A pdb=" N ARG H 139 " --> pdb=" O GLU H 126 " (cutoff:3.500A) 555 hydrogen bonds defined for protein. 1572 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 16 stacking parallelities Total time for adding SS restraints: 2.54 Time building geometry restraints manager: 1.97 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 5103 1.33 - 1.45: 3107 1.45 - 1.57: 10482 1.57 - 1.69: 93 1.69 - 1.81: 78 Bond restraints: 18863 Sorted by residual: bond pdb=" C GLU N 79 " pdb=" N PRO N 80 " ideal model delta sigma weight residual 1.334 1.388 -0.055 2.34e-02 1.83e+03 5.43e+00 bond pdb=" N THR L 133 " pdb=" CA THR L 133 " ideal model delta sigma weight residual 1.457 1.481 -0.024 1.29e-02 6.01e+03 3.32e+00 bond pdb=" N7 A O 37 " pdb=" C5 A O 37 " ideal model delta sigma weight residual 1.388 1.377 0.011 6.00e-03 2.78e+04 3.12e+00 bond pdb=" C ASN I 108 " pdb=" N LYS I 109 " ideal model delta sigma weight residual 1.332 1.309 0.024 1.40e-02 5.10e+03 2.85e+00 bond pdb=" N9 A O 29 " pdb=" C4 A O 29 " ideal model delta sigma weight residual 1.374 1.364 0.010 6.00e-03 2.78e+04 2.70e+00 ... (remaining 18858 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.82: 25062 1.82 - 3.65: 513 3.65 - 5.47: 51 5.47 - 7.30: 23 7.30 - 9.12: 3 Bond angle restraints: 25652 Sorted by residual: angle pdb=" C1' U O 39 " pdb=" N1 U O 39 " pdb=" C2 U O 39 " ideal model delta sigma weight residual 117.70 123.00 -5.30 1.20e+00 6.94e-01 1.95e+01 angle pdb=" C ALA I 235 " pdb=" N VAL I 236 " pdb=" CA VAL I 236 " ideal model delta sigma weight residual 121.70 129.26 -7.56 1.80e+00 3.09e-01 1.76e+01 angle pdb=" C PRO L 77 " pdb=" N ASN L 78 " pdb=" CA ASN L 78 " ideal model delta sigma weight residual 125.02 132.09 -7.07 1.76e+00 3.23e-01 1.61e+01 angle pdb=" O5' A O 37 " pdb=" C5' A O 37 " pdb=" C4' A O 37 " ideal model delta sigma weight residual 109.40 112.59 -3.19 8.00e-01 1.56e+00 1.59e+01 angle pdb=" O5' A O 13 " pdb=" C5' A O 13 " pdb=" C4' A O 13 " ideal model delta sigma weight residual 109.40 112.50 -3.10 8.00e-01 1.56e+00 1.50e+01 ... (remaining 25647 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.98: 11274 35.98 - 71.95: 284 71.95 - 107.93: 36 107.93 - 143.91: 0 143.91 - 179.89: 2 Dihedral angle restraints: 11596 sinusoidal: 5197 harmonic: 6399 Sorted by residual: dihedral pdb=" CD BARG H 45 " pdb=" NE BARG H 45 " pdb=" CZ BARG H 45 " pdb=" NH1BARG H 45 " ideal model delta sinusoidal sigma weight residual 0.00 -179.89 179.89 1 1.00e+01 1.00e-02 1.92e+02 dihedral pdb=" O4' U O 39 " pdb=" C1' U O 39 " pdb=" N1 U O 39 " pdb=" C2 U O 39 " ideal model delta sinusoidal sigma weight residual 232.00 53.06 178.94 1 1.70e+01 3.46e-03 6.64e+01 dihedral pdb=" CA SER K 29 " pdb=" C SER K 29 " pdb=" N ALA K 30 " pdb=" CA ALA K 30 " ideal model delta harmonic sigma weight residual 180.00 153.97 26.03 0 5.00e+00 4.00e-02 2.71e+01 ... (remaining 11593 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 2354 0.054 - 0.108: 480 0.108 - 0.163: 106 0.163 - 0.217: 4 0.217 - 0.271: 2 Chirality restraints: 2946 Sorted by residual: chirality pdb=" CB ILE K 31 " pdb=" CA ILE K 31 " pdb=" CG1 ILE K 31 " pdb=" CG2 ILE K 31 " both_signs ideal model delta sigma weight residual False 2.64 2.37 0.27 2.00e-01 2.50e+01 1.83e+00 chirality pdb=" CA THR L 133 " pdb=" N THR L 133 " pdb=" C THR L 133 " pdb=" CB THR L 133 " both_signs ideal model delta sigma weight residual False 2.53 2.31 0.22 2.00e-01 2.50e+01 1.20e+00 chirality pdb=" CA TYR D 8 " pdb=" N TYR D 8 " pdb=" C TYR D 8 " pdb=" CB TYR D 8 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 9.10e-01 ... (remaining 2943 not shown) Planarity restraints: 3158 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP N 129 " 0.039 5.00e-02 4.00e+02 5.95e-02 5.66e+00 pdb=" N PRO N 130 " -0.103 5.00e-02 4.00e+02 pdb=" CA PRO N 130 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO N 130 " 0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS J 76 " -0.038 5.00e-02 4.00e+02 5.78e-02 5.34e+00 pdb=" N PRO J 77 " 0.100 5.00e-02 4.00e+02 pdb=" CA PRO J 77 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO J 77 " -0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS H 76 " -0.037 5.00e-02 4.00e+02 5.62e-02 5.05e+00 pdb=" N PRO H 77 " 0.097 5.00e-02 4.00e+02 pdb=" CA PRO H 77 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO H 77 " -0.031 5.00e-02 4.00e+02 ... (remaining 3155 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 4476 2.79 - 3.32: 14637 3.32 - 3.85: 28358 3.85 - 4.37: 35038 4.37 - 4.90: 60619 Nonbonded interactions: 143128 Sorted by model distance: nonbonded pdb=" O MET K 95 " pdb=" O2' A O 29 " model vdw 2.263 3.040 nonbonded pdb=" OG SER C 99 " pdb=" OD1 ASP C 101 " model vdw 2.303 3.040 nonbonded pdb=" OG SER F 99 " pdb=" OD1 ASP F 101 " model vdw 2.303 3.040 nonbonded pdb=" OG1 THR G 15 " pdb=" O LYS G 208 " model vdw 2.320 3.040 nonbonded pdb=" O LEU D 36 " pdb=" OG1 THR D 40 " model vdw 2.320 3.040 ... (remaining 143123 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 'C' selection = (chain 'D' and resid 2 through 125) selection = (chain 'E' and resid 2 through 125) selection = chain 'F' } ncs_group { reference = (chain 'H' and (resid 2 through 44 or resid 46 through 235 or (resid 236 and (na \ me N or name CA or name C or name O or name CB or name CG1 or name CG2)))) selection = (chain 'I' and (resid 2 through 44 or resid 46 through 235 or (resid 236 and (na \ me N or name CA or name C or name O or name CB or name CG1 or name CG2)))) selection = (chain 'J' and (resid 2 through 44 or resid 46 through 235 or (resid 236 and (na \ me N or name CA or name C or name O or name CB or name CG1 or name CG2)))) selection = (chain 'K' and (resid 2 through 44 or resid 46 through 235 or (resid 236 and (na \ me N or name CA or name C or name O or name CB or name CG1 or name CG2)))) selection = (chain 'L' and (resid 2 through 44 or resid 46 through 236)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=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: 8.850 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: 0.010 Extract box with map and model: 0.300 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 19.350 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.050 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: 0.000 Load rotamer database and sin/cos tables:1.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8741 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 18863 Z= 0.186 Angle : 0.672 9.123 25652 Z= 0.425 Chirality : 0.046 0.271 2946 Planarity : 0.006 0.059 3158 Dihedral : 15.439 179.886 7490 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 3.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 5.46 % Allowed : 8.41 % Favored : 86.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.02 (0.13), residues: 2194 helix: -4.85 (0.05), residues: 809 sheet: -1.45 (0.27), residues: 332 loop : -2.59 (0.15), residues: 1053 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG J 59 TYR 0.023 0.002 TYR D 8 PHE 0.018 0.001 PHE N 317 TRP 0.006 0.001 TRP N 77 HIS 0.003 0.001 HIS N 32 Details of bonding type rmsd/Z covalent geometry : bond 0.00358 / 0.19 (18863) covalent geometry : angle 0.67216 / 0.42 (25652) hydrogen bonds : bond 0.32657 / 22.18 ( 538) hydrogen bonds : angle 9.64955 / 6.65 ( 1572) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4388 Ramachandran restraints generated. 2194 Oldfield, 0 Emsley, 2194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4388 Ramachandran restraints generated. 2194 Oldfield, 0 Emsley, 2194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 402 residues out of total 1857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 301 time to evaluate : 0.723 Fit side-chains revert: symmetry clash REVERT: G 135 LYS cc_start: 0.7359 (tmtt) cc_final: 0.7156 (pttp) REVERT: G 143 ARG cc_start: 0.7885 (ptt180) cc_final: 0.7004 (ptt-90) REVERT: G 145 ILE cc_start: 0.7791 (pt) cc_final: 0.7306 (pt) REVERT: G 206 GLN cc_start: 0.7229 (tt0) cc_final: 0.6982 (tt0) REVERT: N 56 LYS cc_start: 0.8804 (tmtt) cc_final: 0.7993 (ttpp) REVERT: N 94 GLU cc_start: 0.7368 (tt0) cc_final: 0.6910 (tt0) REVERT: N 254 VAL cc_start: 0.9226 (OUTLIER) cc_final: 0.8937 (p) REVERT: L 36 LYS cc_start: 0.8103 (mttt) cc_final: 0.7777 (mtpt) REVERT: L 149 GLU cc_start: 0.7736 (OUTLIER) cc_final: 0.7406 (mt-10) REVERT: L 168 LYS cc_start: 0.8618 (tmtt) cc_final: 0.8292 (tptt) REVERT: J 28 PHE cc_start: 0.7209 (OUTLIER) cc_final: 0.6433 (m-80) REVERT: I 54 LEU cc_start: 0.9237 (OUTLIER) cc_final: 0.8938 (tt) REVERT: I 194 ASP cc_start: 0.7987 (OUTLIER) cc_final: 0.7754 (t70) REVERT: H 168 LYS cc_start: 0.7700 (mmtm) cc_final: 0.7473 (mmtm) REVERT: H 215 ARG cc_start: 0.6915 (ttp80) cc_final: 0.6676 (ttp80) REVERT: F 13 GLU cc_start: 0.8218 (tm-30) cc_final: 0.7903 (tt0) REVERT: F 43 LEU cc_start: 0.9132 (OUTLIER) cc_final: 0.8819 (tt) REVERT: F 46 GLU cc_start: 0.7986 (mt-10) cc_final: 0.7713 (mt-10) REVERT: F 73 GLN cc_start: 0.8417 (tp-100) cc_final: 0.8091 (tp40) REVERT: F 76 ARG cc_start: 0.7964 (OUTLIER) cc_final: 0.7201 (ptt-90) REVERT: F 95 GLN cc_start: 0.8503 (OUTLIER) cc_final: 0.7337 (mp-120) REVERT: F 103 LEU cc_start: 0.8383 (OUTLIER) cc_final: 0.8030 (tt) REVERT: E 21 LYS cc_start: 0.8451 (mmtt) cc_final: 0.8198 (mmmt) REVERT: D 22 LYS cc_start: 0.8507 (mtpp) cc_final: 0.8160 (tppt) REVERT: C 10 LYS cc_start: 0.8437 (OUTLIER) cc_final: 0.8117 (mtmm) REVERT: C 86 ARG cc_start: 0.7651 (ttm170) cc_final: 0.7402 (mtt180) REVERT: B 83 PHE cc_start: 0.6487 (OUTLIER) cc_final: 0.5609 (t80) outliers start: 101 outliers final: 44 residues processed: 387 average time/residue: 0.1613 time to fit residues: 89.5449 Evaluate side-chains 301 residues out of total 1857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 246 time to evaluate : 0.614 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 110 ASP Chi-restraints excluded: chain K residue 166 GLU Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain G residue 137 ASN Chi-restraints excluded: chain N residue 4 TYR Chi-restraints excluded: chain N residue 27 THR Chi-restraints excluded: chain N residue 38 VAL Chi-restraints excluded: chain N residue 44 GLU Chi-restraints excluded: chain N residue 46 LEU Chi-restraints excluded: chain N residue 81 ASN Chi-restraints excluded: chain N residue 129 ASP Chi-restraints excluded: chain N residue 155 HIS Chi-restraints excluded: chain N residue 191 ASN Chi-restraints excluded: chain N residue 254 VAL Chi-restraints excluded: chain N residue 259 THR Chi-restraints excluded: chain N residue 345 LEU Chi-restraints excluded: chain L residue 11 THR Chi-restraints excluded: chain L residue 15 THR Chi-restraints excluded: chain L residue 87 LEU Chi-restraints excluded: chain L residue 96 THR Chi-restraints excluded: chain L residue 149 GLU Chi-restraints excluded: chain L residue 155 VAL Chi-restraints excluded: chain L residue 207 VAL Chi-restraints excluded: chain J residue 28 PHE Chi-restraints excluded: chain J residue 35 ASP Chi-restraints excluded: chain J residue 218 VAL Chi-restraints excluded: chain I residue 2 THR Chi-restraints excluded: chain I residue 31 ILE Chi-restraints excluded: chain I residue 54 LEU Chi-restraints excluded: chain I residue 194 ASP Chi-restraints excluded: chain I residue 218 VAL Chi-restraints excluded: chain I residue 226 LEU Chi-restraints excluded: chain H residue 15 THR Chi-restraints excluded: chain H residue 54 LEU Chi-restraints excluded: chain H residue 233 LEU Chi-restraints excluded: chain F residue 43 LEU Chi-restraints excluded: chain F residue 68 VAL Chi-restraints excluded: chain F residue 76 ARG Chi-restraints excluded: chain F residue 91 ASP Chi-restraints excluded: chain F residue 95 GLN Chi-restraints excluded: chain F residue 103 LEU Chi-restraints excluded: chain E residue 29 THR Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 91 ASP Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 40 THR Chi-restraints excluded: chain D residue 59 LEU Chi-restraints excluded: chain C residue 10 LYS Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 43 LEU Chi-restraints excluded: chain B residue 68 VAL Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 83 PHE Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain B residue 104 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 216 optimal weight: 0.9980 chunk 98 optimal weight: 0.0570 chunk 194 optimal weight: 0.9980 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 0.6980 chunk 66 optimal weight: 0.5980 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 0.0670 chunk 103 optimal weight: 2.9990 chunk 200 optimal weight: 1.9990 chunk 212 optimal weight: 10.0000 overall best weight: 0.4836 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... K 78 ASN K 127 ASN K 182 ASN G 206 GLN N 53 HIS N 283 GLN N 338 HIS L 21 GLN L 182 ASN L 230 ASN J 78 ASN I 21 GLN H 78 ASN F 73 GLN E 5 GLN E 11 GLN E 42 GLN E 73 GLN D 32 GLN D 48 GLN C 32 GLN B 32 GLN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.128756 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.097888 restraints weight = 56909.915| |-----------------------------------------------------------------------------| r_work (start): 0.3237 rms_B_bonded: 4.49 r_work: 0.2874 rms_B_bonded: 4.60 restraints_weight: 0.5000 r_work (final): 0.2874 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2881 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2881 r_free = 0.2881 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2881 r_free = 0.2881 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.2881 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8946 moved from start: 0.1444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 18863 Z= 0.124 Angle : 0.584 9.020 25652 Z= 0.316 Chirality : 0.041 0.143 2946 Planarity : 0.005 0.050 3158 Dihedral : 13.720 179.851 3285 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 3.64 % Allowed : 11.57 % Favored : 84.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.56 (0.15), residues: 2194 helix: -2.96 (0.13), residues: 826 sheet: -1.09 (0.28), residues: 328 loop : -2.18 (0.16), residues: 1040 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 17 TYR 0.017 0.001 TYR D 8 PHE 0.013 0.001 PHE N 317 TRP 0.003 0.000 TRP N 77 HIS 0.003 0.001 HIS N 32 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.12 (18863) covalent geometry : angle 0.58381 / 0.32 (25652) hydrogen bonds : bond 0.05885 / 4.05 ( 538) hydrogen bonds : angle 5.03682 / 3.44 ( 1572) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4388 Ramachandran restraints generated. 2194 Oldfield, 0 Emsley, 2194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4388 Ramachandran restraints generated. 2194 Oldfield, 0 Emsley, 2194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 1857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 250 time to evaluate : 0.716 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: N 81 ASN cc_start: 0.7265 (OUTLIER) cc_final: 0.6542 (p0) REVERT: N 94 GLU cc_start: 0.7592 (tt0) cc_final: 0.7382 (tt0) REVERT: N 174 GLN cc_start: 0.7373 (mt0) cc_final: 0.7143 (mm-40) REVERT: L 36 LYS cc_start: 0.8165 (mttt) cc_final: 0.7870 (mtpt) REVERT: L 149 GLU cc_start: 0.8450 (OUTLIER) cc_final: 0.8221 (mt-10) REVERT: J 28 PHE cc_start: 0.7045 (OUTLIER) cc_final: 0.6112 (m-80) REVERT: H 160 PHE cc_start: 0.7698 (m-80) cc_final: 0.6849 (t80) REVERT: H 168 LYS cc_start: 0.7468 (mmtm) cc_final: 0.7232 (mmtm) REVERT: H 215 ARG cc_start: 0.7624 (ttp80) cc_final: 0.7178 (ttp80) REVERT: F 73 GLN cc_start: 0.8714 (tp40) cc_final: 0.8170 (tp40) REVERT: F 76 ARG cc_start: 0.8235 (OUTLIER) cc_final: 0.7939 (ptp-170) REVERT: E 21 LYS cc_start: 0.8378 (mmtt) cc_final: 0.8116 (mmmt) REVERT: D 22 LYS cc_start: 0.8463 (mtpp) cc_final: 0.8075 (tppt) REVERT: D 59 LEU cc_start: 0.9143 (OUTLIER) cc_final: 0.8804 (tt) REVERT: C 86 ARG cc_start: 0.7815 (ttm170) cc_final: 0.7552 (mtt180) REVERT: C 101 ASP cc_start: 0.8271 (p0) cc_final: 0.7899 (p0) REVERT: C 105 LYS cc_start: 0.8934 (mmtm) cc_final: 0.8638 (mmtt) REVERT: B 83 PHE cc_start: 0.6322 (OUTLIER) cc_final: 0.5542 (t80) outliers start: 67 outliers final: 46 residues processed: 306 average time/residue: 0.1584 time to fit residues: 70.5280 Evaluate side-chains 289 residues out of total 1857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 237 time to evaluate : 0.569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 110 ASP Chi-restraints excluded: chain K residue 166 GLU Chi-restraints excluded: chain K residue 167 GLN Chi-restraints excluded: chain K residue 218 VAL Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain G residue 137 ASN Chi-restraints excluded: chain G residue 196 LEU Chi-restraints excluded: chain N residue 4 TYR Chi-restraints excluded: chain N residue 27 THR Chi-restraints excluded: chain N residue 46 LEU Chi-restraints excluded: chain N residue 81 ASN Chi-restraints excluded: chain N residue 100 ILE Chi-restraints excluded: chain N residue 129 ASP Chi-restraints excluded: chain N residue 259 THR Chi-restraints excluded: chain N residue 299 ILE Chi-restraints excluded: chain N residue 300 VAL Chi-restraints excluded: chain N residue 327 VAL Chi-restraints excluded: chain N residue 339 VAL Chi-restraints excluded: chain N residue 345 LEU Chi-restraints excluded: chain L residue 11 THR Chi-restraints excluded: chain L residue 87 LEU Chi-restraints excluded: chain L residue 96 THR Chi-restraints excluded: chain L residue 149 GLU Chi-restraints excluded: chain L residue 155 VAL Chi-restraints excluded: chain J residue 28 PHE Chi-restraints excluded: chain J residue 171 LEU Chi-restraints excluded: chain J residue 218 VAL Chi-restraints excluded: chain I residue 2 THR Chi-restraints excluded: chain I residue 218 VAL Chi-restraints excluded: chain I residue 226 LEU Chi-restraints excluded: chain H residue 54 LEU Chi-restraints excluded: chain H residue 233 LEU Chi-restraints excluded: chain F residue 33 LEU Chi-restraints excluded: chain F residue 43 LEU Chi-restraints excluded: chain F residue 68 VAL Chi-restraints excluded: chain F residue 76 ARG Chi-restraints excluded: chain F residue 95 GLN Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 25 ASP Chi-restraints excluded: chain E residue 29 THR Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 91 ASP Chi-restraints excluded: chain D residue 10 LYS Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 59 LEU Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain B residue 15 VAL Chi-restraints excluded: chain B residue 68 VAL Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 83 PHE Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain B residue 104 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 123 optimal weight: 0.6980 chunk 219 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 chunk 4 optimal weight: 3.9990 chunk 213 optimal weight: 0.9980 chunk 187 optimal weight: 3.9990 chunk 145 optimal weight: 3.9990 chunk 8 optimal weight: 2.9990 chunk 60 optimal weight: 5.9990 chunk 94 optimal weight: 1.9990 chunk 84 optimal weight: 0.1980 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** G 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 140 GLN J 78 ASN C 32 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.126875 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.092663 restraints weight = 58819.889| |-----------------------------------------------------------------------------| r_work (start): 0.3152 rms_B_bonded: 2.81 r_work: 0.2936 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.2936 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2946 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2946 r_free = 0.2946 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2946 r_free = 0.2946 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2946 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8914 moved from start: 0.1711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 18863 Z= 0.150 Angle : 0.554 7.546 25652 Z= 0.297 Chirality : 0.042 0.147 2946 Planarity : 0.004 0.041 3158 Dihedral : 13.343 179.459 3254 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 3.59 % Allowed : 12.64 % Favored : 83.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.78 (0.16), residues: 2194 helix: -2.02 (0.16), residues: 832 sheet: -0.87 (0.28), residues: 328 loop : -1.93 (0.17), residues: 1034 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG F 17 TYR 0.020 0.002 TYR H 204 PHE 0.014 0.001 PHE N 317 TRP 0.002 0.001 TRP N 77 HIS 0.007 0.001 HIS N 32 Details of bonding type rmsd/Z covalent geometry : bond 0.00350 / 0.15 (18863) covalent geometry : angle 0.55355 / 0.30 (25652) hydrogen bonds : bond 0.04954 / 3.41 ( 538) hydrogen bonds : angle 4.47375 / 3.06 ( 1572) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4388 Ramachandran restraints generated. 2194 Oldfield, 0 Emsley, 2194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4388 Ramachandran restraints generated. 2194 Oldfield, 0 Emsley, 2194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 1857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 236 time to evaluate : 0.418 Fit side-chains revert: symmetry clash REVERT: G 120 LEU cc_start: 0.6533 (OUTLIER) cc_final: 0.6015 (mm) REVERT: G 131 ARG cc_start: 0.6443 (OUTLIER) cc_final: 0.4544 (mmt90) REVERT: N 81 ASN cc_start: 0.7182 (OUTLIER) cc_final: 0.6451 (p0) REVERT: N 94 GLU cc_start: 0.7388 (tt0) cc_final: 0.7173 (tt0) REVERT: N 286 TYR cc_start: 0.7433 (OUTLIER) cc_final: 0.6457 (p90) REVERT: L 36 LYS cc_start: 0.8063 (mttt) cc_final: 0.7832 (mtpt) REVERT: L 149 GLU cc_start: 0.8300 (OUTLIER) cc_final: 0.8097 (mt-10) REVERT: J 28 PHE cc_start: 0.7123 (OUTLIER) cc_final: 0.6192 (m-80) REVERT: H 160 PHE cc_start: 0.7548 (m-80) cc_final: 0.6856 (t80) REVERT: H 168 LYS cc_start: 0.7525 (mmtm) cc_final: 0.7307 (mmtm) REVERT: H 215 ARG cc_start: 0.7598 (ttp80) cc_final: 0.7285 (ttp80) REVERT: F 17 ARG cc_start: 0.8560 (mtt90) cc_final: 0.7970 (mtt-85) REVERT: F 73 GLN cc_start: 0.8666 (tp40) cc_final: 0.7955 (tp40) REVERT: F 76 ARG cc_start: 0.8199 (OUTLIER) cc_final: 0.7937 (ptp-170) REVERT: E 21 LYS cc_start: 0.8348 (mmtt) cc_final: 0.8112 (mmmt) REVERT: D 22 LYS cc_start: 0.8424 (mtpp) cc_final: 0.8092 (tppt) REVERT: D 59 LEU cc_start: 0.9150 (OUTLIER) cc_final: 0.8828 (tt) REVERT: C 86 ARG cc_start: 0.7670 (ttm170) cc_final: 0.7439 (mtt180) REVERT: C 101 ASP cc_start: 0.8098 (p0) cc_final: 0.7895 (p0) REVERT: C 105 LYS cc_start: 0.8898 (mmtm) cc_final: 0.8641 (mmtt) REVERT: B 83 PHE cc_start: 0.6300 (OUTLIER) cc_final: 0.5537 (t80) outliers start: 66 outliers final: 47 residues processed: 287 average time/residue: 0.1469 time to fit residues: 60.8222 Evaluate side-chains 279 residues out of total 1857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 223 time to evaluate : 0.582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 11 THR Chi-restraints excluded: chain K residue 48 MET Chi-restraints excluded: chain K residue 75 ARG Chi-restraints excluded: chain K residue 104 THR Chi-restraints excluded: chain K residue 110 ASP Chi-restraints excluded: chain K residue 166 GLU Chi-restraints excluded: chain K residue 167 GLN Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain G residue 120 LEU Chi-restraints excluded: chain G residue 123 VAL Chi-restraints excluded: chain G residue 131 ARG Chi-restraints excluded: chain G residue 196 LEU Chi-restraints excluded: chain N residue 4 TYR Chi-restraints excluded: chain N residue 27 THR Chi-restraints excluded: chain N residue 32 HIS Chi-restraints excluded: chain N residue 46 LEU Chi-restraints excluded: chain N residue 81 ASN Chi-restraints excluded: chain N residue 100 ILE Chi-restraints excluded: chain N residue 129 ASP Chi-restraints excluded: chain N residue 286 TYR Chi-restraints excluded: chain N residue 299 ILE Chi-restraints excluded: chain N residue 300 VAL Chi-restraints excluded: chain N residue 327 VAL Chi-restraints excluded: chain N residue 339 VAL Chi-restraints excluded: chain N residue 345 LEU Chi-restraints excluded: chain L residue 11 THR Chi-restraints excluded: chain L residue 87 LEU Chi-restraints excluded: chain L residue 96 THR Chi-restraints excluded: chain L residue 149 GLU Chi-restraints excluded: chain J residue 28 PHE Chi-restraints excluded: chain J residue 104 THR Chi-restraints excluded: chain I residue 2 THR Chi-restraints excluded: chain I residue 31 ILE Chi-restraints excluded: chain I residue 218 VAL Chi-restraints excluded: chain I residue 226 LEU Chi-restraints excluded: chain H residue 15 THR Chi-restraints excluded: chain H residue 155 VAL Chi-restraints excluded: chain H residue 177 ILE Chi-restraints excluded: chain F residue 33 LEU Chi-restraints excluded: chain F residue 43 LEU Chi-restraints excluded: chain F residue 68 VAL Chi-restraints excluded: chain F residue 76 ARG Chi-restraints excluded: chain F residue 95 GLN Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 25 ASP Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain D residue 59 LEU Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain B residue 15 VAL Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 68 VAL Chi-restraints excluded: chain B residue 83 PHE Chi-restraints excluded: chain B residue 90 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 190 optimal weight: 4.9990 chunk 60 optimal weight: 5.9990 chunk 185 optimal weight: 3.9990 chunk 22 optimal weight: 0.9980 chunk 10 optimal weight: 1.9990 chunk 137 optimal weight: 0.9990 chunk 146 optimal weight: 2.9990 chunk 109 optimal weight: 0.8980 chunk 194 optimal weight: 1.9990 chunk 88 optimal weight: 3.9990 chunk 172 optimal weight: 5.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** G 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 32 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.126718 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.092157 restraints weight = 66660.612| |-----------------------------------------------------------------------------| r_work (start): 0.3148 rms_B_bonded: 3.42 r_work: 0.2878 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.2878 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2885 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2885 r_free = 0.2885 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2885 r_free = 0.2885 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2885 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8956 moved from start: 0.1882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 18863 Z= 0.165 Angle : 0.555 6.346 25652 Z= 0.298 Chirality : 0.042 0.148 2946 Planarity : 0.004 0.039 3158 Dihedral : 13.209 179.333 3238 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 3.91 % Allowed : 12.43 % Favored : 83.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.28 (0.17), residues: 2194 helix: -1.43 (0.17), residues: 830 sheet: -0.82 (0.28), residues: 338 loop : -1.73 (0.18), residues: 1026 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 17 TYR 0.019 0.002 TYR H 204 PHE 0.015 0.001 PHE N 317 TRP 0.002 0.001 TRP N 77 HIS 0.005 0.001 HIS N 32 Details of bonding type rmsd/Z covalent geometry : bond 0.00388 / 0.16 (18863) covalent geometry : angle 0.55522 / 0.30 (25652) hydrogen bonds : bond 0.04377 / 3.02 ( 538) hydrogen bonds : angle 4.24447 / 2.91 ( 1572) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4388 Ramachandran restraints generated. 2194 Oldfield, 0 Emsley, 2194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4388 Ramachandran restraints generated. 2194 Oldfield, 0 Emsley, 2194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 1857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 227 time to evaluate : 0.631 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 120 LEU cc_start: 0.6497 (OUTLIER) cc_final: 0.5943 (mm) REVERT: G 131 ARG cc_start: 0.6537 (OUTLIER) cc_final: 0.3802 (mmt90) REVERT: N 81 ASN cc_start: 0.7131 (OUTLIER) cc_final: 0.6392 (p0) REVERT: N 94 GLU cc_start: 0.7463 (tt0) cc_final: 0.7191 (tt0) REVERT: N 286 TYR cc_start: 0.7491 (OUTLIER) cc_final: 0.6349 (p90) REVERT: J 28 PHE cc_start: 0.7173 (OUTLIER) cc_final: 0.6196 (m-80) REVERT: H 160 PHE cc_start: 0.7569 (m-80) cc_final: 0.6858 (t80) REVERT: H 168 LYS cc_start: 0.7609 (mmtm) cc_final: 0.7390 (mmtm) REVERT: H 215 ARG cc_start: 0.7687 (ttp80) cc_final: 0.7314 (ttp80) REVERT: F 73 GLN cc_start: 0.8766 (tp40) cc_final: 0.8007 (tp40) REVERT: F 76 ARG cc_start: 0.8275 (OUTLIER) cc_final: 0.7950 (ptp-170) REVERT: E 21 LYS cc_start: 0.8312 (mmtt) cc_final: 0.8088 (mmmt) REVERT: D 22 LYS cc_start: 0.8485 (mtpp) cc_final: 0.8120 (tppt) REVERT: D 59 LEU cc_start: 0.9174 (OUTLIER) cc_final: 0.8824 (tt) REVERT: C 85 GLU cc_start: 0.8031 (pp20) cc_final: 0.7800 (pp20) REVERT: C 86 ARG cc_start: 0.7733 (ttm170) cc_final: 0.7417 (mtt180) REVERT: C 101 ASP cc_start: 0.8066 (p0) cc_final: 0.7842 (p0) REVERT: C 105 LYS cc_start: 0.8907 (mmtm) cc_final: 0.8623 (mmtt) REVERT: B 83 PHE cc_start: 0.6295 (OUTLIER) cc_final: 0.5576 (t80) outliers start: 72 outliers final: 51 residues processed: 281 average time/residue: 0.1529 time to fit residues: 61.6770 Evaluate side-chains 281 residues out of total 1857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 222 time to evaluate : 0.609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 48 MET Chi-restraints excluded: chain K residue 75 ARG Chi-restraints excluded: chain K residue 104 THR Chi-restraints excluded: chain K residue 110 ASP Chi-restraints excluded: chain K residue 166 GLU Chi-restraints excluded: chain K residue 167 GLN Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain G residue 120 LEU Chi-restraints excluded: chain G residue 123 VAL Chi-restraints excluded: chain G residue 131 ARG Chi-restraints excluded: chain G residue 137 ASN Chi-restraints excluded: chain G residue 196 LEU Chi-restraints excluded: chain N residue 4 TYR Chi-restraints excluded: chain N residue 27 THR Chi-restraints excluded: chain N residue 32 HIS Chi-restraints excluded: chain N residue 46 LEU Chi-restraints excluded: chain N residue 81 ASN Chi-restraints excluded: chain N residue 100 ILE Chi-restraints excluded: chain N residue 129 ASP Chi-restraints excluded: chain N residue 286 TYR Chi-restraints excluded: chain N residue 300 VAL Chi-restraints excluded: chain N residue 327 VAL Chi-restraints excluded: chain N residue 339 VAL Chi-restraints excluded: chain N residue 375 GLU Chi-restraints excluded: chain L residue 11 THR Chi-restraints excluded: chain L residue 87 LEU Chi-restraints excluded: chain L residue 96 THR Chi-restraints excluded: chain L residue 129 ILE Chi-restraints excluded: chain J residue 28 PHE Chi-restraints excluded: chain J residue 104 THR Chi-restraints excluded: chain J residue 218 VAL Chi-restraints excluded: chain I residue 2 THR Chi-restraints excluded: chain I residue 31 ILE Chi-restraints excluded: chain I residue 218 VAL Chi-restraints excluded: chain I residue 226 LEU Chi-restraints excluded: chain H residue 15 THR Chi-restraints excluded: chain H residue 155 VAL Chi-restraints excluded: chain F residue 5 GLN Chi-restraints excluded: chain F residue 33 LEU Chi-restraints excluded: chain F residue 43 LEU Chi-restraints excluded: chain F residue 68 VAL Chi-restraints excluded: chain F residue 76 ARG Chi-restraints excluded: chain F residue 81 ARG Chi-restraints excluded: chain F residue 95 GLN Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 25 ASP Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain D residue 10 LYS Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 59 LEU Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain B residue 15 VAL Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 68 VAL Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 83 PHE Chi-restraints excluded: chain B residue 90 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 41 optimal weight: 10.0000 chunk 11 optimal weight: 2.9990 chunk 216 optimal weight: 5.9990 chunk 39 optimal weight: 9.9990 chunk 82 optimal weight: 2.9990 chunk 36 optimal weight: 8.9990 chunk 181 optimal weight: 2.9990 chunk 185 optimal weight: 0.0770 chunk 73 optimal weight: 0.2980 chunk 69 optimal weight: 3.9990 chunk 175 optimal weight: 0.5980 overall best weight: 1.3942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** G 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 32 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.126948 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.092625 restraints weight = 59422.704| |-----------------------------------------------------------------------------| r_work (start): 0.3137 rms_B_bonded: 2.90 r_work: 0.2909 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.2909 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2916 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2916 r_free = 0.2916 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2916 r_free = 0.2916 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2916 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8934 moved from start: 0.2000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 18863 Z= 0.165 Angle : 0.555 11.157 25652 Z= 0.295 Chirality : 0.042 0.148 2946 Planarity : 0.004 0.040 3158 Dihedral : 13.115 179.457 3233 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 4.12 % Allowed : 12.53 % Favored : 83.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.01 (0.17), residues: 2194 helix: -1.13 (0.18), residues: 831 sheet: -0.71 (0.28), residues: 338 loop : -1.65 (0.18), residues: 1025 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 102 TYR 0.019 0.002 TYR H 204 PHE 0.015 0.001 PHE N 317 TRP 0.003 0.001 TRP N 77 HIS 0.006 0.001 HIS N 32 Details of bonding type rmsd/Z covalent geometry : bond 0.00392 / 0.16 (18863) covalent geometry : angle 0.55511 / 0.29 (25652) hydrogen bonds : bond 0.04173 / 2.89 ( 538) hydrogen bonds : angle 4.14604 / 2.83 ( 1572) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4388 Ramachandran restraints generated. 2194 Oldfield, 0 Emsley, 2194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4388 Ramachandran restraints generated. 2194 Oldfield, 0 Emsley, 2194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 1857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 228 time to evaluate : 0.729 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 120 LEU cc_start: 0.6517 (OUTLIER) cc_final: 0.5966 (mm) REVERT: G 131 ARG cc_start: 0.6470 (OUTLIER) cc_final: 0.3639 (mmt90) REVERT: N 81 ASN cc_start: 0.7152 (OUTLIER) cc_final: 0.6425 (p0) REVERT: N 94 GLU cc_start: 0.7426 (tt0) cc_final: 0.7128 (tt0) REVERT: N 286 TYR cc_start: 0.7504 (OUTLIER) cc_final: 0.6319 (p90) REVERT: L 206 GLN cc_start: 0.8793 (OUTLIER) cc_final: 0.8189 (tt0) REVERT: J 28 PHE cc_start: 0.7147 (OUTLIER) cc_final: 0.6188 (m-80) REVERT: H 160 PHE cc_start: 0.7586 (m-80) cc_final: 0.6879 (t80) REVERT: H 168 LYS cc_start: 0.7582 (mmtm) cc_final: 0.7360 (mmtm) REVERT: H 215 ARG cc_start: 0.7620 (ttp80) cc_final: 0.7298 (ttp80) REVERT: F 13 GLU cc_start: 0.8704 (tm-30) cc_final: 0.8259 (tm-30) REVERT: F 17 ARG cc_start: 0.8532 (mtt-85) cc_final: 0.8046 (mtt-85) REVERT: F 73 GLN cc_start: 0.8759 (tp40) cc_final: 0.7937 (tp40) REVERT: F 76 ARG cc_start: 0.8261 (OUTLIER) cc_final: 0.7895 (ptp-170) REVERT: F 95 GLN cc_start: 0.8819 (OUTLIER) cc_final: 0.7604 (mp-120) REVERT: E 21 LYS cc_start: 0.8300 (mmtt) cc_final: 0.8094 (mmmt) REVERT: D 22 LYS cc_start: 0.8481 (mtpp) cc_final: 0.8118 (tppt) REVERT: D 59 LEU cc_start: 0.9187 (OUTLIER) cc_final: 0.8849 (tt) REVERT: C 85 GLU cc_start: 0.8016 (pp20) cc_final: 0.7785 (pp20) REVERT: C 86 ARG cc_start: 0.7695 (ttm170) cc_final: 0.7367 (mtt180) REVERT: C 101 ASP cc_start: 0.7987 (p0) cc_final: 0.7721 (p0) REVERT: C 105 LYS cc_start: 0.8866 (mmtm) cc_final: 0.8590 (mmtt) REVERT: B 83 PHE cc_start: 0.6289 (OUTLIER) cc_final: 0.5591 (t80) outliers start: 76 outliers final: 59 residues processed: 284 average time/residue: 0.1596 time to fit residues: 65.2348 Evaluate side-chains 290 residues out of total 1857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 221 time to evaluate : 0.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 11 THR Chi-restraints excluded: chain K residue 48 MET Chi-restraints excluded: chain K residue 75 ARG Chi-restraints excluded: chain K residue 104 THR Chi-restraints excluded: chain K residue 110 ASP Chi-restraints excluded: chain K residue 166 GLU Chi-restraints excluded: chain K residue 167 GLN Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain G residue 120 LEU Chi-restraints excluded: chain G residue 123 VAL Chi-restraints excluded: chain G residue 131 ARG Chi-restraints excluded: chain G residue 137 ASN Chi-restraints excluded: chain G residue 196 LEU Chi-restraints excluded: chain N residue 4 TYR Chi-restraints excluded: chain N residue 27 THR Chi-restraints excluded: chain N residue 32 HIS Chi-restraints excluded: chain N residue 46 LEU Chi-restraints excluded: chain N residue 81 ASN Chi-restraints excluded: chain N residue 100 ILE Chi-restraints excluded: chain N residue 104 ARG Chi-restraints excluded: chain N residue 129 ASP Chi-restraints excluded: chain N residue 286 TYR Chi-restraints excluded: chain N residue 299 ILE Chi-restraints excluded: chain N residue 300 VAL Chi-restraints excluded: chain N residue 327 VAL Chi-restraints excluded: chain N residue 339 VAL Chi-restraints excluded: chain N residue 345 LEU Chi-restraints excluded: chain N residue 375 GLU Chi-restraints excluded: chain L residue 11 THR Chi-restraints excluded: chain L residue 87 LEU Chi-restraints excluded: chain L residue 96 THR Chi-restraints excluded: chain L residue 129 ILE Chi-restraints excluded: chain L residue 206 GLN Chi-restraints excluded: chain L residue 210 SER Chi-restraints excluded: chain J residue 28 PHE Chi-restraints excluded: chain J residue 52 THR Chi-restraints excluded: chain J residue 104 THR Chi-restraints excluded: chain J residue 171 LEU Chi-restraints excluded: chain I residue 2 THR Chi-restraints excluded: chain I residue 31 ILE Chi-restraints excluded: chain I residue 218 VAL Chi-restraints excluded: chain I residue 226 LEU Chi-restraints excluded: chain H residue 15 THR Chi-restraints excluded: chain H residue 155 VAL Chi-restraints excluded: chain H residue 177 ILE Chi-restraints excluded: chain F residue 5 GLN Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 33 LEU Chi-restraints excluded: chain F residue 43 LEU Chi-restraints excluded: chain F residue 68 VAL Chi-restraints excluded: chain F residue 76 ARG Chi-restraints excluded: chain F residue 81 ARG Chi-restraints excluded: chain F residue 95 GLN Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain D residue 10 LYS Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 59 LEU Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain B residue 15 VAL Chi-restraints excluded: chain B residue 40 THR Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 68 VAL Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 83 PHE Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain B residue 104 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 88 optimal weight: 2.9990 chunk 82 optimal weight: 2.9990 chunk 121 optimal weight: 0.6980 chunk 105 optimal weight: 4.9990 chunk 48 optimal weight: 0.0070 chunk 165 optimal weight: 0.0060 chunk 164 optimal weight: 2.9990 chunk 140 optimal weight: 0.9980 chunk 184 optimal weight: 0.8980 chunk 142 optimal weight: 0.9980 chunk 152 optimal weight: 2.9990 overall best weight: 0.5214 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** G 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 137 ASN ** I 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 32 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.128603 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.093759 restraints weight = 57784.172| |-----------------------------------------------------------------------------| r_work (start): 0.3169 rms_B_bonded: 2.81 r_work: 0.2955 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.2955 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2962 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2962 r_free = 0.2962 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2962 r_free = 0.2962 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2962 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8892 moved from start: 0.2134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 18863 Z= 0.098 Angle : 0.496 6.694 25652 Z= 0.267 Chirality : 0.040 0.142 2946 Planarity : 0.004 0.038 3158 Dihedral : 13.063 179.895 3233 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 3.59 % Allowed : 13.12 % Favored : 83.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.72 (0.17), residues: 2194 helix: -0.81 (0.18), residues: 832 sheet: -0.64 (0.28), residues: 344 loop : -1.52 (0.18), residues: 1018 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 102 TYR 0.017 0.001 TYR F 65 PHE 0.011 0.001 PHE F 26 TRP 0.002 0.000 TRP N 264 HIS 0.005 0.001 HIS N 32 Details of bonding type rmsd/Z covalent geometry : bond 0.00220 / 0.10 (18863) covalent geometry : angle 0.49568 / 0.27 (25652) hydrogen bonds : bond 0.03368 / 2.33 ( 538) hydrogen bonds : angle 3.95343 / 2.70 ( 1572) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4388 Ramachandran restraints generated. 2194 Oldfield, 0 Emsley, 2194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4388 Ramachandran restraints generated. 2194 Oldfield, 0 Emsley, 2194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 1857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 235 time to evaluate : 0.755 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: N 81 ASN cc_start: 0.7152 (OUTLIER) cc_final: 0.6422 (p0) REVERT: N 94 GLU cc_start: 0.7375 (tt0) cc_final: 0.7099 (tt0) REVERT: N 224 MET cc_start: 0.5281 (mtp) cc_final: 0.4759 (mpp) REVERT: N 282 ASN cc_start: 0.8358 (t0) cc_final: 0.8115 (t0) REVERT: N 286 TYR cc_start: 0.7497 (OUTLIER) cc_final: 0.6495 (p90) REVERT: J 28 PHE cc_start: 0.7046 (OUTLIER) cc_final: 0.6075 (m-80) REVERT: H 160 PHE cc_start: 0.7559 (m-80) cc_final: 0.6880 (t80) REVERT: H 168 LYS cc_start: 0.7521 (mmtm) cc_final: 0.7300 (mmtm) REVERT: F 17 ARG cc_start: 0.8460 (mtt-85) cc_final: 0.8074 (mtt-85) REVERT: F 73 GLN cc_start: 0.8693 (tp40) cc_final: 0.7845 (tp40) REVERT: F 76 ARG cc_start: 0.8227 (OUTLIER) cc_final: 0.7905 (ptp-170) REVERT: D 22 LYS cc_start: 0.8474 (mtpp) cc_final: 0.8119 (tppt) REVERT: D 59 LEU cc_start: 0.9142 (OUTLIER) cc_final: 0.8814 (tt) REVERT: C 85 GLU cc_start: 0.7940 (pp20) cc_final: 0.7731 (pp20) REVERT: C 86 ARG cc_start: 0.7650 (ttm170) cc_final: 0.7343 (mtt90) REVERT: B 83 PHE cc_start: 0.6198 (OUTLIER) cc_final: 0.5489 (t80) outliers start: 66 outliers final: 50 residues processed: 286 average time/residue: 0.1628 time to fit residues: 66.8363 Evaluate side-chains 283 residues out of total 1857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 227 time to evaluate : 0.490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 48 MET Chi-restraints excluded: chain K residue 75 ARG Chi-restraints excluded: chain K residue 104 THR Chi-restraints excluded: chain K residue 110 ASP Chi-restraints excluded: chain K residue 166 GLU Chi-restraints excluded: chain K residue 167 GLN Chi-restraints excluded: chain K residue 218 VAL Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain G residue 123 VAL Chi-restraints excluded: chain G residue 137 ASN Chi-restraints excluded: chain G residue 196 LEU Chi-restraints excluded: chain N residue 4 TYR Chi-restraints excluded: chain N residue 27 THR Chi-restraints excluded: chain N residue 32 HIS Chi-restraints excluded: chain N residue 46 LEU Chi-restraints excluded: chain N residue 81 ASN Chi-restraints excluded: chain N residue 100 ILE Chi-restraints excluded: chain N residue 104 ARG Chi-restraints excluded: chain N residue 129 ASP Chi-restraints excluded: chain N residue 286 TYR Chi-restraints excluded: chain N residue 299 ILE Chi-restraints excluded: chain N residue 300 VAL Chi-restraints excluded: chain N residue 339 VAL Chi-restraints excluded: chain N residue 345 LEU Chi-restraints excluded: chain N residue 375 GLU Chi-restraints excluded: chain L residue 11 THR Chi-restraints excluded: chain L residue 87 LEU Chi-restraints excluded: chain L residue 96 THR Chi-restraints excluded: chain L residue 129 ILE Chi-restraints excluded: chain J residue 28 PHE Chi-restraints excluded: chain J residue 104 THR Chi-restraints excluded: chain J residue 171 LEU Chi-restraints excluded: chain J residue 218 VAL Chi-restraints excluded: chain I residue 2 THR Chi-restraints excluded: chain I residue 31 ILE Chi-restraints excluded: chain I residue 218 VAL Chi-restraints excluded: chain I residue 226 LEU Chi-restraints excluded: chain H residue 155 VAL Chi-restraints excluded: chain F residue 5 GLN Chi-restraints excluded: chain F residue 33 LEU Chi-restraints excluded: chain F residue 43 LEU Chi-restraints excluded: chain F residue 68 VAL Chi-restraints excluded: chain F residue 76 ARG Chi-restraints excluded: chain F residue 81 ARG Chi-restraints excluded: chain F residue 95 GLN Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain D residue 59 LEU Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain B residue 68 VAL Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 83 PHE Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain B residue 104 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 75 optimal weight: 0.7980 chunk 37 optimal weight: 7.9990 chunk 155 optimal weight: 2.9990 chunk 2 optimal weight: 3.9990 chunk 82 optimal weight: 4.9990 chunk 148 optimal weight: 5.9990 chunk 26 optimal weight: 8.9990 chunk 139 optimal weight: 3.9990 chunk 215 optimal weight: 3.9990 chunk 64 optimal weight: 0.0060 chunk 193 optimal weight: 0.9980 overall best weight: 1.7600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 130 ASN G 137 ASN N 283 GLN ** I 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 5 GLN C 32 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.126615 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.091794 restraints weight = 58313.861| |-----------------------------------------------------------------------------| r_work (start): 0.3128 rms_B_bonded: 2.76 r_work: 0.2910 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.2910 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2917 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2917 r_free = 0.2917 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2917 r_free = 0.2917 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2917 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8935 moved from start: 0.2148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 18863 Z= 0.197 Angle : 0.574 8.282 25652 Z= 0.303 Chirality : 0.043 0.156 2946 Planarity : 0.004 0.040 3158 Dihedral : 13.064 179.238 3233 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 3.86 % Allowed : 13.55 % Favored : 82.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.66 (0.17), residues: 2194 helix: -0.72 (0.18), residues: 831 sheet: -0.56 (0.29), residues: 339 loop : -1.54 (0.18), residues: 1024 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG K 115 TYR 0.022 0.002 TYR H 204 PHE 0.016 0.001 PHE N 317 TRP 0.003 0.001 TRP N 77 HIS 0.005 0.001 HIS N 32 Details of bonding type rmsd/Z covalent geometry : bond 0.00474 / 0.20 (18863) covalent geometry : angle 0.57351 / 0.30 (25652) hydrogen bonds : bond 0.04122 / 2.85 ( 538) hydrogen bonds : angle 4.04101 / 2.76 ( 1572) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4388 Ramachandran restraints generated. 2194 Oldfield, 0 Emsley, 2194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4388 Ramachandran restraints generated. 2194 Oldfield, 0 Emsley, 2194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 1857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 228 time to evaluate : 0.646 Fit side-chains revert: symmetry clash REVERT: G 120 LEU cc_start: 0.6569 (OUTLIER) cc_final: 0.5962 (mm) REVERT: G 131 ARG cc_start: 0.6483 (OUTLIER) cc_final: 0.3319 (mmt90) REVERT: N 81 ASN cc_start: 0.7154 (OUTLIER) cc_final: 0.6393 (p0) REVERT: N 94 GLU cc_start: 0.7389 (tt0) cc_final: 0.7081 (tt0) REVERT: N 282 ASN cc_start: 0.8367 (t0) cc_final: 0.8119 (t0) REVERT: N 286 TYR cc_start: 0.7539 (OUTLIER) cc_final: 0.6569 (p90) REVERT: L 206 GLN cc_start: 0.8787 (OUTLIER) cc_final: 0.8190 (tt0) REVERT: H 160 PHE cc_start: 0.7583 (m-80) cc_final: 0.6905 (t80) REVERT: H 168 LYS cc_start: 0.7509 (mmtm) cc_final: 0.7277 (mmtm) REVERT: F 17 ARG cc_start: 0.8467 (mtt-85) cc_final: 0.8071 (mtt-85) REVERT: F 73 GLN cc_start: 0.8747 (tp40) cc_final: 0.7843 (tp40) REVERT: F 76 ARG cc_start: 0.8260 (OUTLIER) cc_final: 0.7890 (ptp-170) REVERT: F 95 GLN cc_start: 0.8786 (OUTLIER) cc_final: 0.7621 (mp10) REVERT: D 59 LEU cc_start: 0.9177 (OUTLIER) cc_final: 0.8835 (tt) REVERT: C 86 ARG cc_start: 0.7767 (ttm170) cc_final: 0.7422 (mtt90) REVERT: B 83 PHE cc_start: 0.6293 (OUTLIER) cc_final: 0.5578 (t80) outliers start: 71 outliers final: 55 residues processed: 278 average time/residue: 0.1771 time to fit residues: 70.3798 Evaluate side-chains 290 residues out of total 1857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 226 time to evaluate : 0.704 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 48 MET Chi-restraints excluded: chain K residue 75 ARG Chi-restraints excluded: chain K residue 104 THR Chi-restraints excluded: chain K residue 110 ASP Chi-restraints excluded: chain K residue 166 GLU Chi-restraints excluded: chain K residue 167 GLN Chi-restraints excluded: chain K residue 218 VAL Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain G residue 120 LEU Chi-restraints excluded: chain G residue 123 VAL Chi-restraints excluded: chain G residue 131 ARG Chi-restraints excluded: chain G residue 196 LEU Chi-restraints excluded: chain N residue 4 TYR Chi-restraints excluded: chain N residue 27 THR Chi-restraints excluded: chain N residue 32 HIS Chi-restraints excluded: chain N residue 46 LEU Chi-restraints excluded: chain N residue 81 ASN Chi-restraints excluded: chain N residue 100 ILE Chi-restraints excluded: chain N residue 104 ARG Chi-restraints excluded: chain N residue 129 ASP Chi-restraints excluded: chain N residue 191 ASN Chi-restraints excluded: chain N residue 286 TYR Chi-restraints excluded: chain N residue 299 ILE Chi-restraints excluded: chain N residue 300 VAL Chi-restraints excluded: chain N residue 317 PHE Chi-restraints excluded: chain N residue 327 VAL Chi-restraints excluded: chain N residue 339 VAL Chi-restraints excluded: chain N residue 345 LEU Chi-restraints excluded: chain N residue 375 GLU Chi-restraints excluded: chain L residue 11 THR Chi-restraints excluded: chain L residue 87 LEU Chi-restraints excluded: chain L residue 129 ILE Chi-restraints excluded: chain L residue 206 GLN Chi-restraints excluded: chain L residue 210 SER Chi-restraints excluded: chain J residue 52 THR Chi-restraints excluded: chain J residue 104 THR Chi-restraints excluded: chain I residue 2 THR Chi-restraints excluded: chain I residue 31 ILE Chi-restraints excluded: chain I residue 218 VAL Chi-restraints excluded: chain I residue 226 LEU Chi-restraints excluded: chain H residue 15 THR Chi-restraints excluded: chain H residue 155 VAL Chi-restraints excluded: chain H residue 177 ILE Chi-restraints excluded: chain F residue 33 LEU Chi-restraints excluded: chain F residue 43 LEU Chi-restraints excluded: chain F residue 68 VAL Chi-restraints excluded: chain F residue 76 ARG Chi-restraints excluded: chain F residue 81 ARG Chi-restraints excluded: chain F residue 95 GLN Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain D residue 10 LYS Chi-restraints excluded: chain D residue 59 LEU Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain B residue 15 VAL Chi-restraints excluded: chain B residue 40 THR Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 68 VAL Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 83 PHE Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain B residue 104 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 180 optimal weight: 1.9990 chunk 183 optimal weight: 0.9980 chunk 121 optimal weight: 1.9990 chunk 91 optimal weight: 6.9990 chunk 105 optimal weight: 3.9990 chunk 102 optimal weight: 1.9990 chunk 125 optimal weight: 0.8980 chunk 18 optimal weight: 0.9980 chunk 57 optimal weight: 3.9990 chunk 62 optimal weight: 2.9990 chunk 75 optimal weight: 0.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** I 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 32 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.126957 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.092816 restraints weight = 59239.751| |-----------------------------------------------------------------------------| r_work (start): 0.3150 rms_B_bonded: 2.98 r_work: 0.2913 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.2913 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2919 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2919 r_free = 0.2919 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2919 r_free = 0.2919 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2919 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8930 moved from start: 0.2205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 18863 Z= 0.145 Angle : 0.540 7.552 25652 Z= 0.288 Chirality : 0.041 0.145 2946 Planarity : 0.004 0.059 3158 Dihedral : 13.028 179.515 3230 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 3.75 % Allowed : 13.93 % Favored : 82.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.54 (0.17), residues: 2194 helix: -0.60 (0.18), residues: 831 sheet: -0.49 (0.29), residues: 338 loop : -1.51 (0.18), residues: 1025 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG E 102 TYR 0.016 0.001 TYR H 204 PHE 0.013 0.001 PHE N 317 TRP 0.002 0.000 TRP N 77 HIS 0.005 0.001 HIS N 32 Details of bonding type rmsd/Z covalent geometry : bond 0.00345 / 0.15 (18863) covalent geometry : angle 0.53971 / 0.29 (25652) hydrogen bonds : bond 0.03761 / 2.60 ( 538) hydrogen bonds : angle 3.94524 / 2.70 ( 1572) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4388 Ramachandran restraints generated. 2194 Oldfield, 0 Emsley, 2194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4388 Ramachandran restraints generated. 2194 Oldfield, 0 Emsley, 2194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 1857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 223 time to evaluate : 0.724 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 120 LEU cc_start: 0.6472 (OUTLIER) cc_final: 0.5832 (mm) REVERT: G 131 ARG cc_start: 0.6463 (OUTLIER) cc_final: 0.2878 (mmt90) REVERT: N 81 ASN cc_start: 0.7160 (OUTLIER) cc_final: 0.6417 (p0) REVERT: N 94 GLU cc_start: 0.7396 (tt0) cc_final: 0.7091 (tt0) REVERT: N 282 ASN cc_start: 0.8377 (t0) cc_final: 0.8127 (t0) REVERT: N 286 TYR cc_start: 0.7496 (OUTLIER) cc_final: 0.6561 (p90) REVERT: L 206 GLN cc_start: 0.8768 (OUTLIER) cc_final: 0.8182 (tt0) REVERT: H 160 PHE cc_start: 0.7590 (m-80) cc_final: 0.6900 (t80) REVERT: H 168 LYS cc_start: 0.7503 (mmtm) cc_final: 0.7270 (mmtm) REVERT: F 17 ARG cc_start: 0.8473 (mtt-85) cc_final: 0.8056 (mtt-85) REVERT: F 73 GLN cc_start: 0.8725 (tp40) cc_final: 0.7807 (tp40) REVERT: F 76 ARG cc_start: 0.8269 (OUTLIER) cc_final: 0.7901 (ptp-170) REVERT: F 95 GLN cc_start: 0.8790 (OUTLIER) cc_final: 0.7590 (mp10) REVERT: D 59 LEU cc_start: 0.9172 (OUTLIER) cc_final: 0.8838 (tt) REVERT: C 86 ARG cc_start: 0.7647 (ttm170) cc_final: 0.7412 (mtt180) REVERT: B 83 PHE cc_start: 0.6274 (OUTLIER) cc_final: 0.5573 (t80) outliers start: 69 outliers final: 55 residues processed: 272 average time/residue: 0.1747 time to fit residues: 68.7459 Evaluate side-chains 286 residues out of total 1857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 222 time to evaluate : 0.713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 11 THR Chi-restraints excluded: chain K residue 48 MET Chi-restraints excluded: chain K residue 75 ARG Chi-restraints excluded: chain K residue 104 THR Chi-restraints excluded: chain K residue 110 ASP Chi-restraints excluded: chain K residue 167 GLN Chi-restraints excluded: chain K residue 218 VAL Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain G residue 120 LEU Chi-restraints excluded: chain G residue 123 VAL Chi-restraints excluded: chain G residue 131 ARG Chi-restraints excluded: chain G residue 196 LEU Chi-restraints excluded: chain N residue 4 TYR Chi-restraints excluded: chain N residue 27 THR Chi-restraints excluded: chain N residue 32 HIS Chi-restraints excluded: chain N residue 46 LEU Chi-restraints excluded: chain N residue 81 ASN Chi-restraints excluded: chain N residue 100 ILE Chi-restraints excluded: chain N residue 104 ARG Chi-restraints excluded: chain N residue 129 ASP Chi-restraints excluded: chain N residue 286 TYR Chi-restraints excluded: chain N residue 299 ILE Chi-restraints excluded: chain N residue 300 VAL Chi-restraints excluded: chain N residue 327 VAL Chi-restraints excluded: chain N residue 339 VAL Chi-restraints excluded: chain N residue 345 LEU Chi-restraints excluded: chain N residue 375 GLU Chi-restraints excluded: chain L residue 11 THR Chi-restraints excluded: chain L residue 87 LEU Chi-restraints excluded: chain L residue 96 THR Chi-restraints excluded: chain L residue 129 ILE Chi-restraints excluded: chain L residue 206 GLN Chi-restraints excluded: chain L residue 210 SER Chi-restraints excluded: chain J residue 104 THR Chi-restraints excluded: chain J residue 171 LEU Chi-restraints excluded: chain I residue 2 THR Chi-restraints excluded: chain I residue 31 ILE Chi-restraints excluded: chain I residue 167 GLN Chi-restraints excluded: chain I residue 218 VAL Chi-restraints excluded: chain I residue 226 LEU Chi-restraints excluded: chain H residue 15 THR Chi-restraints excluded: chain H residue 155 VAL Chi-restraints excluded: chain F residue 5 GLN Chi-restraints excluded: chain F residue 33 LEU Chi-restraints excluded: chain F residue 43 LEU Chi-restraints excluded: chain F residue 68 VAL Chi-restraints excluded: chain F residue 76 ARG Chi-restraints excluded: chain F residue 81 ARG Chi-restraints excluded: chain F residue 95 GLN Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain D residue 10 LYS Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 59 LEU Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain B residue 15 VAL Chi-restraints excluded: chain B residue 40 THR Chi-restraints excluded: chain B residue 68 VAL Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 83 PHE Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain B residue 104 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 50 optimal weight: 6.9990 chunk 45 optimal weight: 0.9990 chunk 66 optimal weight: 8.9990 chunk 158 optimal weight: 3.9990 chunk 99 optimal weight: 0.9990 chunk 154 optimal weight: 1.9990 chunk 178 optimal weight: 0.2980 chunk 4 optimal weight: 0.9980 chunk 216 optimal weight: 4.9990 chunk 15 optimal weight: 0.8980 chunk 21 optimal weight: 2.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** I 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 32 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.128390 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.094574 restraints weight = 63821.040| |-----------------------------------------------------------------------------| r_work (start): 0.3175 rms_B_bonded: 3.06 r_work: 0.2928 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.2928 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2931 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2931 r_free = 0.2931 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2931 r_free = 0.2931 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2931 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8912 moved from start: 0.2273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 18863 Z= 0.120 Angle : 0.513 7.095 25652 Z= 0.276 Chirality : 0.040 0.157 2946 Planarity : 0.004 0.043 3158 Dihedral : 12.951 179.767 3227 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 3.54 % Allowed : 13.87 % Favored : 82.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.32 (0.18), residues: 2194 helix: -0.34 (0.19), residues: 825 sheet: -0.29 (0.30), residues: 313 loop : -1.46 (0.18), residues: 1056 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 102 TYR 0.014 0.001 TYR D 8 PHE 0.011 0.001 PHE N 317 TRP 0.002 0.000 TRP N 77 HIS 0.005 0.001 HIS N 32 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.12 (18863) covalent geometry : angle 0.51295 / 0.28 (25652) hydrogen bonds : bond 0.03393 / 2.34 ( 538) hydrogen bonds : angle 3.83898 / 2.63 ( 1572) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4388 Ramachandran restraints generated. 2194 Oldfield, 0 Emsley, 2194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4388 Ramachandran restraints generated. 2194 Oldfield, 0 Emsley, 2194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 1857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 227 time to evaluate : 0.648 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 20 LEU cc_start: 0.8356 (tp) cc_final: 0.8052 (tp) REVERT: G 120 LEU cc_start: 0.6449 (OUTLIER) cc_final: 0.5825 (mm) REVERT: G 131 ARG cc_start: 0.6530 (OUTLIER) cc_final: 0.2923 (mmt90) REVERT: N 81 ASN cc_start: 0.7131 (OUTLIER) cc_final: 0.6385 (p0) REVERT: N 94 GLU cc_start: 0.7461 (tt0) cc_final: 0.7157 (tt0) REVERT: N 224 MET cc_start: 0.5477 (mtp) cc_final: 0.4841 (mpp) REVERT: N 226 MET cc_start: 0.7838 (mtm) cc_final: 0.7550 (mtt) REVERT: N 282 ASN cc_start: 0.8395 (t0) cc_final: 0.8157 (t0) REVERT: N 286 TYR cc_start: 0.7508 (OUTLIER) cc_final: 0.6685 (p90) REVERT: L 206 GLN cc_start: 0.8736 (OUTLIER) cc_final: 0.8140 (tt0) REVERT: H 160 PHE cc_start: 0.7568 (m-80) cc_final: 0.6902 (t80) REVERT: H 168 LYS cc_start: 0.7477 (mmtm) cc_final: 0.7255 (mmtm) REVERT: F 13 GLU cc_start: 0.8670 (tm-30) cc_final: 0.8381 (tt0) REVERT: F 73 GLN cc_start: 0.8722 (tp40) cc_final: 0.7802 (tp40) REVERT: F 76 ARG cc_start: 0.8244 (OUTLIER) cc_final: 0.7927 (ptp-170) REVERT: F 95 GLN cc_start: 0.8771 (OUTLIER) cc_final: 0.7551 (mp10) REVERT: D 59 LEU cc_start: 0.9159 (OUTLIER) cc_final: 0.8854 (tt) REVERT: C 86 ARG cc_start: 0.7605 (ttm170) cc_final: 0.7387 (mtt180) REVERT: B 83 PHE cc_start: 0.6235 (OUTLIER) cc_final: 0.5529 (t80) outliers start: 65 outliers final: 51 residues processed: 274 average time/residue: 0.1734 time to fit residues: 68.3265 Evaluate side-chains 284 residues out of total 1857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 224 time to evaluate : 0.759 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 48 MET Chi-restraints excluded: chain K residue 104 THR Chi-restraints excluded: chain K residue 110 ASP Chi-restraints excluded: chain K residue 166 GLU Chi-restraints excluded: chain K residue 167 GLN Chi-restraints excluded: chain K residue 218 VAL Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain G residue 120 LEU Chi-restraints excluded: chain G residue 123 VAL Chi-restraints excluded: chain G residue 131 ARG Chi-restraints excluded: chain G residue 196 LEU Chi-restraints excluded: chain N residue 27 THR Chi-restraints excluded: chain N residue 32 HIS Chi-restraints excluded: chain N residue 46 LEU Chi-restraints excluded: chain N residue 81 ASN Chi-restraints excluded: chain N residue 100 ILE Chi-restraints excluded: chain N residue 104 ARG Chi-restraints excluded: chain N residue 129 ASP Chi-restraints excluded: chain N residue 286 TYR Chi-restraints excluded: chain N residue 299 ILE Chi-restraints excluded: chain N residue 300 VAL Chi-restraints excluded: chain N residue 327 VAL Chi-restraints excluded: chain N residue 339 VAL Chi-restraints excluded: chain N residue 345 LEU Chi-restraints excluded: chain N residue 375 GLU Chi-restraints excluded: chain L residue 11 THR Chi-restraints excluded: chain L residue 96 THR Chi-restraints excluded: chain L residue 129 ILE Chi-restraints excluded: chain L residue 206 GLN Chi-restraints excluded: chain J residue 104 THR Chi-restraints excluded: chain J residue 171 LEU Chi-restraints excluded: chain I residue 2 THR Chi-restraints excluded: chain I residue 31 ILE Chi-restraints excluded: chain I residue 167 GLN Chi-restraints excluded: chain I residue 218 VAL Chi-restraints excluded: chain I residue 226 LEU Chi-restraints excluded: chain H residue 15 THR Chi-restraints excluded: chain H residue 155 VAL Chi-restraints excluded: chain F residue 5 GLN Chi-restraints excluded: chain F residue 33 LEU Chi-restraints excluded: chain F residue 43 LEU Chi-restraints excluded: chain F residue 68 VAL Chi-restraints excluded: chain F residue 76 ARG Chi-restraints excluded: chain F residue 81 ARG Chi-restraints excluded: chain F residue 95 GLN Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain D residue 10 LYS Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 59 LEU Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain B residue 15 VAL Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 68 VAL Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 83 PHE Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain B residue 104 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 55 optimal weight: 7.9990 chunk 150 optimal weight: 1.9990 chunk 105 optimal weight: 0.9980 chunk 54 optimal weight: 1.9990 chunk 178 optimal weight: 2.9990 chunk 91 optimal weight: 7.9990 chunk 80 optimal weight: 0.6980 chunk 163 optimal weight: 0.1980 chunk 123 optimal weight: 2.9990 chunk 192 optimal weight: 0.9980 chunk 120 optimal weight: 0.3980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** I 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 32 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.128450 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.093928 restraints weight = 58585.250| |-----------------------------------------------------------------------------| r_work (start): 0.3170 rms_B_bonded: 2.87 r_work: 0.2955 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.2955 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2962 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2962 r_free = 0.2962 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2962 r_free = 0.2962 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2962 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8892 moved from start: 0.2327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 18863 Z= 0.108 Angle : 0.512 9.224 25652 Z= 0.275 Chirality : 0.040 0.149 2946 Planarity : 0.004 0.048 3158 Dihedral : 12.868 179.761 3223 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 3.21 % Allowed : 14.30 % Favored : 82.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.22 (0.18), residues: 2194 helix: -0.23 (0.19), residues: 828 sheet: -0.25 (0.30), residues: 313 loop : -1.42 (0.18), residues: 1053 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG F 17 TYR 0.015 0.001 TYR N 4 PHE 0.010 0.001 PHE N 317 TRP 0.002 0.000 TRP N 77 HIS 0.005 0.001 HIS N 32 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.11 (18863) covalent geometry : angle 0.51160 / 0.27 (25652) hydrogen bonds : bond 0.03271 / 2.26 ( 538) hydrogen bonds : angle 3.77958 / 2.59 ( 1572) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4388 Ramachandran restraints generated. 2194 Oldfield, 0 Emsley, 2194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4388 Ramachandran restraints generated. 2194 Oldfield, 0 Emsley, 2194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 1857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 228 time to evaluate : 0.712 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 20 LEU cc_start: 0.8365 (tp) cc_final: 0.8063 (tp) REVERT: N 81 ASN cc_start: 0.7125 (OUTLIER) cc_final: 0.6397 (p0) REVERT: N 94 GLU cc_start: 0.7435 (tt0) cc_final: 0.7146 (tt0) REVERT: N 224 MET cc_start: 0.5409 (mtp) cc_final: 0.4793 (mpp) REVERT: N 226 MET cc_start: 0.7836 (mtm) cc_final: 0.7547 (mtt) REVERT: N 282 ASN cc_start: 0.8378 (t0) cc_final: 0.8135 (t0) REVERT: N 286 TYR cc_start: 0.7472 (OUTLIER) cc_final: 0.6762 (p90) REVERT: L 206 GLN cc_start: 0.8715 (OUTLIER) cc_final: 0.8105 (tt0) REVERT: H 160 PHE cc_start: 0.7574 (m-80) cc_final: 0.6917 (t80) REVERT: H 168 LYS cc_start: 0.7487 (mmtm) cc_final: 0.7270 (mmtm) REVERT: F 73 GLN cc_start: 0.8708 (tp40) cc_final: 0.7784 (tp40) REVERT: F 76 ARG cc_start: 0.8237 (OUTLIER) cc_final: 0.7904 (ptp-170) REVERT: F 95 GLN cc_start: 0.8751 (OUTLIER) cc_final: 0.7533 (mp10) REVERT: D 59 LEU cc_start: 0.9146 (OUTLIER) cc_final: 0.8839 (tt) REVERT: C 86 ARG cc_start: 0.7592 (ttm170) cc_final: 0.7374 (mtt180) REVERT: B 83 PHE cc_start: 0.6164 (OUTLIER) cc_final: 0.5457 (t80) outliers start: 59 outliers final: 51 residues processed: 272 average time/residue: 0.1774 time to fit residues: 69.2246 Evaluate side-chains 282 residues out of total 1857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 224 time to evaluate : 0.709 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 48 MET Chi-restraints excluded: chain K residue 104 THR Chi-restraints excluded: chain K residue 110 ASP Chi-restraints excluded: chain K residue 166 GLU Chi-restraints excluded: chain K residue 167 GLN Chi-restraints excluded: chain K residue 218 VAL Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain G residue 123 VAL Chi-restraints excluded: chain G residue 196 LEU Chi-restraints excluded: chain N residue 27 THR Chi-restraints excluded: chain N residue 32 HIS Chi-restraints excluded: chain N residue 46 LEU Chi-restraints excluded: chain N residue 81 ASN Chi-restraints excluded: chain N residue 100 ILE Chi-restraints excluded: chain N residue 104 ARG Chi-restraints excluded: chain N residue 129 ASP Chi-restraints excluded: chain N residue 286 TYR Chi-restraints excluded: chain N residue 299 ILE Chi-restraints excluded: chain N residue 300 VAL Chi-restraints excluded: chain N residue 327 VAL Chi-restraints excluded: chain N residue 339 VAL Chi-restraints excluded: chain N residue 345 LEU Chi-restraints excluded: chain N residue 375 GLU Chi-restraints excluded: chain L residue 11 THR Chi-restraints excluded: chain L residue 96 THR Chi-restraints excluded: chain L residue 129 ILE Chi-restraints excluded: chain L residue 206 GLN Chi-restraints excluded: chain J residue 52 THR Chi-restraints excluded: chain J residue 104 THR Chi-restraints excluded: chain J residue 171 LEU Chi-restraints excluded: chain I residue 2 THR Chi-restraints excluded: chain I residue 31 ILE Chi-restraints excluded: chain I residue 218 VAL Chi-restraints excluded: chain I residue 226 LEU Chi-restraints excluded: chain H residue 15 THR Chi-restraints excluded: chain H residue 155 VAL Chi-restraints excluded: chain F residue 5 GLN Chi-restraints excluded: chain F residue 33 LEU Chi-restraints excluded: chain F residue 43 LEU Chi-restraints excluded: chain F residue 68 VAL Chi-restraints excluded: chain F residue 76 ARG Chi-restraints excluded: chain F residue 81 ARG Chi-restraints excluded: chain F residue 95 GLN Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain D residue 10 LYS Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 59 LEU Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain B residue 15 VAL Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 68 VAL Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 83 PHE Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain B residue 104 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 146 optimal weight: 0.9990 chunk 189 optimal weight: 0.8980 chunk 128 optimal weight: 0.9990 chunk 132 optimal weight: 1.9990 chunk 62 optimal weight: 0.0060 chunk 69 optimal weight: 3.9990 chunk 61 optimal weight: 0.9980 chunk 173 optimal weight: 2.9990 chunk 201 optimal weight: 0.9980 chunk 31 optimal weight: 0.9990 chunk 172 optimal weight: 2.9990 overall best weight: 0.7798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** I 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 32 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.128033 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.097841 restraints weight = 57323.446| |-----------------------------------------------------------------------------| r_work (start): 0.3236 rms_B_bonded: 4.33 r_work: 0.2868 rms_B_bonded: 4.57 restraints_weight: 0.5000 r_work (final): 0.2868 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2873 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2873 r_free = 0.2873 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2873 r_free = 0.2873 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2873 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8943 moved from start: 0.2369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 18863 Z= 0.116 Angle : 0.517 9.321 25652 Z= 0.277 Chirality : 0.040 0.153 2946 Planarity : 0.004 0.038 3158 Dihedral : 12.839 179.683 3223 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 3.43 % Allowed : 14.30 % Favored : 82.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.12 (0.18), residues: 2194 helix: -0.10 (0.19), residues: 828 sheet: -0.22 (0.30), residues: 313 loop : -1.40 (0.18), residues: 1053 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 102 TYR 0.015 0.001 TYR N 4 PHE 0.010 0.001 PHE N 317 TRP 0.002 0.000 TRP N 77 HIS 0.005 0.001 HIS N 32 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.12 (18863) covalent geometry : angle 0.51737 / 0.28 (25652) hydrogen bonds : bond 0.03269 / 2.26 ( 538) hydrogen bonds : angle 3.74071 / 2.56 ( 1572) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4768.69 seconds wall clock time: 82 minutes 19.05 seconds (4939.05 seconds total)