Starting phenix.real_space_refine on Sun Aug 24 08:13:44 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8x5d_38066/08_2025/8x5d_38066.cif Found real_map, /net/cci-nas-00/data/ceres_data/8x5d_38066/08_2025/8x5d_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_2025/8x5d_38066.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8x5d_38066/08_2025/8x5d_38066.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8x5d_38066/08_2025/8x5d_38066.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8x5d_38066/08_2025/8x5d_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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/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: 6.39, per 1000 atoms: 0.35 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: 1.65 Conformation dependent library (CDL) restraints added in 1.1 seconds Enol-peptide restraints added in 476.8 nanoseconds 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: 2.99 Time building geometry restraints manager: 2.15 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=" 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=" N GLU I 71 " pdb=" CA GLU I 71 " ideal model delta sigma weight residual 1.460 1.481 -0.021 1.42e-02 4.96e+03 2.27e+00 bond pdb=" N ARG L 98 " pdb=" CA ARG L 98 " ideal model delta sigma weight residual 1.458 1.483 -0.024 1.77e-02 3.19e+03 1.89e+00 ... (remaining 18858 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.82: 25147 1.82 - 3.65: 428 3.65 - 5.47: 51 5.47 - 7.30: 23 7.30 - 9.12: 3 Bond angle restraints: 25652 Sorted by residual: 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=" CA THR L 133 " pdb=" CB THR L 133 " pdb=" CG2 THR L 133 " ideal model delta sigma weight residual 110.50 117.04 -6.54 1.70e+00 3.46e-01 1.48e+01 angle pdb=" C LEU N 345 " pdb=" N ARG N 346 " pdb=" CA ARG N 346 " ideal model delta sigma weight residual 122.82 128.26 -5.44 1.42e+00 4.96e-01 1.47e+01 angle pdb=" C SER H 210 " pdb=" N ASN H 211 " pdb=" CA ASN H 211 " ideal model delta sigma weight residual 122.82 128.08 -5.26 1.42e+00 4.96e-01 1.37e+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: 2401 0.054 - 0.108: 458 0.108 - 0.163: 81 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: 8.400 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: 0.020 Extract box with map and model: 0.320 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 21.190 Find NCS groups from input model: 0.330 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.010 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8496 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= 0.168 Angle : 0.654 9.123 25652 Z= 0.379 Chirality : 0.044 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 aren 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 covalent geometry : bond 0.00356 (18863) covalent geometry : angle 0.65398 (25652) hydrogen bonds : bond 0.32657 ( 538) hydrogen bonds : angle 9.64955 ( 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 : 0.730 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: 0.1819 time to fit residues: 99.5711 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 : 0.751 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: K 78 ASN K 127 ASN K 182 ASN G 140 GLN G 206 GLN N 53 HIS N 282 ASN N 283 GLN N 338 HIS L 21 GLN L 182 ASN L 230 ASN J 78 ASN I 21 GLN H 78 ASN H 211 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: 25 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.129516 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.098723 restraints weight = 57481.757| |-----------------------------------------------------------------------------| r_work (start): 0.3251 rms_B_bonded: 4.60 r_work: 0.2880 rms_B_bonded: 4.72 restraints_weight: 0.5000 r_work (final): 0.2880 ------------------------------------------------------------------------------- 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 = 0.50 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 = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2885 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8745 moved from start: 0.1653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 18863 Z= 0.105 Angle : 0.539 7.844 25652 Z= 0.290 Chirality : 0.040 0.226 2946 Planarity : 0.005 0.047 3158 Dihedral : 13.530 179.733 3285 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 3.21 % Allowed : 11.78 % Favored : 85.00 % 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 aren not related in a simple way. whole: -3.56 (0.15), residues: 2194 helix: -3.05 (0.13), residues: 812 sheet: -1.13 (0.27), residues: 338 loop : -2.10 (0.16), residues: 1044 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 102 TYR 0.018 0.001 TYR D 8 PHE 0.012 0.001 PHE N 317 TRP 0.001 0.000 TRP N 77 HIS 0.005 0.001 HIS N 32 Details of bonding type rmsd covalent geometry : bond 0.00225 (18863) covalent geometry : angle 0.53907 (25652) hydrogen bonds : bond 0.04710 ( 538) hydrogen bonds : angle 4.70849 ( 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 314 residues out of total 1857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 255 time to evaluate : 0.731 Fit side-chains revert: symmetry clash REVERT: G 16 VAL cc_start: 0.5635 (OUTLIER) cc_final: 0.4941 (t) REVERT: G 135 LYS cc_start: 0.7035 (tmtt) cc_final: 0.6792 (pttp) REVERT: G 202 ARG cc_start: 0.7720 (ptt-90) cc_final: 0.7475 (mtm180) REVERT: N 81 ASN cc_start: 0.7184 (OUTLIER) cc_final: 0.6464 (p0) REVERT: N 94 GLU cc_start: 0.7556 (tt0) cc_final: 0.7328 (tt0) REVERT: N 224 MET cc_start: 0.5065 (mtm) cc_final: 0.4817 (mpp) REVERT: L 36 LYS cc_start: 0.8138 (mttt) cc_final: 0.7832 (mtpt) REVERT: L 149 GLU cc_start: 0.8471 (OUTLIER) cc_final: 0.8258 (mt-10) REVERT: J 28 PHE cc_start: 0.7026 (OUTLIER) cc_final: 0.6048 (m-80) REVERT: H 15 THR cc_start: 0.9185 (t) cc_final: 0.8970 (m) REVERT: H 160 PHE cc_start: 0.7640 (m-80) cc_final: 0.6875 (t80) REVERT: H 168 LYS cc_start: 0.7470 (mmtm) cc_final: 0.7234 (mmtm) REVERT: H 215 ARG cc_start: 0.7696 (ttp80) cc_final: 0.7369 (ttp80) REVERT: F 17 ARG cc_start: 0.8646 (mtt90) cc_final: 0.8411 (mtt-85) REVERT: F 73 GLN cc_start: 0.8737 (tp40) cc_final: 0.8093 (tp40) REVERT: F 76 ARG cc_start: 0.8269 (OUTLIER) cc_final: 0.8036 (ptp-170) REVERT: E 21 LYS cc_start: 0.8337 (mmtt) cc_final: 0.8073 (mmmt) REVERT: E 121 ASP cc_start: 0.8246 (t0) cc_final: 0.8026 (t0) REVERT: D 22 LYS cc_start: 0.8464 (mtpp) cc_final: 0.8070 (tppt) REVERT: D 59 LEU cc_start: 0.9166 (OUTLIER) cc_final: 0.8825 (tt) REVERT: C 85 GLU cc_start: 0.8157 (pp20) cc_final: 0.7928 (pp20) REVERT: C 86 ARG cc_start: 0.7707 (ttm170) cc_final: 0.7389 (mtt180) REVERT: C 105 LYS cc_start: 0.8938 (mmtm) cc_final: 0.8682 (mmtt) REVERT: C 118 LYS cc_start: 0.8227 (ttpp) cc_final: 0.7926 (ttpt) REVERT: B 83 PHE cc_start: 0.6306 (OUTLIER) cc_final: 0.5534 (t80) outliers start: 59 outliers final: 36 residues processed: 303 average time/residue: 0.1758 time to fit residues: 75.5024 Evaluate side-chains 273 residues out of total 1857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 230 time to evaluate : 0.824 ------------------------------------------------------------------------------- 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 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 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 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 91 THR 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 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 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 68 VAL Chi-restraints excluded: chain B residue 83 PHE Chi-restraints excluded: chain B residue 90 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 123 optimal weight: 2.9990 chunk 219 optimal weight: 10.0000 chunk 7 optimal weight: 0.9990 chunk 4 optimal weight: 0.0980 chunk 213 optimal weight: 10.0000 chunk 187 optimal weight: 4.9990 chunk 145 optimal weight: 3.9990 chunk 8 optimal weight: 1.9990 chunk 60 optimal weight: 5.9990 chunk 94 optimal weight: 3.9990 chunk 84 optimal weight: 0.9980 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 155 HIS ** 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 = 0.3652 r_free = 0.3652 target = 0.126293 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.092521 restraints weight = 58908.564| |-----------------------------------------------------------------------------| r_work (start): 0.3146 rms_B_bonded: 2.91 r_work: 0.2912 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.2912 ------------------------------------------------------------------------------- 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 = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2919 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8726 moved from start: 0.1861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 18863 Z= 0.173 Angle : 0.567 6.519 25652 Z= 0.301 Chirality : 0.042 0.238 2946 Planarity : 0.004 0.042 3158 Dihedral : 13.181 179.115 3238 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 4.02 % Allowed : 12.21 % 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 aren not related in a simple way. whole: -2.72 (0.16), residues: 2194 helix: -2.01 (0.16), residues: 829 sheet: -0.96 (0.28), residues: 339 loop : -1.82 (0.17), residues: 1026 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 17 TYR 0.020 0.002 TYR H 204 PHE 0.016 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 covalent geometry : bond 0.00410 (18863) covalent geometry : angle 0.56666 (25652) hydrogen bonds : bond 0.04526 ( 538) hydrogen bonds : angle 4.31180 ( 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 311 residues out of total 1857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 237 time to evaluate : 0.733 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 131 ARG cc_start: 0.6420 (mmt90) cc_final: 0.5823 (ttm170) REVERT: G 135 LYS cc_start: 0.7143 (tmtt) cc_final: 0.6763 (pttp) REVERT: N 81 ASN cc_start: 0.7186 (OUTLIER) cc_final: 0.6459 (p0) REVERT: N 224 MET cc_start: 0.5342 (mtm) cc_final: 0.5010 (mpp) REVERT: N 286 TYR cc_start: 0.7493 (OUTLIER) cc_final: 0.6488 (p90) REVERT: L 36 LYS cc_start: 0.8109 (mttt) cc_final: 0.7866 (mtpt) REVERT: J 28 PHE cc_start: 0.7109 (OUTLIER) cc_final: 0.6151 (m-80) REVERT: H 160 PHE cc_start: 0.7599 (m-80) cc_final: 0.6886 (t80) REVERT: H 168 LYS cc_start: 0.7566 (mmtm) cc_final: 0.7342 (mmtm) REVERT: H 215 ARG cc_start: 0.7618 (ttp80) cc_final: 0.7262 (ttp80) REVERT: F 13 GLU cc_start: 0.8584 (tm-30) cc_final: 0.8244 (tm-30) REVERT: F 17 ARG cc_start: 0.8556 (mtt90) cc_final: 0.8263 (mtt-85) REVERT: F 73 GLN cc_start: 0.8768 (tp40) cc_final: 0.7988 (tp40) REVERT: F 76 ARG cc_start: 0.8216 (OUTLIER) cc_final: 0.7933 (ptp-170) REVERT: F 95 GLN cc_start: 0.8828 (OUTLIER) cc_final: 0.7735 (mp10) REVERT: E 21 LYS cc_start: 0.8321 (mmtt) cc_final: 0.8098 (mmmt) REVERT: E 121 ASP cc_start: 0.8341 (t0) cc_final: 0.8129 (t0) REVERT: D 22 LYS cc_start: 0.8461 (mtpp) cc_final: 0.8121 (tppt) REVERT: D 59 LEU cc_start: 0.9188 (OUTLIER) cc_final: 0.8844 (tt) REVERT: C 85 GLU cc_start: 0.8045 (pp20) cc_final: 0.7819 (pp20) REVERT: C 86 ARG cc_start: 0.7730 (ttm170) cc_final: 0.7390 (mtt180) REVERT: C 118 LYS cc_start: 0.8379 (ttpp) cc_final: 0.7967 (ttpp) REVERT: B 83 PHE cc_start: 0.6244 (OUTLIER) cc_final: 0.5574 (t80) outliers start: 74 outliers final: 53 residues processed: 289 average time/residue: 0.1739 time to fit residues: 71.6755 Evaluate side-chains 289 residues out of total 1857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 229 time to evaluate : 0.564 ------------------------------------------------------------------------------- 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 G residue 16 VAL Chi-restraints excluded: chain G residue 52 THR 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 155 HIS 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 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 H residue 177 ILE Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 33 LEU Chi-restraints excluded: chain F residue 38 SER 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 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 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 83 PHE Chi-restraints excluded: chain B residue 89 LEU 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: 1.9990 chunk 185 optimal weight: 0.1980 chunk 22 optimal weight: 0.0980 chunk 10 optimal weight: 0.9990 chunk 137 optimal weight: 3.9990 chunk 146 optimal weight: 2.9990 chunk 109 optimal weight: 2.9990 chunk 194 optimal weight: 0.8980 chunk 88 optimal weight: 3.9990 chunk 172 optimal weight: 0.0980 overall best weight: 0.4582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 32 GLN C 64 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.129669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.096001 restraints weight = 66689.999| |-----------------------------------------------------------------------------| r_work (start): 0.3208 rms_B_bonded: 3.23 r_work: 0.2952 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.2952 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2957 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2957 r_free = 0.2957 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 = 0.2957 r_free = 0.2957 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2957 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8678 moved from start: 0.2140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 18863 Z= 0.093 Angle : 0.490 5.803 25652 Z= 0.262 Chirality : 0.039 0.212 2946 Planarity : 0.004 0.039 3158 Dihedral : 12.999 179.886 3235 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 3.16 % Allowed : 13.07 % 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 aren not related in a simple way. whole: -2.12 (0.17), residues: 2194 helix: -1.33 (0.17), residues: 832 sheet: -0.78 (0.28), residues: 344 loop : -1.58 (0.18), residues: 1018 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 102 TYR 0.016 0.001 TYR D 8 PHE 0.010 0.001 PHE N 317 TRP 0.001 0.000 TRP N 264 HIS 0.015 0.001 HIS N 155 Details of bonding type rmsd covalent geometry : bond 0.00205 (18863) covalent geometry : angle 0.48955 (25652) hydrogen bonds : bond 0.03181 ( 538) hydrogen bonds : angle 3.91507 ( 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 303 residues out of total 1857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 245 time to evaluate : 0.778 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 126 GLU cc_start: 0.8720 (mt-10) cc_final: 0.8505 (mt-10) REVERT: G 131 ARG cc_start: 0.6474 (mmt90) cc_final: 0.5886 (ttm170) REVERT: G 135 LYS cc_start: 0.7159 (tmtt) cc_final: 0.6914 (pttp) REVERT: N 81 ASN cc_start: 0.7164 (OUTLIER) cc_final: 0.6442 (p0) REVERT: N 286 TYR cc_start: 0.7490 (OUTLIER) cc_final: 0.6473 (p90) REVERT: J 28 PHE cc_start: 0.6973 (OUTLIER) cc_final: 0.5984 (m-80) REVERT: H 15 THR cc_start: 0.9126 (t) cc_final: 0.8899 (m) REVERT: H 160 PHE cc_start: 0.7547 (m-80) cc_final: 0.6877 (t80) REVERT: H 168 LYS cc_start: 0.7531 (mmtm) cc_final: 0.7316 (mmtm) REVERT: F 13 GLU cc_start: 0.8571 (tm-30) cc_final: 0.8214 (tm-30) REVERT: F 17 ARG cc_start: 0.8542 (mtt90) cc_final: 0.8301 (mtt-85) REVERT: F 73 GLN cc_start: 0.8719 (tp40) cc_final: 0.7914 (tp40) REVERT: F 76 ARG cc_start: 0.8178 (OUTLIER) cc_final: 0.7918 (ptp-170) REVERT: F 95 GLN cc_start: 0.8765 (OUTLIER) cc_final: 0.7573 (mp10) REVERT: E 21 LYS cc_start: 0.8360 (mmtt) cc_final: 0.8158 (mmmt) REVERT: E 121 ASP cc_start: 0.8283 (t0) cc_final: 0.8075 (t0) REVERT: D 22 LYS cc_start: 0.8480 (mtpp) cc_final: 0.8114 (tppt) REVERT: D 59 LEU cc_start: 0.9149 (OUTLIER) cc_final: 0.8801 (tt) REVERT: C 86 ARG cc_start: 0.7679 (ttm170) cc_final: 0.7450 (mtt180) REVERT: B 83 PHE cc_start: 0.6169 (OUTLIER) cc_final: 0.5543 (t80) outliers start: 58 outliers final: 39 residues processed: 289 average time/residue: 0.1779 time to fit residues: 72.7600 Evaluate side-chains 277 residues out of total 1857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 231 time to evaluate : 0.735 ------------------------------------------------------------------------------- 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 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 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 155 HIS 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 L residue 11 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 155 VAL 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 D residue 59 LEU Chi-restraints excluded: chain C residue 35 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 89 LEU 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: 1.9990 chunk 11 optimal weight: 3.9990 chunk 216 optimal weight: 5.9990 chunk 39 optimal weight: 10.0000 chunk 82 optimal weight: 3.9990 chunk 36 optimal weight: 8.9990 chunk 181 optimal weight: 3.9990 chunk 185 optimal weight: 4.9990 chunk 73 optimal weight: 3.9990 chunk 69 optimal weight: 4.9990 chunk 175 optimal weight: 0.5980 overall best weight: 2.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 155 HIS C 32 GLN B 53 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.123726 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.089318 restraints weight = 57223.104| |-----------------------------------------------------------------------------| r_work (start): 0.3094 rms_B_bonded: 2.94 r_work: 0.2863 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.2863 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2870 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2870 r_free = 0.2870 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2870 r_free = 0.2870 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2870 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8778 moved from start: 0.2164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.071 18863 Z= 0.321 Angle : 0.690 7.594 25652 Z= 0.360 Chirality : 0.048 0.275 2946 Planarity : 0.005 0.047 3158 Dihedral : 13.132 178.657 3225 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.71 % Favored : 94.29 % Rotamer: Outliers : 4.39 % Allowed : 12.64 % Favored : 82.97 % 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 aren not related in a simple way. whole: -2.12 (0.17), residues: 2194 helix: -1.23 (0.17), residues: 823 sheet: -0.78 (0.28), residues: 344 loop : -1.69 (0.18), residues: 1027 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 102 TYR 0.029 0.003 TYR H 204 PHE 0.024 0.002 PHE N 317 TRP 0.005 0.001 TRP N 77 HIS 0.006 0.001 HIS L 81 Details of bonding type rmsd covalent geometry : bond 0.00770 (18863) covalent geometry : angle 0.69048 (25652) hydrogen bonds : bond 0.05276 ( 538) hydrogen bonds : angle 4.37933 ( 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 309 residues out of total 1857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 228 time to evaluate : 0.613 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 131 ARG cc_start: 0.6417 (OUTLIER) cc_final: 0.5782 (ttm170) REVERT: G 135 LYS cc_start: 0.7281 (tmtt) cc_final: 0.6922 (pttp) REVERT: G 137 ASN cc_start: 0.7587 (OUTLIER) cc_final: 0.7354 (p0) REVERT: N 4 TYR cc_start: 0.8576 (OUTLIER) cc_final: 0.8176 (p90) REVERT: N 81 ASN cc_start: 0.7183 (OUTLIER) cc_final: 0.6431 (p0) REVERT: N 286 TYR cc_start: 0.7575 (OUTLIER) cc_final: 0.6423 (p90) REVERT: L 206 GLN cc_start: 0.8829 (OUTLIER) cc_final: 0.8270 (tt0) REVERT: H 160 PHE cc_start: 0.7612 (m-80) cc_final: 0.6914 (t80) REVERT: F 13 GLU cc_start: 0.8699 (tm-30) cc_final: 0.7855 (tm-30) REVERT: F 17 ARG cc_start: 0.8525 (mtt90) cc_final: 0.8248 (ttm-80) REVERT: F 73 GLN cc_start: 0.8853 (tp40) cc_final: 0.7905 (tp40) REVERT: F 95 GLN cc_start: 0.8790 (OUTLIER) cc_final: 0.7679 (mp10) REVERT: E 21 LYS cc_start: 0.8333 (mmtt) cc_final: 0.8095 (mmmt) REVERT: E 121 ASP cc_start: 0.8622 (t0) cc_final: 0.8370 (t0) REVERT: D 59 LEU cc_start: 0.9174 (OUTLIER) cc_final: 0.8817 (tt) REVERT: C 86 ARG cc_start: 0.7777 (ttm170) cc_final: 0.7497 (ttm110) REVERT: B 83 PHE cc_start: 0.6425 (OUTLIER) cc_final: 0.5647 (t80) outliers start: 81 outliers final: 55 residues processed: 288 average time/residue: 0.1721 time to fit residues: 71.0007 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 : 0.668 ------------------------------------------------------------------------------- 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 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 81 ASN 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 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 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 54 LEU 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 39 VAL Chi-restraints excluded: chain H residue 155 VAL Chi-restraints excluded: chain H residue 177 ILE Chi-restraints excluded: chain H residue 233 LEU 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 38 SER Chi-restraints excluded: chain F residue 43 LEU Chi-restraints excluded: chain F residue 68 VAL 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 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 89 LEU 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: 0.9990 chunk 82 optimal weight: 0.7980 chunk 121 optimal weight: 2.9990 chunk 105 optimal weight: 0.9980 chunk 48 optimal weight: 0.0170 chunk 165 optimal weight: 0.0770 chunk 164 optimal weight: 0.9980 chunk 140 optimal weight: 3.9990 chunk 184 optimal weight: 2.9990 chunk 142 optimal weight: 1.9990 chunk 152 optimal weight: 0.9990 overall best weight: 0.5776 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3675 r_free = 0.3675 target = 0.128042 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.098130 restraints weight = 57734.270| |-----------------------------------------------------------------------------| r_work (start): 0.3240 rms_B_bonded: 4.42 r_work: 0.2866 rms_B_bonded: 4.64 restraints_weight: 0.5000 r_work (final): 0.2866 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2875 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2875 r_free = 0.2875 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2875 r_free = 0.2875 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2875 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8751 moved from start: 0.2284 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= 0.104 Angle : 0.506 8.847 25652 Z= 0.270 Chirality : 0.040 0.226 2946 Planarity : 0.004 0.053 3158 Dihedral : 12.874 179.872 3217 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 3.21 % Allowed : 13.93 % Favored : 82.86 % 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 aren not related in a simple way. whole: -1.64 (0.17), residues: 2194 helix: -0.73 (0.18), residues: 814 sheet: -0.66 (0.29), residues: 339 loop : -1.45 (0.18), residues: 1041 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 102 TYR 0.015 0.001 TYR D 8 PHE 0.010 0.001 PHE J 101 TRP 0.002 0.000 TRP N 264 HIS 0.005 0.001 HIS N 32 Details of bonding type rmsd covalent geometry : bond 0.00235 (18863) covalent geometry : angle 0.50627 (25652) hydrogen bonds : bond 0.03182 ( 538) hydrogen bonds : angle 3.88155 ( 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 292 residues out of total 1857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 233 time to evaluate : 0.678 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 131 ARG cc_start: 0.6572 (mmt90) cc_final: 0.6089 (ttm170) REVERT: G 135 LYS cc_start: 0.7086 (tmtt) cc_final: 0.6619 (pttp) REVERT: N 81 ASN cc_start: 0.7141 (OUTLIER) cc_final: 0.6414 (p0) REVERT: N 226 MET cc_start: 0.7649 (mtm) cc_final: 0.7349 (mtt) REVERT: N 286 TYR cc_start: 0.7456 (OUTLIER) cc_final: 0.6503 (p90) REVERT: L 206 GLN cc_start: 0.8791 (OUTLIER) cc_final: 0.8189 (tt0) REVERT: H 160 PHE cc_start: 0.7600 (m-80) cc_final: 0.6907 (t80) REVERT: F 21 LYS cc_start: 0.7904 (OUTLIER) cc_final: 0.7649 (mmtp) REVERT: F 73 GLN cc_start: 0.8755 (tp40) cc_final: 0.7869 (tp40) REVERT: F 95 GLN cc_start: 0.8800 (OUTLIER) cc_final: 0.7649 (mp10) REVERT: E 121 ASP cc_start: 0.8473 (t0) cc_final: 0.8235 (t0) REVERT: D 59 LEU cc_start: 0.9176 (OUTLIER) cc_final: 0.8841 (tt) REVERT: C 86 ARG cc_start: 0.7733 (ttm170) cc_final: 0.7484 (mtt180) outliers start: 59 outliers final: 51 residues processed: 276 average time/residue: 0.1779 time to fit residues: 70.4268 Evaluate side-chains 282 residues out of total 1857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 225 time to evaluate : 0.689 ------------------------------------------------------------------------------- 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 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 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 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 155 VAL Chi-restraints excluded: chain H residue 233 LEU Chi-restraints excluded: chain F residue 5 GLN Chi-restraints excluded: chain F residue 21 LYS 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 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 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 89 LEU 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: 2.9990 chunk 37 optimal weight: 7.9990 chunk 155 optimal weight: 3.9990 chunk 2 optimal weight: 3.9990 chunk 82 optimal weight: 2.9990 chunk 148 optimal weight: 2.9990 chunk 26 optimal weight: 8.9990 chunk 139 optimal weight: 3.9990 chunk 215 optimal weight: 0.9980 chunk 64 optimal weight: 5.9990 chunk 193 optimal weight: 0.7980 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 283 GLN C 32 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.124784 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.089688 restraints weight = 58310.967| |-----------------------------------------------------------------------------| r_work (start): 0.3102 rms_B_bonded: 2.98 r_work: 0.2873 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.2873 ------------------------------------------------------------------------------- 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 = 0.35 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 = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2885 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8764 moved from start: 0.2287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 18863 Z= 0.241 Angle : 0.623 8.903 25652 Z= 0.326 Chirality : 0.045 0.259 2946 Planarity : 0.004 0.044 3158 Dihedral : 12.949 178.904 3215 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 3.37 % Allowed : 14.35 % 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 aren not related in a simple way. whole: -1.68 (0.17), residues: 2194 helix: -0.71 (0.18), residues: 819 sheet: -0.66 (0.28), residues: 344 loop : -1.55 (0.18), residues: 1031 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 102 TYR 0.023 0.002 TYR H 204 PHE 0.020 0.002 PHE N 317 TRP 0.004 0.001 TRP N 77 HIS 0.005 0.001 HIS N 32 Details of bonding type rmsd covalent geometry : bond 0.00578 (18863) covalent geometry : angle 0.62298 (25652) hydrogen bonds : bond 0.04537 ( 538) hydrogen bonds : angle 4.12086 ( 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 289 residues out of total 1857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 227 time to evaluate : 0.796 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 131 ARG cc_start: 0.6466 (OUTLIER) cc_final: 0.5990 (ttm170) REVERT: G 135 LYS cc_start: 0.7186 (tmtt) cc_final: 0.6779 (pttp) REVERT: G 137 ASN cc_start: 0.7486 (OUTLIER) cc_final: 0.7245 (p0) REVERT: N 4 TYR cc_start: 0.8528 (OUTLIER) cc_final: 0.8164 (p90) REVERT: N 81 ASN cc_start: 0.7211 (OUTLIER) cc_final: 0.6468 (p0) REVERT: N 286 TYR cc_start: 0.7439 (OUTLIER) cc_final: 0.6560 (p90) REVERT: L 206 GLN cc_start: 0.8816 (OUTLIER) cc_final: 0.8258 (tt0) REVERT: H 160 PHE cc_start: 0.7615 (m-80) cc_final: 0.6890 (t80) REVERT: F 21 LYS cc_start: 0.8036 (OUTLIER) cc_final: 0.7675 (tppt) REVERT: F 73 GLN cc_start: 0.8805 (tp40) cc_final: 0.7789 (tp40) REVERT: F 95 GLN cc_start: 0.8811 (OUTLIER) cc_final: 0.7646 (mp10) REVERT: E 121 ASP cc_start: 0.8592 (t0) cc_final: 0.8345 (t0) REVERT: D 59 LEU cc_start: 0.9193 (OUTLIER) cc_final: 0.8844 (tt) REVERT: C 86 ARG cc_start: 0.7768 (ttm170) cc_final: 0.7490 (mtt180) outliers start: 62 outliers final: 49 residues processed: 271 average time/residue: 0.1910 time to fit residues: 73.3988 Evaluate side-chains 280 residues out of total 1857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 222 time to evaluate : 0.715 ------------------------------------------------------------------------------- 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 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 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 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 H residue 233 LEU Chi-restraints excluded: chain F residue 5 GLN Chi-restraints excluded: chain F residue 21 LYS Chi-restraints excluded: chain F residue 33 LEU Chi-restraints excluded: chain F residue 38 SER Chi-restraints excluded: chain F residue 43 LEU Chi-restraints excluded: chain F residue 68 VAL 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 15 VAL Chi-restraints excluded: chain B residue 68 VAL Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 89 LEU 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: 0.9980 chunk 183 optimal weight: 3.9990 chunk 121 optimal weight: 1.9990 chunk 91 optimal weight: 3.9990 chunk 105 optimal weight: 2.9990 chunk 102 optimal weight: 0.9980 chunk 125 optimal weight: 1.9990 chunk 18 optimal weight: 0.8980 chunk 57 optimal weight: 0.4980 chunk 62 optimal weight: 3.9990 chunk 75 optimal weight: 0.8980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 283 GLN ** 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 = 0.3669 r_free = 0.3669 target = 0.127687 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.092821 restraints weight = 59357.594| |-----------------------------------------------------------------------------| r_work (start): 0.3158 rms_B_bonded: 2.84 r_work: 0.2946 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.2946 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2949 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2949 r_free = 0.2949 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2949 r_free = 0.2949 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2949 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8699 moved from start: 0.2366 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= 0.121 Angle : 0.526 8.899 25652 Z= 0.279 Chirality : 0.041 0.236 2946 Planarity : 0.004 0.041 3158 Dihedral : 12.837 179.816 3215 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 3.37 % Allowed : 14.89 % Favored : 81.74 % 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 aren not related in a simple way. whole: -1.40 (0.17), residues: 2194 helix: -0.40 (0.19), residues: 813 sheet: -0.56 (0.28), residues: 339 loop : -1.42 (0.18), residues: 1042 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 102 TYR 0.015 0.001 TYR D 8 PHE 0.012 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 covalent geometry : bond 0.00283 (18863) covalent geometry : angle 0.52558 (25652) hydrogen bonds : bond 0.03380 ( 538) hydrogen bonds : angle 3.82834 ( 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 283 residues out of total 1857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 221 time to evaluate : 0.786 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 135 LYS cc_start: 0.7098 (tmtt) cc_final: 0.6892 (pttp) REVERT: N 81 ASN cc_start: 0.7172 (OUTLIER) cc_final: 0.6434 (p0) REVERT: N 104 ARG cc_start: 0.5020 (OUTLIER) cc_final: 0.4511 (mtm180) REVERT: N 226 MET cc_start: 0.7753 (mtm) cc_final: 0.7438 (mtt) REVERT: N 286 TYR cc_start: 0.7440 (OUTLIER) cc_final: 0.6622 (p90) REVERT: L 206 GLN cc_start: 0.8716 (OUTLIER) cc_final: 0.8116 (tt0) REVERT: H 160 PHE cc_start: 0.7590 (m-80) cc_final: 0.6943 (t80) REVERT: F 21 LYS cc_start: 0.7977 (OUTLIER) cc_final: 0.7682 (mmtp) REVERT: F 73 GLN cc_start: 0.8725 (tp40) cc_final: 0.7746 (tp40) REVERT: F 95 GLN cc_start: 0.8738 (OUTLIER) cc_final: 0.7529 (mp10) REVERT: E 121 ASP cc_start: 0.8467 (t0) cc_final: 0.8217 (t0) REVERT: D 59 LEU cc_start: 0.9148 (OUTLIER) cc_final: 0.8851 (tt) REVERT: C 14 GLN cc_start: 0.7359 (pp30) cc_final: 0.7151 (pt0) REVERT: C 86 ARG cc_start: 0.7709 (ttm170) cc_final: 0.7455 (mtt180) outliers start: 62 outliers final: 50 residues processed: 263 average time/residue: 0.1877 time to fit residues: 70.5567 Evaluate side-chains 276 residues out of total 1857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 219 time to evaluate : 0.784 ------------------------------------------------------------------------------- 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 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 137 ASN 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 L residue 11 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 75 ARG 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 233 LEU Chi-restraints excluded: chain F residue 5 GLN Chi-restraints excluded: chain F residue 21 LYS 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 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 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 89 LEU Chi-restraints excluded: chain B residue 90 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: 6.9990 chunk 66 optimal weight: 9.9990 chunk 158 optimal weight: 4.9990 chunk 99 optimal weight: 0.4980 chunk 154 optimal weight: 3.9990 chunk 178 optimal weight: 0.2980 chunk 4 optimal weight: 0.8980 chunk 216 optimal weight: 0.7980 chunk 15 optimal weight: 1.9990 chunk 21 optimal weight: 5.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3670 r_free = 0.3670 target = 0.127759 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.093695 restraints weight = 63980.385| |-----------------------------------------------------------------------------| r_work (start): 0.3165 rms_B_bonded: 3.17 r_work: 0.2925 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.2925 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2932 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2932 r_free = 0.2932 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2932 r_free = 0.2932 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2932 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8712 moved from start: 0.2421 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= 0.126 Angle : 0.527 9.270 25652 Z= 0.279 Chirality : 0.041 0.228 2946 Planarity : 0.004 0.038 3158 Dihedral : 12.755 179.528 3213 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 3.05 % Allowed : 15.10 % Favored : 81.84 % 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 aren not related in a simple way. whole: -1.22 (0.18), residues: 2194 helix: -0.20 (0.19), residues: 811 sheet: -0.33 (0.30), residues: 314 loop : -1.40 (0.18), residues: 1069 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 102 TYR 0.016 0.001 TYR D 8 PHE 0.012 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 covalent geometry : bond 0.00296 (18863) covalent geometry : angle 0.52722 (25652) hydrogen bonds : bond 0.03366 ( 538) hydrogen bonds : angle 3.75298 ( 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 282 residues out of total 1857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 226 time to evaluate : 0.822 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 135 LYS cc_start: 0.7083 (tmtt) cc_final: 0.6847 (pttp) REVERT: N 81 ASN cc_start: 0.7252 (OUTLIER) cc_final: 0.6541 (p0) REVERT: N 104 ARG cc_start: 0.4968 (OUTLIER) cc_final: 0.4456 (mtm180) REVERT: N 226 MET cc_start: 0.7650 (mtm) cc_final: 0.7334 (mtt) REVERT: N 286 TYR cc_start: 0.7427 (OUTLIER) cc_final: 0.6516 (p90) REVERT: H 160 PHE cc_start: 0.7613 (m-80) cc_final: 0.6936 (t80) REVERT: F 21 LYS cc_start: 0.7955 (OUTLIER) cc_final: 0.7654 (mmtp) REVERT: F 73 GLN cc_start: 0.8742 (tp40) cc_final: 0.7701 (tp40) REVERT: F 95 GLN cc_start: 0.8772 (OUTLIER) cc_final: 0.7639 (mp-120) REVERT: E 121 ASP cc_start: 0.8418 (t0) cc_final: 0.8186 (t0) REVERT: D 59 LEU cc_start: 0.9171 (OUTLIER) cc_final: 0.8889 (tt) REVERT: C 14 GLN cc_start: 0.7396 (pp30) cc_final: 0.7151 (pt0) REVERT: C 86 ARG cc_start: 0.7657 (ttm170) cc_final: 0.7396 (mtt180) REVERT: B 72 TYR cc_start: 0.7714 (t80) cc_final: 0.7478 (t80) outliers start: 56 outliers final: 49 residues processed: 265 average time/residue: 0.1776 time to fit residues: 67.4475 Evaluate side-chains 275 residues out of total 1857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 220 time to evaluate : 0.438 ------------------------------------------------------------------------------- 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 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 L residue 11 THR Chi-restraints excluded: chain L residue 31 ILE Chi-restraints excluded: chain L residue 129 ILE 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 233 LEU Chi-restraints excluded: chain F residue 5 GLN Chi-restraints excluded: chain F residue 21 LYS Chi-restraints excluded: chain F residue 33 LEU Chi-restraints excluded: chain F residue 38 SER Chi-restraints excluded: chain F residue 43 LEU Chi-restraints excluded: chain F residue 68 VAL 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 15 VAL Chi-restraints excluded: chain B residue 68 VAL Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 90 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 55 optimal weight: 1.9990 chunk 150 optimal weight: 0.8980 chunk 105 optimal weight: 2.9990 chunk 54 optimal weight: 6.9990 chunk 178 optimal weight: 3.9990 chunk 91 optimal weight: 3.9990 chunk 80 optimal weight: 0.9980 chunk 163 optimal weight: 0.9980 chunk 123 optimal weight: 1.9990 chunk 192 optimal weight: 0.2980 chunk 120 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.128284 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.097569 restraints weight = 58662.207| |-----------------------------------------------------------------------------| r_work (start): 0.3229 rms_B_bonded: 4.51 r_work: 0.2867 rms_B_bonded: 4.57 restraints_weight: 0.5000 r_work (final): 0.2867 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2876 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2876 r_free = 0.2876 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2876 r_free = 0.2876 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2876 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8750 moved from start: 0.2482 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= 0.117 Angle : 0.520 9.361 25652 Z= 0.275 Chirality : 0.040 0.225 2946 Planarity : 0.004 0.039 3158 Dihedral : 12.732 179.739 3213 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 3.21 % Allowed : 15.00 % Favored : 81.79 % 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 aren not related in a simple way. whole: -1.10 (0.18), residues: 2194 helix: -0.06 (0.19), residues: 814 sheet: -0.29 (0.30), residues: 314 loop : -1.36 (0.18), residues: 1066 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 102 TYR 0.016 0.001 TYR D 8 PHE 0.012 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 covalent geometry : bond 0.00275 (18863) covalent geometry : angle 0.52026 (25652) hydrogen bonds : bond 0.03221 ( 538) hydrogen bonds : angle 3.70159 ( 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 : 0.741 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 135 LYS cc_start: 0.7037 (tmtt) cc_final: 0.6763 (pttp) REVERT: N 81 ASN cc_start: 0.7150 (OUTLIER) cc_final: 0.6419 (p0) REVERT: N 104 ARG cc_start: 0.4889 (OUTLIER) cc_final: 0.4331 (mtm180) REVERT: N 226 MET cc_start: 0.7641 (mtm) cc_final: 0.7334 (mtt) REVERT: N 286 TYR cc_start: 0.7444 (OUTLIER) cc_final: 0.6524 (p90) REVERT: H 160 PHE cc_start: 0.7637 (m-80) cc_final: 0.6931 (t80) REVERT: F 21 LYS cc_start: 0.7999 (OUTLIER) cc_final: 0.7680 (mmtp) REVERT: F 73 GLN cc_start: 0.8769 (tp40) cc_final: 0.7764 (tp40) REVERT: F 91 ASP cc_start: 0.8257 (m-30) cc_final: 0.7659 (m-30) REVERT: F 95 GLN cc_start: 0.8774 (OUTLIER) cc_final: 0.7648 (mp-120) REVERT: E 121 ASP cc_start: 0.8426 (t0) cc_final: 0.8188 (t0) REVERT: D 59 LEU cc_start: 0.9188 (OUTLIER) cc_final: 0.8882 (tt) REVERT: C 14 GLN cc_start: 0.7426 (pp30) cc_final: 0.7224 (pt0) REVERT: C 86 ARG cc_start: 0.7700 (ttm170) cc_final: 0.7451 (mtt180) outliers start: 59 outliers final: 52 residues processed: 268 average time/residue: 0.1530 time to fit residues: 59.0214 Evaluate side-chains 280 residues out of total 1857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 222 time to evaluate : 0.614 ------------------------------------------------------------------------------- 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 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 123 VAL Chi-restraints excluded: chain G residue 137 ASN 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 L residue 11 THR Chi-restraints excluded: chain L residue 31 ILE Chi-restraints excluded: chain L residue 129 ILE Chi-restraints excluded: chain L residue 210 SER Chi-restraints excluded: chain J residue 52 THR Chi-restraints excluded: chain J residue 75 ARG 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 233 LEU Chi-restraints excluded: chain F residue 5 GLN Chi-restraints excluded: chain F residue 21 LYS Chi-restraints excluded: chain F residue 33 LEU Chi-restraints excluded: chain F residue 38 SER Chi-restraints excluded: chain F residue 43 LEU Chi-restraints excluded: chain F residue 68 VAL 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 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 89 LEU Chi-restraints excluded: chain B residue 90 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 146 optimal weight: 2.9990 chunk 189 optimal weight: 1.9990 chunk 128 optimal weight: 0.8980 chunk 132 optimal weight: 1.9990 chunk 62 optimal weight: 4.9990 chunk 69 optimal weight: 3.9990 chunk 61 optimal weight: 0.9990 chunk 173 optimal weight: 2.9990 chunk 201 optimal weight: 6.9990 chunk 31 optimal weight: 0.8980 chunk 172 optimal weight: 2.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.126625 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.095791 restraints weight = 57490.759| |-----------------------------------------------------------------------------| r_work (start): 0.3199 rms_B_bonded: 4.60 r_work: 0.2825 rms_B_bonded: 4.63 restraints_weight: 0.5000 r_work (final): 0.2825 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2834 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2834 r_free = 0.2834 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2834 r_free = 0.2834 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2834 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8790 moved from start: 0.2461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 18863 Z= 0.166 Angle : 0.565 9.464 25652 Z= 0.297 Chirality : 0.042 0.240 2946 Planarity : 0.004 0.038 3158 Dihedral : 12.770 179.329 3213 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 3.37 % Allowed : 14.89 % Favored : 81.74 % 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 aren not related in a simple way. whole: -1.13 (0.18), residues: 2194 helix: -0.08 (0.19), residues: 810 sheet: -0.42 (0.28), residues: 344 loop : -1.36 (0.18), residues: 1040 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 102 TYR 0.018 0.002 TYR D 8 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 covalent geometry : bond 0.00396 (18863) covalent geometry : angle 0.56495 (25652) hydrogen bonds : bond 0.03815 ( 538) hydrogen bonds : angle 3.83525 ( 1572) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4904.78 seconds wall clock time: 84 minutes 44.91 seconds (5084.91 seconds total)