Starting phenix.real_space_refine on Thu Feb 13 21:57:58 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8gqy_34203/02_2025/8gqy_34203.cif Found real_map, /net/cci-nas-00/data/ceres_data/8gqy_34203/02_2025/8gqy_34203.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8gqy_34203/02_2025/8gqy_34203.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8gqy_34203/02_2025/8gqy_34203.map" model { file = "/net/cci-nas-00/data/ceres_data/8gqy_34203/02_2025/8gqy_34203.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8gqy_34203/02_2025/8gqy_34203.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 60 5.16 5 C 6230 2.51 5 N 1505 2.21 5 O 1720 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 9515 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 1903 Number of conformers: 1 Conformer: "" Number of residues, atoms: 253, 1903 Classifications: {'peptide': 253} Link IDs: {'PTRANS': 11, 'TRANS': 241} Chain: "B" Number of atoms: 1903 Number of conformers: 1 Conformer: "" Number of residues, atoms: 253, 1903 Classifications: {'peptide': 253} Link IDs: {'PTRANS': 11, 'TRANS': 241} Chain: "C" Number of atoms: 1903 Number of conformers: 1 Conformer: "" Number of residues, atoms: 253, 1903 Classifications: {'peptide': 253} Link IDs: {'PTRANS': 11, 'TRANS': 241} Chain: "D" Number of atoms: 1903 Number of conformers: 1 Conformer: "" Number of residues, atoms: 253, 1903 Classifications: {'peptide': 253} Link IDs: {'PTRANS': 11, 'TRANS': 241} Chain: "E" Number of atoms: 1903 Number of conformers: 1 Conformer: "" Number of residues, atoms: 253, 1903 Classifications: {'peptide': 253} Link IDs: {'PTRANS': 11, 'TRANS': 241} Time building chain proxies: 6.33, per 1000 atoms: 0.67 Number of scatterers: 9515 At special positions: 0 Unit cell: (88.2, 88.2, 101.7, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 60 16.00 O 1720 8.00 N 1505 7.00 C 6230 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: 2.51 Conformation dependent library (CDL) restraints added in 1.2 seconds 2510 Ramachandran restraints generated. 1255 Oldfield, 0 Emsley, 1255 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2310 Finding SS restraints... Secondary structure from input PDB file: 89 helices and 0 sheets defined 82.1% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.91 Creating SS restraints... Processing helix chain 'A' and resid 5 through 14 removed outlier: 3.768A pdb=" N ALA A 12 " --> pdb=" O GLY A 8 " (cutoff:3.500A) Processing helix chain 'A' and resid 17 through 22 Processing helix chain 'A' and resid 31 through 35 Processing helix chain 'A' and resid 38 through 45 Processing helix chain 'A' and resid 51 through 60 Processing helix chain 'A' and resid 61 through 65 Processing helix chain 'A' and resid 72 through 77 Processing helix chain 'A' and resid 77 through 90 Processing helix chain 'A' and resid 98 through 104 Processing helix chain 'A' and resid 106 through 119 removed outlier: 3.891A pdb=" N ASP A 111 " --> pdb=" O PRO A 107 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLY A 119 " --> pdb=" O MET A 115 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 125 Processing helix chain 'A' and resid 128 through 134 Processing helix chain 'A' and resid 140 through 148 removed outlier: 3.786A pdb=" N VAL A 146 " --> pdb=" O THR A 142 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N TRP A 147 " --> pdb=" O GLU A 143 " (cutoff:3.500A) Processing helix chain 'A' and resid 149 through 154 Processing helix chain 'A' and resid 157 through 173 removed outlier: 3.739A pdb=" N LEU A 163 " --> pdb=" O MET A 159 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N GLN A 168 " --> pdb=" O ILE A 164 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N MET A 169 " --> pdb=" O GLY A 165 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ASN A 172 " --> pdb=" O GLN A 168 " (cutoff:3.500A) Processing helix chain 'A' and resid 175 through 178 Processing helix chain 'A' and resid 179 through 200 removed outlier: 3.563A pdb=" N ALA A 186 " --> pdb=" O GLY A 182 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N THR A 189 " --> pdb=" O VAL A 185 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N THR A 190 " --> pdb=" O ALA A 186 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N GLY A 193 " --> pdb=" O THR A 189 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ALA A 197 " --> pdb=" O GLY A 193 " (cutoff:3.500A) Processing helix chain 'A' and resid 200 through 211 removed outlier: 4.204A pdb=" N LYS A 209 " --> pdb=" O ALA A 205 " (cutoff:3.500A) Processing helix chain 'A' and resid 211 through 231 removed outlier: 3.550A pdb=" N LEU A 217 " --> pdb=" O ASP A 213 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ILE A 223 " --> pdb=" O LYS A 219 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N GLU A 224 " --> pdb=" O THR A 220 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N LYS A 231 " --> pdb=" O GLU A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 234 through 247 removed outlier: 3.775A pdb=" N LYS A 239 " --> pdb=" O PRO A 235 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLN A 240 " --> pdb=" O ASN A 236 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ILE A 244 " --> pdb=" O GLN A 240 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N MET A 245 " --> pdb=" O GLU A 241 " (cutoff:3.500A) Processing helix chain 'B' and resid 9 through 24 removed outlier: 4.032A pdb=" N LEU B 15 " --> pdb=" O ALA B 11 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N ILE B 16 " --> pdb=" O ALA B 12 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N LEU B 17 " --> pdb=" O PHE B 13 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N SER B 19 " --> pdb=" O LEU B 15 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N ILE B 20 " --> pdb=" O ILE B 16 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N GLY B 23 " --> pdb=" O SER B 19 " (cutoff:3.500A) Processing helix chain 'B' and resid 25 through 29 removed outlier: 3.807A pdb=" N ALA B 28 " --> pdb=" O SER B 25 " (cutoff:3.500A) Processing helix chain 'B' and resid 31 through 33 No H-bonds generated for 'chain 'B' and resid 31 through 33' Processing helix chain 'B' and resid 34 through 39 removed outlier: 3.991A pdb=" N VAL B 38 " --> pdb=" O SER B 34 " (cutoff:3.500A) Processing helix chain 'B' and resid 51 through 60 removed outlier: 3.591A pdb=" N ILE B 56 " --> pdb=" O LEU B 52 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLY B 58 " --> pdb=" O ASP B 54 " (cutoff:3.500A) Processing helix chain 'B' and resid 72 through 91 removed outlier: 3.597A pdb=" N ILE B 77 " --> pdb=" O LEU B 73 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N GLU B 78 " --> pdb=" O ASN B 74 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ILE B 80 " --> pdb=" O VAL B 76 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLU B 82 " --> pdb=" O GLU B 78 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N SER B 85 " --> pdb=" O GLY B 81 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LYS B 86 " --> pdb=" O GLU B 82 " (cutoff:3.500A) Processing helix chain 'B' and resid 92 through 97 removed outlier: 3.581A pdb=" N LEU B 95 " --> pdb=" O ILE B 92 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N GLU B 96 " --> pdb=" O LEU B 93 " (cutoff:3.500A) removed outlier: 4.968A pdb=" N GLY B 97 " --> pdb=" O ALA B 94 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 92 through 97' Processing helix chain 'B' and resid 98 through 106 removed outlier: 3.700A pdb=" N GLN B 104 " --> pdb=" O GLU B 100 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LYS B 105 " --> pdb=" O LEU B 101 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N ASP B 106 " --> pdb=" O TYR B 102 " (cutoff:3.500A) Processing helix chain 'B' and resid 106 through 119 removed outlier: 3.892A pdb=" N ASP B 111 " --> pdb=" O PRO B 107 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLY B 119 " --> pdb=" O MET B 115 " (cutoff:3.500A) Processing helix chain 'B' and resid 121 through 130 removed outlier: 4.452A pdb=" N ALA B 127 " --> pdb=" O ASN B 123 " (cutoff:3.500A) Processing helix chain 'B' and resid 130 through 148 removed outlier: 3.991A pdb=" N GLU B 138 " --> pdb=" O ALA B 134 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N LYS B 139 " --> pdb=" O GLN B 135 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N MET B 140 " --> pdb=" O LEU B 136 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N GLU B 143 " --> pdb=" O LYS B 139 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N TRP B 147 " --> pdb=" O GLU B 143 " (cutoff:3.500A) Processing helix chain 'B' and resid 149 through 154 Processing helix chain 'B' and resid 157 through 172 removed outlier: 3.600A pdb=" N GLN B 168 " --> pdb=" O ILE B 164 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N MET B 169 " --> pdb=" O GLY B 165 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N ASN B 172 " --> pdb=" O GLN B 168 " (cutoff:3.500A) Processing helix chain 'B' and resid 175 through 178 Processing helix chain 'B' and resid 179 through 200 removed outlier: 3.542A pdb=" N VAL B 185 " --> pdb=" O PRO B 181 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N THR B 189 " --> pdb=" O VAL B 185 " (cutoff:3.500A) removed outlier: 4.740A pdb=" N THR B 190 " --> pdb=" O ALA B 186 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N GLY B 193 " --> pdb=" O THR B 189 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N LEU B 196 " --> pdb=" O TYR B 192 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ASN B 198 " --> pdb=" O ALA B 194 " (cutoff:3.500A) Processing helix chain 'B' and resid 200 through 211 removed outlier: 3.726A pdb=" N VAL B 204 " --> pdb=" O PHE B 200 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N LYS B 209 " --> pdb=" O ALA B 205 " (cutoff:3.500A) Processing helix chain 'B' and resid 211 through 231 removed outlier: 3.524A pdb=" N GLU B 227 " --> pdb=" O ILE B 223 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N LYS B 228 " --> pdb=" O GLU B 224 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LYS B 231 " --> pdb=" O GLU B 227 " (cutoff:3.500A) Processing helix chain 'B' and resid 234 through 239 removed outlier: 3.558A pdb=" N LYS B 239 " --> pdb=" O PRO B 235 " (cutoff:3.500A) Processing helix chain 'B' and resid 239 through 247 removed outlier: 3.758A pdb=" N ILE B 244 " --> pdb=" O GLN B 240 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N MET B 245 " --> pdb=" O GLU B 241 " (cutoff:3.500A) Processing helix chain 'C' and resid 17 through 24 removed outlier: 4.125A pdb=" N GLY C 23 " --> pdb=" O SER C 19 " (cutoff:3.500A) Processing helix chain 'C' and resid 31 through 33 No H-bonds generated for 'chain 'C' and resid 31 through 33' Processing helix chain 'C' and resid 34 through 45 removed outlier: 3.623A pdb=" N VAL C 38 " --> pdb=" O SER C 34 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N MET C 43 " --> pdb=" O VAL C 39 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ALA C 44 " --> pdb=" O GLY C 40 " (cutoff:3.500A) Processing helix chain 'C' and resid 51 through 60 removed outlier: 3.516A pdb=" N ILE C 56 " --> pdb=" O LEU C 52 " (cutoff:3.500A) Processing helix chain 'C' and resid 61 through 67 removed outlier: 3.635A pdb=" N LEU C 67 " --> pdb=" O LYS C 63 " (cutoff:3.500A) Processing helix chain 'C' and resid 72 through 77 removed outlier: 3.604A pdb=" N ILE C 77 " --> pdb=" O LEU C 73 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 91 removed outlier: 3.502A pdb=" N SER C 85 " --> pdb=" O GLY C 81 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LYS C 89 " --> pdb=" O SER C 85 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLU C 90 " --> pdb=" O LYS C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 92 through 96 removed outlier: 3.718A pdb=" N GLU C 96 " --> pdb=" O LEU C 93 " (cutoff:3.500A) Processing helix chain 'C' and resid 98 through 106 removed outlier: 3.978A pdb=" N GLN C 104 " --> pdb=" O GLU C 100 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LYS C 105 " --> pdb=" O LEU C 101 " (cutoff:3.500A) Processing helix chain 'C' and resid 106 through 119 removed outlier: 3.566A pdb=" N GLY C 110 " --> pdb=" O ASP C 106 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N ASP C 111 " --> pdb=" O PRO C 107 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N MET C 115 " --> pdb=" O ASP C 111 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLY C 119 " --> pdb=" O MET C 115 " (cutoff:3.500A) Processing helix chain 'C' and resid 121 through 135 removed outlier: 3.525A pdb=" N LYS C 126 " --> pdb=" O ILE C 122 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ALA C 127 " --> pdb=" O ASN C 123 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ALA C 129 " --> pdb=" O ILE C 125 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N MET C 131 " --> pdb=" O ALA C 127 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLN C 135 " --> pdb=" O MET C 131 " (cutoff:3.500A) Processing helix chain 'C' and resid 136 through 151 removed outlier: 3.746A pdb=" N THR C 142 " --> pdb=" O GLU C 138 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N GLU C 143 " --> pdb=" O LYS C 139 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N VAL C 146 " --> pdb=" O THR C 142 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N TRP C 147 " --> pdb=" O GLU C 143 " (cutoff:3.500A) Processing helix chain 'C' and resid 157 through 171 removed outlier: 3.703A pdb=" N GLN C 168 " --> pdb=" O ILE C 164 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N MET C 169 " --> pdb=" O GLY C 165 " (cutoff:3.500A) Processing helix chain 'C' and resid 175 through 178 Processing helix chain 'C' and resid 179 through 200 removed outlier: 3.614A pdb=" N ALA C 186 " --> pdb=" O GLY C 182 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N THR C 189 " --> pdb=" O VAL C 185 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N THR C 190 " --> pdb=" O ALA C 186 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LEU C 191 " --> pdb=" O LEU C 187 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N GLY C 193 " --> pdb=" O THR C 189 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LEU C 196 " --> pdb=" O TYR C 192 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ALA C 197 " --> pdb=" O GLY C 193 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ASN C 198 " --> pdb=" O ALA C 194 " (cutoff:3.500A) Processing helix chain 'C' and resid 200 through 231 removed outlier: 3.790A pdb=" N VAL C 204 " --> pdb=" O PHE C 200 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N LYS C 209 " --> pdb=" O ALA C 205 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LYS C 210 " --> pdb=" O ASN C 206 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N MET C 214 " --> pdb=" O LYS C 210 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N GLU C 215 " --> pdb=" O ALA C 211 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N VAL C 218 " --> pdb=" O MET C 214 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LYS C 219 " --> pdb=" O GLU C 215 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLU C 224 " --> pdb=" O THR C 220 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLU C 227 " --> pdb=" O ILE C 223 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ILE C 229 " --> pdb=" O ALA C 225 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LYS C 231 " --> pdb=" O GLU C 227 " (cutoff:3.500A) Processing helix chain 'C' and resid 234 through 247 removed outlier: 3.501A pdb=" N VAL C 238 " --> pdb=" O ASN C 234 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LYS C 239 " --> pdb=" O PRO C 235 " (cutoff:3.500A) Processing helix chain 'D' and resid 5 through 10 Processing helix chain 'D' and resid 11 through 24 removed outlier: 3.620A pdb=" N LEU D 15 " --> pdb=" O ALA D 11 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LEU D 17 " --> pdb=" O PHE D 13 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N SER D 19 " --> pdb=" O LEU D 15 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLY D 23 " --> pdb=" O SER D 19 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N GLY D 24 " --> pdb=" O ILE D 20 " (cutoff:3.500A) Processing helix chain 'D' and resid 31 through 33 No H-bonds generated for 'chain 'D' and resid 31 through 33' Processing helix chain 'D' and resid 34 through 45 removed outlier: 3.775A pdb=" N VAL D 38 " --> pdb=" O SER D 34 " (cutoff:3.500A) Processing helix chain 'D' and resid 51 through 60 removed outlier: 3.553A pdb=" N ARG D 57 " --> pdb=" O LYS D 53 " (cutoff:3.500A) Processing helix chain 'D' and resid 62 through 67 Processing helix chain 'D' and resid 72 through 91 removed outlier: 3.757A pdb=" N ILE D 77 " --> pdb=" O LEU D 73 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N GLU D 78 " --> pdb=" O ASN D 74 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLU D 82 " --> pdb=" O GLU D 78 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N SER D 85 " --> pdb=" O GLY D 81 " (cutoff:3.500A) Processing helix chain 'D' and resid 92 through 97 removed outlier: 4.272A pdb=" N GLU D 96 " --> pdb=" O LEU D 93 " (cutoff:3.500A) removed outlier: 5.046A pdb=" N GLY D 97 " --> pdb=" O ALA D 94 " (cutoff:3.500A) Processing helix chain 'D' and resid 98 through 104 Processing helix chain 'D' and resid 106 through 118 removed outlier: 3.653A pdb=" N GLY D 110 " --> pdb=" O ASP D 106 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N MET D 115 " --> pdb=" O ASP D 111 " (cutoff:3.500A) Processing helix chain 'D' and resid 121 through 135 removed outlier: 3.944A pdb=" N ALA D 127 " --> pdb=" O ASN D 123 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N MET D 131 " --> pdb=" O ALA D 127 " (cutoff:3.500A) Processing helix chain 'D' and resid 139 through 154 removed outlier: 3.878A pdb=" N GLU D 143 " --> pdb=" O LYS D 139 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N TRP D 147 " --> pdb=" O GLU D 143 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ASP D 152 " --> pdb=" O GLU D 148 " (cutoff:3.500A) Processing helix chain 'D' and resid 157 through 172 removed outlier: 3.561A pdb=" N GLY D 165 " --> pdb=" O GLY D 161 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ILE D 167 " --> pdb=" O LEU D 163 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLN D 168 " --> pdb=" O ILE D 164 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N MET D 169 " --> pdb=" O GLY D 165 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N LEU D 170 " --> pdb=" O LEU D 166 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ASN D 172 " --> pdb=" O GLN D 168 " (cutoff:3.500A) Processing helix chain 'D' and resid 175 through 178 Processing helix chain 'D' and resid 179 through 200 removed outlier: 3.949A pdb=" N THR D 189 " --> pdb=" O VAL D 185 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N THR D 190 " --> pdb=" O ALA D 186 " (cutoff:3.500A) Processing helix chain 'D' and resid 202 through 207 Processing helix chain 'D' and resid 208 through 231 removed outlier: 3.532A pdb=" N MET D 214 " --> pdb=" O LYS D 210 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LEU D 217 " --> pdb=" O ASP D 213 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N VAL D 218 " --> pdb=" O MET D 214 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N LYS D 219 " --> pdb=" O GLU D 215 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ILE D 221 " --> pdb=" O LEU D 217 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N TYR D 222 " --> pdb=" O VAL D 218 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N GLU D 224 " --> pdb=" O THR D 220 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N GLU D 227 " --> pdb=" O ILE D 223 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ILE D 229 " --> pdb=" O ALA D 225 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N LYS D 231 " --> pdb=" O GLU D 227 " (cutoff:3.500A) Processing helix chain 'D' and resid 234 through 245 removed outlier: 3.511A pdb=" N VAL D 238 " --> pdb=" O ASN D 234 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLN D 240 " --> pdb=" O ASN D 236 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ILE D 244 " --> pdb=" O GLN D 240 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N MET D 245 " --> pdb=" O GLU D 241 " (cutoff:3.500A) Processing helix chain 'E' and resid 5 through 24 removed outlier: 3.830A pdb=" N ALA E 12 " --> pdb=" O GLY E 8 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ILE E 18 " --> pdb=" O LEU E 14 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N GLY E 23 " --> pdb=" O SER E 19 " (cutoff:3.500A) Processing helix chain 'E' and resid 31 through 33 No H-bonds generated for 'chain 'E' and resid 31 through 33' Processing helix chain 'E' and resid 34 through 43 removed outlier: 4.137A pdb=" N VAL E 38 " --> pdb=" O SER E 34 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 49 Processing helix chain 'E' and resid 51 through 60 removed outlier: 3.835A pdb=" N ARG E 57 " --> pdb=" O LYS E 53 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLY E 58 " --> pdb=" O ASP E 54 " (cutoff:3.500A) Processing helix chain 'E' and resid 76 through 91 removed outlier: 3.944A pdb=" N ILE E 80 " --> pdb=" O VAL E 76 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N GLU E 82 " --> pdb=" O GLU E 78 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N SER E 85 " --> pdb=" O GLY E 81 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LYS E 86 " --> pdb=" O GLU E 82 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLU E 90 " --> pdb=" O LYS E 86 " (cutoff:3.500A) Processing helix chain 'E' and resid 92 through 97 removed outlier: 3.540A pdb=" N LEU E 95 " --> pdb=" O ILE E 92 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N GLU E 96 " --> pdb=" O LEU E 93 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N GLY E 97 " --> pdb=" O ALA E 94 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 92 through 97' Processing helix chain 'E' and resid 98 through 106 removed outlier: 3.651A pdb=" N GLN E 104 " --> pdb=" O GLU E 100 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N LYS E 105 " --> pdb=" O LEU E 101 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N ASP E 106 " --> pdb=" O TYR E 102 " (cutoff:3.500A) Processing helix chain 'E' and resid 106 through 118 removed outlier: 3.635A pdb=" N ARG E 114 " --> pdb=" O GLY E 110 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N MET E 115 " --> pdb=" O ASP E 111 " (cutoff:3.500A) Processing helix chain 'E' and resid 121 through 154 removed outlier: 3.685A pdb=" N ALA E 127 " --> pdb=" O ASN E 123 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLU E 130 " --> pdb=" O LYS E 126 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N MET E 131 " --> pdb=" O ALA E 127 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N LYS E 139 " --> pdb=" O GLN E 135 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N MET E 140 " --> pdb=" O LEU E 136 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N THR E 142 " --> pdb=" O GLU E 138 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLU E 143 " --> pdb=" O LYS E 139 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N TRP E 147 " --> pdb=" O GLU E 143 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LYS E 149 " --> pdb=" O ALA E 145 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N ASP E 152 " --> pdb=" O GLU E 148 " (cutoff:3.500A) Processing helix chain 'E' and resid 157 through 172 removed outlier: 3.524A pdb=" N LEU E 163 " --> pdb=" O MET E 159 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N GLY E 165 " --> pdb=" O GLY E 161 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N GLN E 168 " --> pdb=" O ILE E 164 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N MET E 169 " --> pdb=" O GLY E 165 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N LEU E 170 " --> pdb=" O LEU E 166 " (cutoff:3.500A) Processing helix chain 'E' and resid 179 through 200 removed outlier: 3.783A pdb=" N THR E 189 " --> pdb=" O VAL E 185 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N THR E 190 " --> pdb=" O ALA E 186 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N GLY E 193 " --> pdb=" O THR E 189 " (cutoff:3.500A) Processing helix chain 'E' and resid 200 through 208 removed outlier: 3.630A pdb=" N VAL E 204 " --> pdb=" O PHE E 200 " (cutoff:3.500A) Processing helix chain 'E' and resid 211 through 228 removed outlier: 3.654A pdb=" N TYR E 222 " --> pdb=" O VAL E 218 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N LYS E 228 " --> pdb=" O GLU E 224 " (cutoff:3.500A) Processing helix chain 'E' and resid 235 through 247 removed outlier: 3.736A pdb=" N GLU E 241 " --> pdb=" O VAL E 237 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N MET E 245 " --> pdb=" O GLU E 241 " (cutoff:3.500A) 495 hydrogen bonds defined for protein. 1446 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.54 Time building geometry restraints manager: 2.90 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3007 1.34 - 1.46: 1035 1.46 - 1.57: 5493 1.57 - 1.69: 0 1.69 - 1.80: 120 Bond restraints: 9655 Sorted by residual: bond pdb=" C VAL C 32 " pdb=" N PRO C 33 " ideal model delta sigma weight residual 1.334 1.348 -0.014 8.40e-03 1.42e+04 2.79e+00 bond pdb=" C GLY C 119 " pdb=" N ILE C 120 " ideal model delta sigma weight residual 1.334 1.318 0.016 1.29e-02 6.01e+03 1.47e+00 bond pdb=" CG1 ILE D 221 " pdb=" CD1 ILE D 221 " ideal model delta sigma weight residual 1.513 1.467 0.046 3.90e-02 6.57e+02 1.41e+00 bond pdb=" CG1 ILE E 221 " pdb=" CD1 ILE E 221 " ideal model delta sigma weight residual 1.513 1.474 0.039 3.90e-02 6.57e+02 1.01e+00 bond pdb=" CB ASP D 137 " pdb=" CG ASP D 137 " ideal model delta sigma weight residual 1.516 1.491 0.025 2.50e-02 1.60e+03 9.77e-01 ... (remaining 9650 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.15: 12148 1.15 - 2.29: 782 2.29 - 3.44: 106 3.44 - 4.59: 25 4.59 - 5.74: 14 Bond angle restraints: 13075 Sorted by residual: angle pdb=" C ASN A 31 " pdb=" N VAL A 32 " pdb=" CA VAL A 32 " ideal model delta sigma weight residual 120.24 123.93 -3.69 6.30e-01 2.52e+00 3.43e+01 angle pdb=" N VAL B 3 " pdb=" CA VAL B 3 " pdb=" C VAL B 3 " ideal model delta sigma weight residual 111.91 108.15 3.76 8.90e-01 1.26e+00 1.78e+01 angle pdb=" N ILE C 7 " pdb=" CA ILE C 7 " pdb=" C ILE C 7 " ideal model delta sigma weight residual 112.90 108.95 3.95 9.60e-01 1.09e+00 1.69e+01 angle pdb=" C VAL A 32 " pdb=" CA VAL A 32 " pdb=" CB VAL A 32 " ideal model delta sigma weight residual 114.35 110.75 3.60 1.06e+00 8.90e-01 1.15e+01 angle pdb=" N VAL A 3 " pdb=" CA VAL A 3 " pdb=" C VAL A 3 " ideal model delta sigma weight residual 111.91 109.17 2.74 8.90e-01 1.26e+00 9.46e+00 ... (remaining 13070 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.50: 5309 14.50 - 29.00: 412 29.00 - 43.49: 126 43.49 - 57.99: 38 57.99 - 72.49: 5 Dihedral angle restraints: 5890 sinusoidal: 2300 harmonic: 3590 Sorted by residual: dihedral pdb=" CA GLN E 135 " pdb=" C GLN E 135 " pdb=" N LEU E 136 " pdb=" CA LEU E 136 " ideal model delta harmonic sigma weight residual 180.00 157.63 22.37 0 5.00e+00 4.00e-02 2.00e+01 dihedral pdb=" CA GLN A 135 " pdb=" C GLN A 135 " pdb=" N LEU A 136 " pdb=" CA LEU A 136 " ideal model delta harmonic sigma weight residual 180.00 163.19 16.81 0 5.00e+00 4.00e-02 1.13e+01 dihedral pdb=" CA ALA B 46 " pdb=" C ALA B 46 " pdb=" N MET B 47 " pdb=" CA MET B 47 " ideal model delta harmonic sigma weight residual 180.00 163.61 16.39 0 5.00e+00 4.00e-02 1.07e+01 ... (remaining 5887 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 682 0.025 - 0.051: 591 0.051 - 0.076: 265 0.076 - 0.101: 56 0.101 - 0.126: 16 Chirality restraints: 1610 Sorted by residual: chirality pdb=" CB VAL C 3 " pdb=" CA VAL C 3 " pdb=" CG1 VAL C 3 " pdb=" CG2 VAL C 3 " both_signs ideal model delta sigma weight residual False -2.63 -2.50 -0.13 2.00e-01 2.50e+01 3.98e-01 chirality pdb=" CA ILE A 120 " pdb=" N ILE A 120 " pdb=" C ILE A 120 " pdb=" CB ILE A 120 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.11 2.00e-01 2.50e+01 3.15e-01 chirality pdb=" CB VAL B 3 " pdb=" CA VAL B 3 " pdb=" CG1 VAL B 3 " pdb=" CG2 VAL B 3 " both_signs ideal model delta sigma weight residual False -2.63 -2.52 -0.11 2.00e-01 2.50e+01 3.11e-01 ... (remaining 1607 not shown) Planarity restraints: 1630 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE C 202 " -0.029 5.00e-02 4.00e+02 4.30e-02 2.96e+00 pdb=" N PRO C 203 " 0.074 5.00e-02 4.00e+02 pdb=" CA PRO C 203 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO C 203 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE E 202 " 0.027 5.00e-02 4.00e+02 4.08e-02 2.66e+00 pdb=" N PRO E 203 " -0.071 5.00e-02 4.00e+02 pdb=" CA PRO E 203 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO E 203 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE B 202 " 0.025 5.00e-02 4.00e+02 3.75e-02 2.25e+00 pdb=" N PRO B 203 " -0.065 5.00e-02 4.00e+02 pdb=" CA PRO B 203 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO B 203 " 0.021 5.00e-02 4.00e+02 ... (remaining 1627 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.67: 123 2.67 - 3.23: 9442 3.23 - 3.79: 13488 3.79 - 4.34: 21454 4.34 - 4.90: 33480 Nonbonded interactions: 77987 Sorted by model distance: nonbonded pdb=" O PHE D 29 " pdb=" OH TYR D 192 " model vdw 2.117 3.040 nonbonded pdb=" O PHE B 29 " pdb=" OH TYR B 192 " model vdw 2.120 3.040 nonbonded pdb=" O PHE A 29 " pdb=" OH TYR A 192 " model vdw 2.142 3.040 nonbonded pdb=" O PHE C 29 " pdb=" OH TYR C 192 " model vdw 2.143 3.040 nonbonded pdb=" O PHE E 29 " pdb=" OH TYR E 192 " model vdw 2.216 3.040 ... (remaining 77982 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.810 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.390 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 24.300 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 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 : 0.005 0.046 9655 Z= 0.324 Angle : 0.657 5.736 13075 Z= 0.389 Chirality : 0.040 0.126 1610 Planarity : 0.004 0.043 1630 Dihedral : 12.578 72.490 3580 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 5.67 % Allowed : 9.25 % Favored : 85.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -7.14 (0.13), residues: 1255 helix: -4.90 (0.06), residues: 985 sheet: None (None), residues: 0 loop : -2.58 (0.29), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP C 147 HIS 0.001 0.000 HIS B 0 PHE 0.008 0.001 PHE A 55 TYR 0.007 0.001 TYR D 222 ARG 0.002 0.000 ARG D 88 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2510 Ramachandran restraints generated. 1255 Oldfield, 0 Emsley, 1255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2510 Ramachandran restraints generated. 1255 Oldfield, 0 Emsley, 1255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 202 time to evaluate : 0.962 Fit side-chains REVERT: A 53 LYS cc_start: 0.8001 (mmtp) cc_final: 0.7725 (mmtm) REVERT: A 62 ILE cc_start: 0.8002 (OUTLIER) cc_final: 0.7749 (mt) REVERT: A 217 LEU cc_start: 0.8636 (OUTLIER) cc_final: 0.8386 (tt) REVERT: B 43 MET cc_start: 0.8434 (mmm) cc_final: 0.8227 (mtt) REVERT: B 88 ARG cc_start: 0.7484 (ttm-80) cc_final: 0.7038 (ttt90) REVERT: B 159 MET cc_start: 0.7673 (tmm) cc_final: 0.7107 (ptm) REVERT: C 2 ASP cc_start: 0.7499 (OUTLIER) cc_final: 0.7252 (t70) REVERT: C 69 LYS cc_start: 0.8806 (OUTLIER) cc_final: 0.8522 (mttt) REVERT: C 118 ASP cc_start: 0.7258 (m-30) cc_final: 0.6909 (m-30) REVERT: C 206 ASN cc_start: 0.8825 (t0) cc_final: 0.8569 (t0) REVERT: C 249 GLU cc_start: 0.6967 (tm-30) cc_final: 0.6738 (tm-30) REVERT: D 95 LEU cc_start: 0.6075 (OUTLIER) cc_final: 0.5490 (mp) REVERT: D 115 MET cc_start: 0.8292 (mtp) cc_final: 0.8026 (mtt) REVERT: E 86 LYS cc_start: 0.8200 (tptt) cc_final: 0.7976 (tptm) REVERT: E 139 LYS cc_start: 0.8839 (mmtp) cc_final: 0.8288 (mttt) outliers start: 57 outliers final: 20 residues processed: 246 average time/residue: 0.1880 time to fit residues: 66.1354 Evaluate side-chains 179 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 154 time to evaluate : 1.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue -1 VAL Chi-restraints excluded: chain A residue 62 ILE Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 137 ASP Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain C residue 2 ASP Chi-restraints excluded: chain C residue 59 VAL Chi-restraints excluded: chain C residue 67 LEU Chi-restraints excluded: chain C residue 69 LYS Chi-restraints excluded: chain C residue 121 ASP Chi-restraints excluded: chain C residue 226 ILE Chi-restraints excluded: chain D residue 22 ILE Chi-restraints excluded: chain D residue 67 LEU Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain D residue 121 ASP Chi-restraints excluded: chain D residue 157 PHE Chi-restraints excluded: chain E residue -1 VAL Chi-restraints excluded: chain E residue 159 MET Chi-restraints excluded: chain E residue 228 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 105 optimal weight: 0.6980 chunk 94 optimal weight: 0.6980 chunk 52 optimal weight: 3.9990 chunk 32 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 chunk 50 optimal weight: 6.9990 chunk 97 optimal weight: 0.9980 chunk 37 optimal weight: 1.9990 chunk 59 optimal weight: 5.9990 chunk 72 optimal weight: 0.9980 chunk 113 optimal weight: 0.6980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 198 ASN C 168 GLN C 198 ASN C 240 GLN D 198 ASN D 240 GLN E 104 GLN E 198 ASN E 240 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.131651 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.109418 restraints weight = 11209.541| |-----------------------------------------------------------------------------| r_work (start): 0.3033 rms_B_bonded: 1.52 r_work: 0.2908 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2775 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.2775 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8377 moved from start: 0.1903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 9655 Z= 0.221 Angle : 0.647 10.427 13075 Z= 0.335 Chirality : 0.039 0.121 1610 Planarity : 0.006 0.035 1630 Dihedral : 8.132 59.737 1351 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 3.68 % Allowed : 14.73 % Favored : 81.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.51 (0.16), residues: 1255 helix: -3.61 (0.11), residues: 1040 sheet: None (None), residues: 0 loop : -2.07 (0.31), residues: 215 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP E 147 HIS 0.001 0.000 HIS B 0 PHE 0.007 0.001 PHE D 66 TYR 0.008 0.001 TYR C 192 ARG 0.005 0.001 ARG D 57 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2510 Ramachandran restraints generated. 1255 Oldfield, 0 Emsley, 1255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2510 Ramachandran restraints generated. 1255 Oldfield, 0 Emsley, 1255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 155 time to evaluate : 1.039 Fit side-chains REVERT: A 53 LYS cc_start: 0.8177 (mmtp) cc_final: 0.7800 (mmtm) REVERT: A 217 LEU cc_start: 0.8397 (OUTLIER) cc_final: 0.8147 (tt) REVERT: B 159 MET cc_start: 0.8196 (tmm) cc_final: 0.7838 (ptm) REVERT: B 221 ILE cc_start: 0.8263 (OUTLIER) cc_final: 0.7749 (mp) REVERT: B 236 ASN cc_start: 0.8483 (m-40) cc_final: 0.7925 (m-40) REVERT: C 2 ASP cc_start: 0.7767 (OUTLIER) cc_final: 0.7358 (t70) REVERT: C 43 MET cc_start: 0.8727 (OUTLIER) cc_final: 0.8359 (mmt) REVERT: C 69 LYS cc_start: 0.8979 (OUTLIER) cc_final: 0.8695 (mttt) REVERT: C 112 MET cc_start: 0.8354 (ttp) cc_final: 0.8110 (ttp) REVERT: C 118 ASP cc_start: 0.7200 (m-30) cc_final: 0.6793 (m-30) REVERT: C 138 GLU cc_start: 0.8283 (mm-30) cc_final: 0.7237 (tt0) REVERT: C 206 ASN cc_start: 0.9008 (t0) cc_final: 0.8574 (t0) REVERT: C 249 GLU cc_start: 0.6861 (tm-30) cc_final: 0.6654 (tm-30) REVERT: E 139 LYS cc_start: 0.8889 (mmtp) cc_final: 0.8292 (mttt) outliers start: 37 outliers final: 19 residues processed: 185 average time/residue: 0.1856 time to fit residues: 50.8062 Evaluate side-chains 163 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 139 time to evaluate : 1.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue -1 VAL Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 112 MET Chi-restraints excluded: chain A residue 137 ASP Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain B residue 9 ILE Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain B residue 198 ASN Chi-restraints excluded: chain B residue 221 ILE Chi-restraints excluded: chain C residue 2 ASP Chi-restraints excluded: chain C residue 43 MET Chi-restraints excluded: chain C residue 59 VAL Chi-restraints excluded: chain C residue 67 LEU Chi-restraints excluded: chain C residue 69 LYS Chi-restraints excluded: chain C residue 226 ILE Chi-restraints excluded: chain C residue 229 ILE Chi-restraints excluded: chain D residue 22 ILE Chi-restraints excluded: chain D residue 67 LEU Chi-restraints excluded: chain D residue 157 PHE Chi-restraints excluded: chain E residue 159 MET Chi-restraints excluded: chain E residue 223 ILE Chi-restraints excluded: chain E residue 228 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 22 optimal weight: 0.7980 chunk 107 optimal weight: 0.9990 chunk 63 optimal weight: 5.9990 chunk 84 optimal weight: 0.0980 chunk 54 optimal weight: 3.9990 chunk 53 optimal weight: 0.0980 chunk 37 optimal weight: 2.9990 chunk 17 optimal weight: 0.0980 chunk 66 optimal weight: 3.9990 chunk 124 optimal weight: 0.6980 chunk 3 optimal weight: 0.0470 overall best weight: 0.2078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 198 ASN C 198 ASN ** E 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.128817 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.106983 restraints weight = 11144.183| |-----------------------------------------------------------------------------| r_work (start): 0.3097 rms_B_bonded: 1.44 r_work: 0.2988 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.2861 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.2861 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 moved from start: 0.2434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 9655 Z= 0.142 Angle : 0.528 7.934 13075 Z= 0.274 Chirality : 0.038 0.112 1610 Planarity : 0.004 0.032 1630 Dihedral : 6.861 59.366 1335 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 3.58 % Allowed : 16.22 % Favored : 80.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.95 (0.20), residues: 1255 helix: -2.47 (0.14), residues: 1010 sheet: None (None), residues: 0 loop : -2.10 (0.30), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 147 HIS 0.001 0.000 HIS B 0 PHE 0.006 0.001 PHE A 200 TYR 0.010 0.001 TYR A 222 ARG 0.002 0.000 ARG E 88 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2510 Ramachandran restraints generated. 1255 Oldfield, 0 Emsley, 1255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2510 Ramachandran restraints generated. 1255 Oldfield, 0 Emsley, 1255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 148 time to evaluate : 1.074 Fit side-chains REVERT: A 53 LYS cc_start: 0.8155 (mmtp) cc_final: 0.7807 (mmtm) REVERT: B 7 ILE cc_start: 0.8398 (tt) cc_final: 0.7933 (pt) REVERT: B 159 MET cc_start: 0.8116 (tmm) cc_final: 0.7682 (ptm) REVERT: B 172 ASN cc_start: 0.6490 (m-40) cc_final: 0.4972 (p0) REVERT: B 183 MET cc_start: 0.7988 (tpt) cc_final: 0.7623 (tpp) REVERT: B 221 ILE cc_start: 0.8189 (OUTLIER) cc_final: 0.7766 (mp) REVERT: C 2 ASP cc_start: 0.7653 (OUTLIER) cc_final: 0.7315 (t70) REVERT: C 43 MET cc_start: 0.8531 (OUTLIER) cc_final: 0.8187 (mmt) REVERT: C 118 ASP cc_start: 0.7191 (m-30) cc_final: 0.6849 (m-30) REVERT: C 138 GLU cc_start: 0.8059 (mm-30) cc_final: 0.7167 (tt0) REVERT: C 206 ASN cc_start: 0.8964 (t0) cc_final: 0.8444 (t0) REVERT: D 159 MET cc_start: 0.8301 (tmm) cc_final: 0.7824 (ttt) REVERT: E 137 ASP cc_start: 0.8340 (t0) cc_final: 0.8028 (t0) outliers start: 36 outliers final: 20 residues processed: 174 average time/residue: 0.1709 time to fit residues: 44.5046 Evaluate side-chains 158 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 135 time to evaluate : 1.090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue -1 VAL Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 112 MET Chi-restraints excluded: chain A residue 137 ASP Chi-restraints excluded: chain A residue 142 THR Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain B residue 9 ILE Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain B residue 221 ILE Chi-restraints excluded: chain C residue 2 ASP Chi-restraints excluded: chain C residue 43 MET Chi-restraints excluded: chain C residue 67 LEU Chi-restraints excluded: chain C residue 198 ASN Chi-restraints excluded: chain C residue 226 ILE Chi-restraints excluded: chain D residue 67 LEU Chi-restraints excluded: chain D residue 113 ILE Chi-restraints excluded: chain D residue 169 MET Chi-restraints excluded: chain E residue 67 LEU Chi-restraints excluded: chain E residue 189 THR Chi-restraints excluded: chain E residue 221 ILE Chi-restraints excluded: chain E residue 228 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 94 optimal weight: 2.9990 chunk 20 optimal weight: 0.9980 chunk 114 optimal weight: 0.6980 chunk 67 optimal weight: 0.1980 chunk 51 optimal weight: 2.9990 chunk 48 optimal weight: 0.6980 chunk 34 optimal weight: 0.6980 chunk 12 optimal weight: 0.0980 chunk 19 optimal weight: 0.9990 chunk 103 optimal weight: 2.9990 chunk 68 optimal weight: 0.6980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 198 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 = 0.3416 r_free = 0.3416 target = 0.126472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.104286 restraints weight = 11103.119| |-----------------------------------------------------------------------------| r_work (start): 0.3068 rms_B_bonded: 1.44 r_work: 0.2953 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.2823 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.2823 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8302 moved from start: 0.2644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 9655 Z= 0.154 Angle : 0.502 6.601 13075 Z= 0.258 Chirality : 0.038 0.113 1610 Planarity : 0.004 0.033 1630 Dihedral : 6.166 59.806 1320 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 3.08 % Allowed : 15.92 % Favored : 81.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.05 (0.21), residues: 1255 helix: -1.80 (0.15), residues: 1000 sheet: None (None), residues: 0 loop : -2.03 (0.30), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 147 HIS 0.001 0.000 HIS E 0 PHE 0.007 0.001 PHE A 200 TYR 0.006 0.001 TYR A 222 ARG 0.002 0.000 ARG E 88 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2510 Ramachandran restraints generated. 1255 Oldfield, 0 Emsley, 1255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2510 Ramachandran restraints generated. 1255 Oldfield, 0 Emsley, 1255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 144 time to evaluate : 0.964 Fit side-chains REVERT: A 53 LYS cc_start: 0.8134 (mmtp) cc_final: 0.7807 (mmtm) REVERT: A 106 ASP cc_start: 0.8361 (p0) cc_final: 0.8046 (p0) REVERT: B 7 ILE cc_start: 0.8496 (OUTLIER) cc_final: 0.8012 (pt) REVERT: B 159 MET cc_start: 0.8171 (tmm) cc_final: 0.7680 (ptm) REVERT: B 183 MET cc_start: 0.8032 (tpt) cc_final: 0.7717 (tpp) REVERT: B 221 ILE cc_start: 0.8211 (OUTLIER) cc_final: 0.7775 (mp) REVERT: B 227 GLU cc_start: 0.8076 (tm-30) cc_final: 0.7764 (tt0) REVERT: C 2 ASP cc_start: 0.7649 (OUTLIER) cc_final: 0.7329 (t70) REVERT: C 43 MET cc_start: 0.8433 (tpp) cc_final: 0.8105 (mmt) REVERT: C 69 LYS cc_start: 0.8992 (OUTLIER) cc_final: 0.8768 (mttt) REVERT: C 138 GLU cc_start: 0.8026 (mm-30) cc_final: 0.7185 (tt0) REVERT: C 206 ASN cc_start: 0.8966 (t0) cc_final: 0.8479 (t0) REVERT: C 223 ILE cc_start: 0.8431 (OUTLIER) cc_final: 0.7836 (mp) REVERT: D 90 GLU cc_start: 0.8446 (mp0) cc_final: 0.8086 (mt-10) REVERT: D 159 MET cc_start: 0.8326 (tmm) cc_final: 0.7863 (ttt) REVERT: D 227 GLU cc_start: 0.7865 (tt0) cc_final: 0.7570 (tt0) REVERT: E 136 LEU cc_start: 0.8592 (tt) cc_final: 0.8340 (tp) REVERT: E 137 ASP cc_start: 0.8387 (t0) cc_final: 0.8071 (t0) REVERT: E 241 GLU cc_start: 0.8018 (mt-10) cc_final: 0.7768 (mt-10) outliers start: 31 outliers final: 20 residues processed: 167 average time/residue: 0.1759 time to fit residues: 43.9160 Evaluate side-chains 162 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 137 time to evaluate : 1.046 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue -1 VAL Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 112 MET Chi-restraints excluded: chain A residue 137 ASP Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain B residue 7 ILE Chi-restraints excluded: chain B residue 9 ILE Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain B residue 221 ILE Chi-restraints excluded: chain C residue 2 ASP Chi-restraints excluded: chain C residue 67 LEU Chi-restraints excluded: chain C residue 69 LYS Chi-restraints excluded: chain C residue 198 ASN Chi-restraints excluded: chain C residue 223 ILE Chi-restraints excluded: chain C residue 226 ILE Chi-restraints excluded: chain D residue 67 LEU Chi-restraints excluded: chain D residue 88 ARG Chi-restraints excluded: chain D residue 113 ILE Chi-restraints excluded: chain D residue 157 PHE Chi-restraints excluded: chain D residue 169 MET Chi-restraints excluded: chain E residue 67 LEU Chi-restraints excluded: chain E residue 159 MET Chi-restraints excluded: chain E residue 221 ILE Chi-restraints excluded: chain E residue 228 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 110 optimal weight: 3.9990 chunk 111 optimal weight: 1.9990 chunk 64 optimal weight: 0.9980 chunk 66 optimal weight: 0.7980 chunk 30 optimal weight: 0.6980 chunk 8 optimal weight: 0.9990 chunk 83 optimal weight: 0.9980 chunk 89 optimal weight: 1.9990 chunk 35 optimal weight: 3.9990 chunk 11 optimal weight: 5.9990 chunk 87 optimal weight: 3.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 198 ASN D 31 ASN D 198 ASN ** E 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.135380 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.112697 restraints weight = 10962.412| |-----------------------------------------------------------------------------| r_work (start): 0.2996 rms_B_bonded: 1.52 r_work: 0.2877 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.2742 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.2742 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 moved from start: 0.2760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 9655 Z= 0.193 Angle : 0.517 7.280 13075 Z= 0.262 Chirality : 0.039 0.113 1610 Planarity : 0.004 0.032 1630 Dihedral : 6.140 59.915 1320 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 4.08 % Allowed : 16.62 % Favored : 79.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.49 (0.22), residues: 1255 helix: -1.40 (0.16), residues: 1000 sheet: None (None), residues: 0 loop : -1.83 (0.31), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 147 HIS 0.001 0.000 HIS B 0 PHE 0.010 0.001 PHE E 157 TYR 0.007 0.001 TYR D 222 ARG 0.001 0.000 ARG C 57 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2510 Ramachandran restraints generated. 1255 Oldfield, 0 Emsley, 1255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2510 Ramachandran restraints generated. 1255 Oldfield, 0 Emsley, 1255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 146 time to evaluate : 1.014 Fit side-chains REVERT: A 53 LYS cc_start: 0.8127 (mmtp) cc_final: 0.7795 (mmtm) REVERT: A 106 ASP cc_start: 0.8402 (p0) cc_final: 0.8085 (p0) REVERT: B 7 ILE cc_start: 0.8537 (OUTLIER) cc_final: 0.8195 (tt) REVERT: B 88 ARG cc_start: 0.7441 (ttm-80) cc_final: 0.7047 (ttt90) REVERT: B 159 MET cc_start: 0.8254 (tmm) cc_final: 0.7742 (ptm) REVERT: B 221 ILE cc_start: 0.8221 (OUTLIER) cc_final: 0.7732 (mp) REVERT: B 227 GLU cc_start: 0.8097 (tm-30) cc_final: 0.7793 (tt0) REVERT: B 236 ASN cc_start: 0.8113 (m-40) cc_final: 0.7896 (m-40) REVERT: C 2 ASP cc_start: 0.7717 (OUTLIER) cc_final: 0.7397 (t70) REVERT: C 43 MET cc_start: 0.8421 (tpp) cc_final: 0.8081 (mmt) REVERT: C 69 LYS cc_start: 0.9024 (OUTLIER) cc_final: 0.8769 (mttt) REVERT: C 89 LYS cc_start: 0.8124 (tptt) cc_final: 0.7711 (mptt) REVERT: C 206 ASN cc_start: 0.9007 (t0) cc_final: 0.8429 (t0) REVERT: C 223 ILE cc_start: 0.8436 (OUTLIER) cc_final: 0.7808 (mp) REVERT: D 90 GLU cc_start: 0.8473 (mp0) cc_final: 0.8160 (mt-10) REVERT: D 159 MET cc_start: 0.8392 (tmm) cc_final: 0.7947 (ttt) REVERT: D 227 GLU cc_start: 0.7929 (tt0) cc_final: 0.7697 (tt0) REVERT: E 136 LEU cc_start: 0.8561 (tt) cc_final: 0.8341 (tp) REVERT: E 137 ASP cc_start: 0.8430 (t0) cc_final: 0.8111 (t0) REVERT: E 228 LYS cc_start: 0.7783 (OUTLIER) cc_final: 0.7412 (mttt) outliers start: 41 outliers final: 25 residues processed: 176 average time/residue: 0.1734 time to fit residues: 45.1037 Evaluate side-chains 169 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 138 time to evaluate : 1.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue -1 VAL Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 112 MET Chi-restraints excluded: chain A residue 137 ASP Chi-restraints excluded: chain A residue 142 THR Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain B residue 7 ILE Chi-restraints excluded: chain B residue 9 ILE Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain B residue 187 LEU Chi-restraints excluded: chain B residue 221 ILE Chi-restraints excluded: chain C residue 2 ASP Chi-restraints excluded: chain C residue 67 LEU Chi-restraints excluded: chain C residue 69 LYS Chi-restraints excluded: chain C residue 223 ILE Chi-restraints excluded: chain C residue 226 ILE Chi-restraints excluded: chain D residue 22 ILE Chi-restraints excluded: chain D residue 67 LEU Chi-restraints excluded: chain D residue 88 ARG Chi-restraints excluded: chain D residue 113 ILE Chi-restraints excluded: chain D residue 185 VAL Chi-restraints excluded: chain D residue 198 ASN Chi-restraints excluded: chain E residue 21 LEU Chi-restraints excluded: chain E residue 67 LEU Chi-restraints excluded: chain E residue 159 MET Chi-restraints excluded: chain E residue 221 ILE Chi-restraints excluded: chain E residue 228 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 73 optimal weight: 4.9990 chunk 19 optimal weight: 2.9990 chunk 44 optimal weight: 1.9990 chunk 26 optimal weight: 0.8980 chunk 32 optimal weight: 0.4980 chunk 11 optimal weight: 0.7980 chunk 29 optimal weight: 0.5980 chunk 25 optimal weight: 4.9990 chunk 67 optimal weight: 6.9990 chunk 51 optimal weight: 0.9980 chunk 58 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 198 ASN ** E 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.136247 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.113504 restraints weight = 10945.284| |-----------------------------------------------------------------------------| r_work (start): 0.3077 rms_B_bonded: 1.52 r_work: 0.2954 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.2818 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.2818 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 moved from start: 0.2895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9655 Z= 0.177 Angle : 0.503 5.350 13075 Z= 0.257 Chirality : 0.038 0.113 1610 Planarity : 0.004 0.035 1630 Dihedral : 6.075 59.715 1320 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 3.68 % Allowed : 17.31 % Favored : 79.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.06 (0.22), residues: 1255 helix: -1.10 (0.16), residues: 1000 sheet: None (None), residues: 0 loop : -1.69 (0.32), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 147 HIS 0.001 0.000 HIS E 0 PHE 0.007 0.001 PHE A 200 TYR 0.007 0.001 TYR D 222 ARG 0.001 0.000 ARG E 57 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2510 Ramachandran restraints generated. 1255 Oldfield, 0 Emsley, 1255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2510 Ramachandran restraints generated. 1255 Oldfield, 0 Emsley, 1255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 143 time to evaluate : 1.076 Fit side-chains REVERT: A 53 LYS cc_start: 0.8132 (mmtp) cc_final: 0.7801 (mmtm) REVERT: A 106 ASP cc_start: 0.8393 (p0) cc_final: 0.8054 (p0) REVERT: A 244 ILE cc_start: 0.8366 (OUTLIER) cc_final: 0.8160 (mm) REVERT: B 7 ILE cc_start: 0.8553 (OUTLIER) cc_final: 0.8209 (tt) REVERT: B 17 LEU cc_start: 0.8267 (OUTLIER) cc_final: 0.7936 (tp) REVERT: B 88 ARG cc_start: 0.7561 (ttm-80) cc_final: 0.7150 (ttt90) REVERT: B 122 ILE cc_start: 0.7862 (mp) cc_final: 0.7546 (mm) REVERT: B 159 MET cc_start: 0.8210 (tmm) cc_final: 0.7694 (ptm) REVERT: B 221 ILE cc_start: 0.8227 (OUTLIER) cc_final: 0.7762 (mp) REVERT: B 227 GLU cc_start: 0.8096 (tm-30) cc_final: 0.7818 (tt0) REVERT: B 236 ASN cc_start: 0.8118 (m-40) cc_final: 0.7904 (m-40) REVERT: C 2 ASP cc_start: 0.7704 (OUTLIER) cc_final: 0.7375 (t70) REVERT: C 17 LEU cc_start: 0.8648 (OUTLIER) cc_final: 0.8392 (tp) REVERT: C 43 MET cc_start: 0.8429 (tpp) cc_final: 0.8089 (mmt) REVERT: C 69 LYS cc_start: 0.9042 (OUTLIER) cc_final: 0.8823 (mttt) REVERT: C 89 LYS cc_start: 0.8120 (tptt) cc_final: 0.7683 (mptt) REVERT: C 206 ASN cc_start: 0.9017 (t0) cc_final: 0.8497 (t0) REVERT: C 223 ILE cc_start: 0.8425 (OUTLIER) cc_final: 0.7827 (mp) REVERT: D 90 GLU cc_start: 0.8480 (mp0) cc_final: 0.7991 (mt-10) REVERT: D 112 MET cc_start: 0.8439 (ttp) cc_final: 0.8168 (mtp) REVERT: D 159 MET cc_start: 0.8367 (tmm) cc_final: 0.7928 (ttt) REVERT: D 227 GLU cc_start: 0.7953 (tt0) cc_final: 0.7646 (tt0) REVERT: E 136 LEU cc_start: 0.8541 (tt) cc_final: 0.8313 (tp) REVERT: E 137 ASP cc_start: 0.8462 (t0) cc_final: 0.8139 (t0) REVERT: E 228 LYS cc_start: 0.7736 (OUTLIER) cc_final: 0.7368 (mttt) outliers start: 37 outliers final: 24 residues processed: 169 average time/residue: 0.1783 time to fit residues: 44.3928 Evaluate side-chains 175 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 142 time to evaluate : 0.995 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 112 MET Chi-restraints excluded: chain A residue 137 ASP Chi-restraints excluded: chain A residue 152 ASP Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain A residue 244 ILE Chi-restraints excluded: chain B residue 7 ILE Chi-restraints excluded: chain B residue 9 ILE Chi-restraints excluded: chain B residue 17 LEU Chi-restraints excluded: chain B residue 43 MET Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain B residue 187 LEU Chi-restraints excluded: chain B residue 221 ILE Chi-restraints excluded: chain C residue 2 ASP Chi-restraints excluded: chain C residue 17 LEU Chi-restraints excluded: chain C residue 67 LEU Chi-restraints excluded: chain C residue 69 LYS Chi-restraints excluded: chain C residue 223 ILE Chi-restraints excluded: chain C residue 226 ILE Chi-restraints excluded: chain C residue 229 ILE Chi-restraints excluded: chain D residue 22 ILE Chi-restraints excluded: chain D residue 67 LEU Chi-restraints excluded: chain D residue 88 ARG Chi-restraints excluded: chain D residue 113 ILE Chi-restraints excluded: chain D residue 198 ASN Chi-restraints excluded: chain E residue -1 VAL Chi-restraints excluded: chain E residue 21 LEU Chi-restraints excluded: chain E residue 67 LEU Chi-restraints excluded: chain E residue 221 ILE Chi-restraints excluded: chain E residue 226 ILE Chi-restraints excluded: chain E residue 228 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 71 optimal weight: 0.6980 chunk 15 optimal weight: 0.5980 chunk 58 optimal weight: 2.9990 chunk 116 optimal weight: 0.7980 chunk 115 optimal weight: 0.8980 chunk 33 optimal weight: 0.9990 chunk 84 optimal weight: 0.7980 chunk 112 optimal weight: 2.9990 chunk 117 optimal weight: 0.0050 chunk 49 optimal weight: 0.7980 chunk 38 optimal weight: 2.9990 overall best weight: 0.5794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 198 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 = 0.3431 r_free = 0.3431 target = 0.127477 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.105003 restraints weight = 11034.921| |-----------------------------------------------------------------------------| r_work (start): 0.3127 rms_B_bonded: 1.45 r_work: 0.3014 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.2884 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.2884 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8287 moved from start: 0.3019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9655 Z= 0.160 Angle : 0.486 5.200 13075 Z= 0.249 Chirality : 0.038 0.112 1610 Planarity : 0.003 0.033 1630 Dihedral : 5.945 59.530 1319 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 3.98 % Allowed : 17.21 % Favored : 78.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.60 (0.23), residues: 1255 helix: -0.77 (0.16), residues: 980 sheet: None (None), residues: 0 loop : -1.51 (0.31), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 147 HIS 0.002 0.000 HIS A 0 PHE 0.007 0.001 PHE A 200 TYR 0.007 0.001 TYR D 222 ARG 0.001 0.000 ARG E 88 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2510 Ramachandran restraints generated. 1255 Oldfield, 0 Emsley, 1255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2510 Ramachandran restraints generated. 1255 Oldfield, 0 Emsley, 1255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 145 time to evaluate : 1.033 Fit side-chains REVERT: A 53 LYS cc_start: 0.8119 (mmtp) cc_final: 0.7783 (mmtm) REVERT: A 106 ASP cc_start: 0.8364 (p0) cc_final: 0.8035 (p0) REVERT: A 244 ILE cc_start: 0.8334 (OUTLIER) cc_final: 0.8134 (mm) REVERT: B 7 ILE cc_start: 0.8571 (OUTLIER) cc_final: 0.8240 (tt) REVERT: B 17 LEU cc_start: 0.8220 (OUTLIER) cc_final: 0.7880 (tp) REVERT: B 88 ARG cc_start: 0.7573 (ttm-80) cc_final: 0.7215 (ttt90) REVERT: B 159 MET cc_start: 0.8135 (tmm) cc_final: 0.7593 (ptm) REVERT: B 221 ILE cc_start: 0.8198 (OUTLIER) cc_final: 0.7744 (mp) REVERT: B 236 ASN cc_start: 0.8091 (m-40) cc_final: 0.7888 (m-40) REVERT: C 2 ASP cc_start: 0.7683 (OUTLIER) cc_final: 0.7362 (t70) REVERT: C 43 MET cc_start: 0.8382 (tpp) cc_final: 0.8049 (mmt) REVERT: C 69 LYS cc_start: 0.9038 (OUTLIER) cc_final: 0.8803 (mttt) REVERT: C 89 LYS cc_start: 0.8102 (tptt) cc_final: 0.7670 (mptt) REVERT: C 206 ASN cc_start: 0.8980 (t0) cc_final: 0.8440 (t0) REVERT: C 223 ILE cc_start: 0.8418 (OUTLIER) cc_final: 0.7800 (mp) REVERT: C 245 MET cc_start: 0.8007 (mtm) cc_final: 0.7750 (mtp) REVERT: D 90 GLU cc_start: 0.8499 (OUTLIER) cc_final: 0.8037 (mt-10) REVERT: D 138 GLU cc_start: 0.8149 (mm-30) cc_final: 0.6722 (mt-10) REVERT: D 159 MET cc_start: 0.8318 (tmm) cc_final: 0.7882 (ttt) REVERT: D 198 ASN cc_start: 0.8655 (OUTLIER) cc_final: 0.8383 (t0) REVERT: D 227 GLU cc_start: 0.7889 (tt0) cc_final: 0.7598 (tt0) REVERT: E 136 LEU cc_start: 0.8499 (tt) cc_final: 0.8286 (tp) REVERT: E 137 ASP cc_start: 0.8430 (t0) cc_final: 0.8093 (t0) REVERT: E 228 LYS cc_start: 0.7700 (mptm) cc_final: 0.7386 (mttt) outliers start: 40 outliers final: 22 residues processed: 174 average time/residue: 0.1807 time to fit residues: 46.3152 Evaluate side-chains 171 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 140 time to evaluate : 1.051 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue -1 VAL Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 142 THR Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain A residue 244 ILE Chi-restraints excluded: chain B residue 7 ILE Chi-restraints excluded: chain B residue 9 ILE Chi-restraints excluded: chain B residue 17 LEU Chi-restraints excluded: chain B residue 43 MET Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain B residue 221 ILE Chi-restraints excluded: chain C residue 2 ASP Chi-restraints excluded: chain C residue 67 LEU Chi-restraints excluded: chain C residue 69 LYS Chi-restraints excluded: chain C residue 223 ILE Chi-restraints excluded: chain C residue 226 ILE Chi-restraints excluded: chain C residue 229 ILE Chi-restraints excluded: chain D residue 67 LEU Chi-restraints excluded: chain D residue 88 ARG Chi-restraints excluded: chain D residue 90 GLU Chi-restraints excluded: chain D residue 113 ILE Chi-restraints excluded: chain D residue 185 VAL Chi-restraints excluded: chain D residue 198 ASN Chi-restraints excluded: chain E residue -1 VAL Chi-restraints excluded: chain E residue 32 VAL Chi-restraints excluded: chain E residue 59 VAL Chi-restraints excluded: chain E residue 67 LEU Chi-restraints excluded: chain E residue 221 ILE Chi-restraints excluded: chain E residue 226 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 113 optimal weight: 0.9980 chunk 71 optimal weight: 1.9990 chunk 11 optimal weight: 0.7980 chunk 5 optimal weight: 0.7980 chunk 82 optimal weight: 0.0770 chunk 58 optimal weight: 2.9990 chunk 9 optimal weight: 5.9990 chunk 114 optimal weight: 0.9980 chunk 55 optimal weight: 0.3980 chunk 47 optimal weight: 2.9990 chunk 123 optimal weight: 1.9990 overall best weight: 0.6138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 206 ASN D 135 GLN D 198 ASN ** E 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.137343 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.116714 restraints weight = 10975.039| |-----------------------------------------------------------------------------| r_work (start): 0.3305 rms_B_bonded: 1.31 r_work: 0.3181 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.3058 rms_B_bonded: 3.38 restraints_weight: 0.2500 r_work (final): 0.3058 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8278 moved from start: 0.3156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 9655 Z= 0.165 Angle : 0.491 5.250 13075 Z= 0.251 Chirality : 0.038 0.112 1610 Planarity : 0.003 0.034 1630 Dihedral : 5.690 59.593 1313 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 3.78 % Allowed : 18.01 % Favored : 78.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.23 (0.23), residues: 1255 helix: -0.49 (0.17), residues: 980 sheet: None (None), residues: 0 loop : -1.46 (0.31), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 147 HIS 0.002 0.000 HIS A 0 PHE 0.010 0.001 PHE E 157 TYR 0.006 0.001 TYR D 222 ARG 0.001 0.000 ARG E 57 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2510 Ramachandran restraints generated. 1255 Oldfield, 0 Emsley, 1255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2510 Ramachandran restraints generated. 1255 Oldfield, 0 Emsley, 1255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 148 time to evaluate : 1.027 Fit side-chains REVERT: A 53 LYS cc_start: 0.8124 (mmtp) cc_final: 0.7782 (mmtm) REVERT: A 106 ASP cc_start: 0.8372 (p0) cc_final: 0.8034 (p0) REVERT: B 7 ILE cc_start: 0.8554 (OUTLIER) cc_final: 0.8228 (tt) REVERT: B 17 LEU cc_start: 0.8151 (OUTLIER) cc_final: 0.7808 (tp) REVERT: B 159 MET cc_start: 0.8130 (tmm) cc_final: 0.7583 (ptm) REVERT: B 221 ILE cc_start: 0.8222 (OUTLIER) cc_final: 0.7781 (mp) REVERT: C 2 ASP cc_start: 0.7653 (OUTLIER) cc_final: 0.7347 (t70) REVERT: C 17 LEU cc_start: 0.8599 (OUTLIER) cc_final: 0.8363 (tp) REVERT: C 43 MET cc_start: 0.8388 (tpp) cc_final: 0.8061 (mmt) REVERT: C 69 LYS cc_start: 0.9067 (OUTLIER) cc_final: 0.8844 (mttt) REVERT: C 89 LYS cc_start: 0.8094 (tptt) cc_final: 0.7647 (mptt) REVERT: C 206 ASN cc_start: 0.8912 (t0) cc_final: 0.8485 (t0) REVERT: C 223 ILE cc_start: 0.8447 (OUTLIER) cc_final: 0.7815 (mp) REVERT: C 230 GLN cc_start: 0.6889 (OUTLIER) cc_final: 0.6669 (tt0) REVERT: D 90 GLU cc_start: 0.8535 (OUTLIER) cc_final: 0.8078 (mt-10) REVERT: D 138 GLU cc_start: 0.8061 (mm-30) cc_final: 0.6622 (mt-10) REVERT: D 159 MET cc_start: 0.8302 (tmm) cc_final: 0.7847 (ttt) REVERT: D 227 GLU cc_start: 0.7814 (tt0) cc_final: 0.7542 (tt0) REVERT: E 17 LEU cc_start: 0.8403 (OUTLIER) cc_final: 0.8100 (tp) REVERT: E 137 ASP cc_start: 0.8477 (t0) cc_final: 0.8162 (t0) REVERT: E 224 GLU cc_start: 0.7922 (mm-30) cc_final: 0.7701 (mp0) REVERT: E 228 LYS cc_start: 0.7776 (mptm) cc_final: 0.7459 (mttt) outliers start: 38 outliers final: 23 residues processed: 179 average time/residue: 0.1873 time to fit residues: 49.5026 Evaluate side-chains 174 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 141 time to evaluate : 1.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue -1 VAL Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 142 THR Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain B residue 7 ILE Chi-restraints excluded: chain B residue 9 ILE Chi-restraints excluded: chain B residue 17 LEU Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain B residue 221 ILE Chi-restraints excluded: chain C residue 2 ASP Chi-restraints excluded: chain C residue 17 LEU Chi-restraints excluded: chain C residue 67 LEU Chi-restraints excluded: chain C residue 69 LYS Chi-restraints excluded: chain C residue 223 ILE Chi-restraints excluded: chain C residue 226 ILE Chi-restraints excluded: chain C residue 229 ILE Chi-restraints excluded: chain C residue 230 GLN Chi-restraints excluded: chain D residue 22 ILE Chi-restraints excluded: chain D residue 67 LEU Chi-restraints excluded: chain D residue 88 ARG Chi-restraints excluded: chain D residue 90 GLU Chi-restraints excluded: chain D residue 113 ILE Chi-restraints excluded: chain D residue 137 ASP Chi-restraints excluded: chain D residue 185 VAL Chi-restraints excluded: chain D residue 198 ASN Chi-restraints excluded: chain D residue 229 ILE Chi-restraints excluded: chain E residue 17 LEU Chi-restraints excluded: chain E residue 32 VAL Chi-restraints excluded: chain E residue 59 VAL Chi-restraints excluded: chain E residue 67 LEU Chi-restraints excluded: chain E residue 221 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 6 optimal weight: 3.9990 chunk 10 optimal weight: 0.2980 chunk 14 optimal weight: 0.9990 chunk 89 optimal weight: 0.9980 chunk 70 optimal weight: 0.5980 chunk 80 optimal weight: 0.3980 chunk 36 optimal weight: 0.6980 chunk 1 optimal weight: 3.9990 chunk 33 optimal weight: 0.7980 chunk 28 optimal weight: 0.2980 chunk 62 optimal weight: 3.9990 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 206 ASN ** E 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.138231 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.117424 restraints weight = 10853.446| |-----------------------------------------------------------------------------| r_work (start): 0.3147 rms_B_bonded: 1.31 r_work: 0.3026 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.2902 rms_B_bonded: 3.29 restraints_weight: 0.2500 r_work (final): 0.2902 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 moved from start: 0.3276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 9655 Z= 0.149 Angle : 0.484 6.656 13075 Z= 0.246 Chirality : 0.038 0.110 1610 Planarity : 0.003 0.035 1630 Dihedral : 5.608 59.658 1313 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 3.18 % Allowed : 18.91 % Favored : 77.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.94 (0.23), residues: 1255 helix: -0.26 (0.17), residues: 985 sheet: None (None), residues: 0 loop : -1.51 (0.31), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 147 HIS 0.001 0.000 HIS E 0 PHE 0.006 0.001 PHE A 200 TYR 0.007 0.001 TYR D 222 ARG 0.001 0.000 ARG B 88 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2510 Ramachandran restraints generated. 1255 Oldfield, 0 Emsley, 1255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2510 Ramachandran restraints generated. 1255 Oldfield, 0 Emsley, 1255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 144 time to evaluate : 0.930 Fit side-chains REVERT: A 53 LYS cc_start: 0.8128 (mmtp) cc_final: 0.7795 (mmtm) REVERT: A 106 ASP cc_start: 0.8352 (p0) cc_final: 0.8015 (p0) REVERT: B 7 ILE cc_start: 0.8548 (OUTLIER) cc_final: 0.8220 (tt) REVERT: B 17 LEU cc_start: 0.8163 (OUTLIER) cc_final: 0.7814 (tp) REVERT: B 159 MET cc_start: 0.8174 (tmm) cc_final: 0.7600 (ptm) REVERT: B 221 ILE cc_start: 0.8207 (OUTLIER) cc_final: 0.7795 (mp) REVERT: C 2 ASP cc_start: 0.7628 (OUTLIER) cc_final: 0.7330 (t70) REVERT: C 17 LEU cc_start: 0.8588 (OUTLIER) cc_final: 0.8356 (tp) REVERT: C 43 MET cc_start: 0.8254 (tpp) cc_final: 0.7964 (mmt) REVERT: C 69 LYS cc_start: 0.9064 (OUTLIER) cc_final: 0.8846 (mttt) REVERT: C 89 LYS cc_start: 0.8124 (tptt) cc_final: 0.7692 (mptt) REVERT: C 206 ASN cc_start: 0.8922 (t0) cc_final: 0.8395 (t0) REVERT: C 223 ILE cc_start: 0.8419 (OUTLIER) cc_final: 0.7789 (mp) REVERT: C 230 GLN cc_start: 0.6872 (OUTLIER) cc_final: 0.6561 (tt0) REVERT: D 90 GLU cc_start: 0.8525 (OUTLIER) cc_final: 0.8087 (mt-10) REVERT: D 138 GLU cc_start: 0.7980 (mm-30) cc_final: 0.6579 (mt-10) REVERT: D 159 MET cc_start: 0.8281 (tmm) cc_final: 0.7836 (ttt) REVERT: D 227 GLU cc_start: 0.7801 (tt0) cc_final: 0.7518 (tt0) REVERT: E 17 LEU cc_start: 0.8375 (OUTLIER) cc_final: 0.8069 (tp) REVERT: E 82 GLU cc_start: 0.7623 (tt0) cc_final: 0.7218 (mt-10) REVERT: E 137 ASP cc_start: 0.8335 (t0) cc_final: 0.8030 (t0) REVERT: E 224 GLU cc_start: 0.7933 (mm-30) cc_final: 0.7677 (mp0) REVERT: E 228 LYS cc_start: 0.7762 (mptm) cc_final: 0.7346 (mttt) outliers start: 32 outliers final: 19 residues processed: 169 average time/residue: 0.1850 time to fit residues: 46.6298 Evaluate side-chains 167 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 138 time to evaluate : 1.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 142 THR Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain B residue 7 ILE Chi-restraints excluded: chain B residue 9 ILE Chi-restraints excluded: chain B residue 17 LEU Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain B residue 221 ILE Chi-restraints excluded: chain C residue 2 ASP Chi-restraints excluded: chain C residue 17 LEU Chi-restraints excluded: chain C residue 67 LEU Chi-restraints excluded: chain C residue 69 LYS Chi-restraints excluded: chain C residue 223 ILE Chi-restraints excluded: chain C residue 226 ILE Chi-restraints excluded: chain C residue 229 ILE Chi-restraints excluded: chain C residue 230 GLN Chi-restraints excluded: chain D residue 22 ILE Chi-restraints excluded: chain D residue 67 LEU Chi-restraints excluded: chain D residue 88 ARG Chi-restraints excluded: chain D residue 90 GLU Chi-restraints excluded: chain D residue 113 ILE Chi-restraints excluded: chain D residue 137 ASP Chi-restraints excluded: chain D residue 229 ILE Chi-restraints excluded: chain E residue 17 LEU Chi-restraints excluded: chain E residue 59 VAL Chi-restraints excluded: chain E residue 67 LEU Chi-restraints excluded: chain E residue 221 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 15 optimal weight: 0.5980 chunk 18 optimal weight: 2.9990 chunk 23 optimal weight: 0.7980 chunk 13 optimal weight: 4.9990 chunk 56 optimal weight: 0.7980 chunk 91 optimal weight: 1.9990 chunk 79 optimal weight: 3.9990 chunk 110 optimal weight: 0.0050 chunk 104 optimal weight: 1.9990 chunk 90 optimal weight: 0.5980 chunk 75 optimal weight: 5.9990 overall best weight: 0.5594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 198 ASN C 206 ASN D 198 ASN ** E 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.131228 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.108658 restraints weight = 10971.337| |-----------------------------------------------------------------------------| r_work (start): 0.3100 rms_B_bonded: 1.49 r_work: 0.2985 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.2852 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.2852 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8270 moved from start: 0.3350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 9655 Z= 0.155 Angle : 0.484 6.627 13075 Z= 0.245 Chirality : 0.038 0.111 1610 Planarity : 0.003 0.035 1630 Dihedral : 5.522 59.717 1313 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 3.18 % Allowed : 19.40 % Favored : 77.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.62 (0.23), residues: 1255 helix: -0.02 (0.17), residues: 985 sheet: None (None), residues: 0 loop : -1.42 (0.31), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 147 HIS 0.001 0.000 HIS E 0 PHE 0.009 0.001 PHE D 36 TYR 0.006 0.001 TYR D 222 ARG 0.002 0.000 ARG B 57 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2510 Ramachandran restraints generated. 1255 Oldfield, 0 Emsley, 1255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2510 Ramachandran restraints generated. 1255 Oldfield, 0 Emsley, 1255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 145 time to evaluate : 1.098 Fit side-chains REVERT: A 53 LYS cc_start: 0.8127 (mmtp) cc_final: 0.7797 (mmtm) REVERT: A 106 ASP cc_start: 0.8374 (p0) cc_final: 0.8039 (p0) REVERT: B 7 ILE cc_start: 0.8530 (OUTLIER) cc_final: 0.8199 (tt) REVERT: B 17 LEU cc_start: 0.8170 (OUTLIER) cc_final: 0.7821 (tp) REVERT: B 221 ILE cc_start: 0.8179 (OUTLIER) cc_final: 0.7719 (mp) REVERT: B 227 GLU cc_start: 0.8093 (tm-30) cc_final: 0.7724 (tt0) REVERT: C 2 ASP cc_start: 0.7664 (OUTLIER) cc_final: 0.7360 (t70) REVERT: C 17 LEU cc_start: 0.8664 (OUTLIER) cc_final: 0.8455 (tp) REVERT: C 43 MET cc_start: 0.8320 (tpp) cc_final: 0.8014 (mmt) REVERT: C 69 LYS cc_start: 0.9053 (OUTLIER) cc_final: 0.8815 (mttt) REVERT: C 89 LYS cc_start: 0.8114 (tptt) cc_final: 0.7659 (mptt) REVERT: C 206 ASN cc_start: 0.8898 (t0) cc_final: 0.8453 (t0) REVERT: C 223 ILE cc_start: 0.8401 (OUTLIER) cc_final: 0.7767 (mp) REVERT: D 90 GLU cc_start: 0.8487 (OUTLIER) cc_final: 0.8046 (mt-10) REVERT: D 138 GLU cc_start: 0.7997 (mm-30) cc_final: 0.6560 (mt-10) REVERT: D 159 MET cc_start: 0.8333 (tmm) cc_final: 0.7909 (ttt) REVERT: D 227 GLU cc_start: 0.7860 (tt0) cc_final: 0.7546 (tt0) REVERT: E 17 LEU cc_start: 0.8345 (OUTLIER) cc_final: 0.8043 (tp) REVERT: E 137 ASP cc_start: 0.8355 (t0) cc_final: 0.8060 (t0) REVERT: E 224 GLU cc_start: 0.7930 (mm-30) cc_final: 0.7659 (mp0) REVERT: E 228 LYS cc_start: 0.7682 (mptm) cc_final: 0.7263 (mttt) outliers start: 32 outliers final: 22 residues processed: 171 average time/residue: 0.1837 time to fit residues: 46.3525 Evaluate side-chains 173 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 142 time to evaluate : 0.989 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 112 MET Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain B residue 7 ILE Chi-restraints excluded: chain B residue 9 ILE Chi-restraints excluded: chain B residue 17 LEU Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain B residue 221 ILE Chi-restraints excluded: chain C residue 2 ASP Chi-restraints excluded: chain C residue 17 LEU Chi-restraints excluded: chain C residue 67 LEU Chi-restraints excluded: chain C residue 69 LYS Chi-restraints excluded: chain C residue 188 ILE Chi-restraints excluded: chain C residue 223 ILE Chi-restraints excluded: chain C residue 226 ILE Chi-restraints excluded: chain D residue 22 ILE Chi-restraints excluded: chain D residue 67 LEU Chi-restraints excluded: chain D residue 88 ARG Chi-restraints excluded: chain D residue 90 GLU Chi-restraints excluded: chain D residue 113 ILE Chi-restraints excluded: chain D residue 137 ASP Chi-restraints excluded: chain D residue 185 VAL Chi-restraints excluded: chain D residue 198 ASN Chi-restraints excluded: chain D residue 229 ILE Chi-restraints excluded: chain E residue 17 LEU Chi-restraints excluded: chain E residue 32 VAL Chi-restraints excluded: chain E residue 59 VAL Chi-restraints excluded: chain E residue 67 LEU Chi-restraints excluded: chain E residue 221 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 86 optimal weight: 0.0370 chunk 88 optimal weight: 3.9990 chunk 111 optimal weight: 0.6980 chunk 87 optimal weight: 0.8980 chunk 71 optimal weight: 1.9990 chunk 110 optimal weight: 0.9990 chunk 59 optimal weight: 4.9990 chunk 82 optimal weight: 0.0050 chunk 65 optimal weight: 0.9980 chunk 76 optimal weight: 1.9990 chunk 53 optimal weight: 0.0170 overall best weight: 0.3310 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 206 ASN ** E 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.138371 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.117626 restraints weight = 10913.091| |-----------------------------------------------------------------------------| r_work (start): 0.3159 rms_B_bonded: 1.34 r_work: 0.3045 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.2923 rms_B_bonded: 3.17 restraints_weight: 0.2500 r_work (final): 0.2923 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8239 moved from start: 0.3375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.083 9655 Z= 0.166 Angle : 0.854 59.200 13075 Z= 0.509 Chirality : 0.038 0.111 1610 Planarity : 0.003 0.035 1630 Dihedral : 5.550 59.725 1313 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 3.28 % Allowed : 19.20 % Favored : 77.51 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.59 (0.23), residues: 1255 helix: 0.00 (0.17), residues: 985 sheet: None (None), residues: 0 loop : -1.41 (0.31), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 147 HIS 0.001 0.000 HIS E 0 PHE 0.009 0.001 PHE E 157 TYR 0.006 0.001 TYR D 222 ARG 0.002 0.000 ARG B 88 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4103.63 seconds wall clock time: 73 minutes 45.36 seconds (4425.36 seconds total)