Starting phenix.real_space_refine on Thu Feb 13 17:07:51 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7yoo_33985/02_2025/7yoo_33985.cif Found real_map, /net/cci-nas-00/data/ceres_data/7yoo_33985/02_2025/7yoo_33985.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.11 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7yoo_33985/02_2025/7yoo_33985.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7yoo_33985/02_2025/7yoo_33985.map" model { file = "/net/cci-nas-00/data/ceres_data/7yoo_33985/02_2025/7yoo_33985.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7yoo_33985/02_2025/7yoo_33985.cif" } resolution = 3.11 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= 0.021 sd= 0.083 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 61 5.16 5 C 5856 2.51 5 N 1559 2.21 5 O 1712 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 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: 9188 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1743 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1743 Classifications: {'peptide': 216} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 213} Chain breaks: 2 Chain: "B" Number of atoms: 2576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2576 Classifications: {'peptide': 335} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 329} Chain: "G" Number of atoms: 418 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 418 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 4, 'TRANS': 49} Chain: "L" Number of atoms: 255 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 255 Classifications: {'peptide': 29} Link IDs: {'PTRANS': 3, 'TRANS': 25} Chain breaks: 1 Chain: "R" Number of atoms: 2402 Number of conformers: 1 Conformer: "" Number of residues, atoms: 302, 2402 Classifications: {'peptide': 302} Link IDs: {'PTRANS': 10, 'TRANS': 291} Chain: "S" Number of atoms: 1794 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1794 Classifications: {'peptide': 233} Link IDs: {'PTRANS': 10, 'TRANS': 222} Chain breaks: 1 Time building chain proxies: 6.72, per 1000 atoms: 0.73 Number of scatterers: 9188 At special positions: 0 Unit cell: (122.018, 138.006, 108.554, 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 61 16.00 O 1712 8.00 N 1559 7.00 C 5856 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS B 121 " - pdb=" SG CYS B 149 " distance=2.04 Simple disulfide: pdb=" SG CYS R 123 " - pdb=" SG CYS R 203 " distance=2.03 Simple disulfide: pdb=" SG CYS S 22 " - pdb=" SG CYS S 96 " distance=2.03 Simple disulfide: pdb=" SG CYS S 159 " - pdb=" SG CYS S 229 " distance=2.03 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: 2.24 Conformation dependent library (CDL) restraints added in 1.1 seconds 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2192 Finding SS restraints... Secondary structure from input PDB file: 33 helices and 15 sheets defined 37.8% alpha, 21.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.93 Creating SS restraints... Processing helix chain 'A' and resid 6 through 28 removed outlier: 3.582A pdb=" N VAL A 13 " --> pdb=" O ASP A 9 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLU A 14 " --> pdb=" O LYS A 10 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ARG A 15 " --> pdb=" O ALA A 11 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ASN A 22 " --> pdb=" O MET A 18 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N GLU A 28 " --> pdb=" O ARG A 24 " (cutoff:3.500A) Processing helix chain 'A' and resid 29 through 33 removed outlier: 4.052A pdb=" N GLU A 33 " --> pdb=" O ALA A 30 " (cutoff:3.500A) Processing helix chain 'A' and resid 46 through 54 removed outlier: 3.647A pdb=" N VAL A 50 " --> pdb=" O LYS A 46 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LYS A 51 " --> pdb=" O SER A 47 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LYS A 54 " --> pdb=" O VAL A 50 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 212 removed outlier: 4.030A pdb=" N TRP A 211 " --> pdb=" O GLU A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 216 removed outlier: 3.500A pdb=" N GLU A 216 " --> pdb=" O HIS A 213 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 213 through 216' Processing helix chain 'A' and resid 242 through 255 removed outlier: 3.747A pdb=" N SER A 246 " --> pdb=" O ARG A 242 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 279 removed outlier: 3.624A pdb=" N GLU A 276 " --> pdb=" O ASP A 272 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N LYS A 279 " --> pdb=" O GLU A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 309 removed outlier: 3.616A pdb=" N ALA A 299 " --> pdb=" O THR A 295 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N PHE A 307 " --> pdb=" O ILE A 303 " (cutoff:3.500A) Processing helix chain 'A' and resid 329 through 351 removed outlier: 3.557A pdb=" N VAL A 335 " --> pdb=" O ASN A 331 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ILE A 344 " --> pdb=" O THR A 340 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LEU A 348 " --> pdb=" O ILE A 344 " (cutoff:3.500A) Processing helix chain 'B' and resid 7 through 26 removed outlier: 3.531A pdb=" N ARG B 19 " --> pdb=" O LYS B 15 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ALA B 24 " --> pdb=" O ASP B 20 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'B' and resid 35 through 37 No H-bonds generated for 'chain 'B' and resid 35 through 37' Processing helix chain 'G' and resid 12 through 24 removed outlier: 4.026A pdb=" N VAL G 16 " --> pdb=" O ALA G 12 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N GLU G 17 " --> pdb=" O ARG G 13 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLN G 18 " --> pdb=" O LYS G 14 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LEU G 19 " --> pdb=" O LEU G 15 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N MET G 21 " --> pdb=" O GLU G 17 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLU G 22 " --> pdb=" O GLN G 18 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N ASN G 24 " --> pdb=" O LYS G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 removed outlier: 3.744A pdb=" N ASP G 36 " --> pdb=" O LYS G 32 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N LEU G 37 " --> pdb=" O ALA G 33 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLU G 42 " --> pdb=" O MET G 38 " (cutoff:3.500A) Processing helix chain 'G' and resid 45 through 48 Processing helix chain 'L' and resid 17 through 32 Processing helix chain 'R' and resid 42 through 45 Processing helix chain 'R' and resid 46 through 78 removed outlier: 3.614A pdb=" N VAL R 52 " --> pdb=" O GLU R 48 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LEU R 70 " --> pdb=" O ILE R 66 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N VAL R 71 " --> pdb=" O GLY R 67 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ILE R 72 " --> pdb=" O ASN R 68 " (cutoff:3.500A) Processing helix chain 'R' and resid 83 through 113 removed outlier: 3.530A pdb=" N PHE R 88 " --> pdb=" O VAL R 84 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ILE R 89 " --> pdb=" O THR R 85 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N LEU R 104 " --> pdb=" O ASN R 100 " (cutoff:3.500A) Proline residue: R 105 - end of helix Processing helix chain 'R' and resid 119 through 124 removed outlier: 4.032A pdb=" N HIS R 124 " --> pdb=" O PRO R 120 " (cutoff:3.500A) Processing helix chain 'R' and resid 125 through 153 removed outlier: 3.960A pdb=" N VAL R 134 " --> pdb=" O GLN R 130 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLN R 135 " --> pdb=" O GLY R 131 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N THR R 142 " --> pdb=" O THR R 138 " (cutoff:3.500A) Processing helix chain 'R' and resid 161 through 180 removed outlier: 3.519A pdb=" N TRP R 173 " --> pdb=" O ILE R 169 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEU R 178 " --> pdb=" O GLY R 174 " (cutoff:3.500A) Processing helix chain 'R' and resid 180 through 186 removed outlier: 4.183A pdb=" N ALA R 184 " --> pdb=" O ALA R 180 " (cutoff:3.500A) Processing helix chain 'R' and resid 213 through 228 removed outlier: 4.264A pdb=" N THR R 217 " --> pdb=" O SER R 213 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N TYR R 219 " --> pdb=" O TYR R 215 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N SER R 220 " --> pdb=" O GLY R 216 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LEU R 221 " --> pdb=" O THR R 217 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LEU R 225 " --> pdb=" O LEU R 221 " (cutoff:3.500A) Processing helix chain 'R' and resid 228 through 248 removed outlier: 3.576A pdb=" N LEU R 232 " --> pdb=" O TYR R 228 " (cutoff:3.500A) Processing helix chain 'R' and resid 255 through 281 removed outlier: 3.542A pdb=" N TYR R 259 " --> pdb=" O ALA R 255 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLN R 264 " --> pdb=" O HIS R 260 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N LYS R 265 " --> pdb=" O GLN R 261 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N THR R 266 " --> pdb=" O ARG R 262 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N THR R 267 " --> pdb=" O ARG R 263 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N LYS R 268 " --> pdb=" O GLN R 264 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N MET R 269 " --> pdb=" O LYS R 265 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N VAL R 273 " --> pdb=" O MET R 269 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N VAL R 274 " --> pdb=" O LEU R 270 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N PHE R 277 " --> pdb=" O VAL R 273 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N TRP R 281 " --> pdb=" O PHE R 277 " (cutoff:3.500A) Processing helix chain 'R' and resid 281 through 294 Processing helix chain 'R' and resid 302 through 315 Processing helix chain 'R' and resid 316 through 319 Processing helix chain 'R' and resid 320 through 325 Processing helix chain 'R' and resid 329 through 341 removed outlier: 4.005A pdb=" N LYS R 334 " --> pdb=" O SER R 330 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N ALA R 335 " --> pdb=" O ASN R 331 " (cutoff:3.500A) Processing helix chain 'S' and resid 28 through 32 removed outlier: 3.525A pdb=" N SER S 31 " --> pdb=" O ALA S 28 " (cutoff:3.500A) Processing helix chain 'S' and resid 220 through 224 removed outlier: 3.976A pdb=" N VAL S 224 " --> pdb=" O ALA S 221 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 190 removed outlier: 3.612A pdb=" N LEU A 38 " --> pdb=" O PHE A 199 " (cutoff:3.500A) removed outlier: 7.067A pdb=" N LYS A 35 " --> pdb=" O ALA A 220 " (cutoff:3.500A) removed outlier: 8.067A pdb=" N ILE A 222 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N LEU A 37 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 7.914A pdb=" N CYS A 224 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 7.467A pdb=" N LEU A 39 " --> pdb=" O CYS A 224 " (cutoff:3.500A) removed outlier: 9.298A pdb=" N ALA A 226 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N ILE A 221 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 7.858A pdb=" N PHE A 267 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N PHE A 223 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 7.296A pdb=" N ASN A 269 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N VAL A 225 " --> pdb=" O ASN A 269 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 51 removed outlier: 3.531A pdb=" N ARG B 46 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 4.020A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.087A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.868A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 4.925A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.054A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 7.139A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 5.469A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 7.147A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.576A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N CYS B 166 " --> pdb=" O THR B 179 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N THR B 179 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N LEU B 168 " --> pdb=" O THR B 177 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N GLN B 175 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.812A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.143A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.433A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.655A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 5.247A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.180A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N PHE B 241 " --> pdb=" O PHE B 253 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 275 through 278 removed outlier: 3.846A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N CYS B 294 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N VAL B 307 " --> pdb=" O CYS B 294 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N VAL B 296 " --> pdb=" O ALA B 305 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'R' and resid 188 through 195 removed outlier: 4.061A pdb=" N SER R 190 " --> pdb=" O ALA R 202 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N PHE R 198 " --> pdb=" O ILE R 194 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'S' and resid 3 through 7 Processing sheet with id=AB2, first strand: chain 'S' and resid 3 through 7 removed outlier: 3.641A pdb=" N PHE S 80 " --> pdb=" O SER S 71 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N SER S 71 " --> pdb=" O PHE S 80 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'S' and resid 11 through 12 Processing sheet with id=AB4, first strand: chain 'S' and resid 58 through 60 removed outlier: 6.603A pdb=" N TRP S 36 " --> pdb=" O VAL S 48 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N TYR S 50 " --> pdb=" O MET S 34 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N MET S 34 " --> pdb=" O TYR S 50 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N TYR S 94 " --> pdb=" O THR S 115 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N THR S 115 " --> pdb=" O TYR S 94 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'S' and resid 158 through 159 removed outlier: 3.992A pdb=" N ALA S 211 " --> pdb=" O SER S 208 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'S' and resid 194 through 195 removed outlier: 5.635A pdb=" N LEU S 187 " --> pdb=" O LEU S 178 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N LEU S 178 " --> pdb=" O LEU S 187 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ILE S 189 " --> pdb=" O TRP S 176 " (cutoff:3.500A) 378 hydrogen bonds defined for protein. 1071 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: 2.65 Time building geometry restraints manager: 2.58 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1484 1.31 - 1.44: 2578 1.44 - 1.57: 5229 1.57 - 1.70: 0 1.70 - 1.83: 88 Bond restraints: 9379 Sorted by residual: bond pdb=" C TYC L 36 " pdb=" NXT TYC L 36 " ideal model delta sigma weight residual 1.340 1.450 -0.110 2.00e-02 2.50e+03 3.05e+01 bond pdb=" CZ TYC L 36 " pdb=" OH TYC L 36 " ideal model delta sigma weight residual 1.350 1.398 -0.048 2.00e-02 2.50e+03 5.74e+00 bond pdb=" C TYC L 36 " pdb=" O TYC L 36 " ideal model delta sigma weight residual 1.231 1.184 0.047 2.00e-02 2.50e+03 5.51e+00 bond pdb=" CB TYC L 36 " pdb=" CG TYC L 36 " ideal model delta sigma weight residual 1.501 1.526 -0.025 2.00e-02 2.50e+03 1.51e+00 bond pdb=" C LEU R 104 " pdb=" N PRO R 105 " ideal model delta sigma weight residual 1.336 1.350 -0.014 1.20e-02 6.94e+03 1.36e+00 ... (remaining 9374 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.14: 12389 1.14 - 2.27: 242 2.27 - 3.41: 52 3.41 - 4.54: 10 4.54 - 5.68: 9 Bond angle restraints: 12702 Sorted by residual: angle pdb=" CA GLY B 216 " pdb=" C GLY B 216 " pdb=" N MET B 217 " ideal model delta sigma weight residual 118.67 115.93 2.74 9.80e-01 1.04e+00 7.82e+00 angle pdb=" C ARG S 191 " pdb=" N MET S 192 " pdb=" CA MET S 192 " ideal model delta sigma weight residual 121.54 126.69 -5.15 1.91e+00 2.74e-01 7.26e+00 angle pdb=" N GLY B 216 " pdb=" CA GLY B 216 " pdb=" C GLY B 216 " ideal model delta sigma weight residual 116.01 111.60 4.41 1.64e+00 3.72e-01 7.24e+00 angle pdb=" CA GLY B 216 " pdb=" C GLY B 216 " pdb=" O GLY B 216 " ideal model delta sigma weight residual 118.77 121.05 -2.28 9.40e-01 1.13e+00 5.90e+00 angle pdb=" CA CYS B 149 " pdb=" CB CYS B 149 " pdb=" SG CYS B 149 " ideal model delta sigma weight residual 114.40 118.73 -4.33 2.30e+00 1.89e-01 3.54e+00 ... (remaining 12697 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.75: 5075 17.75 - 35.50: 409 35.50 - 53.26: 90 53.26 - 71.01: 12 71.01 - 88.76: 3 Dihedral angle restraints: 5589 sinusoidal: 2191 harmonic: 3398 Sorted by residual: dihedral pdb=" CG ARG B 52 " pdb=" CD ARG B 52 " pdb=" NE ARG B 52 " pdb=" CZ ARG B 52 " ideal model delta sinusoidal sigma weight residual -180.00 -135.10 -44.90 2 1.50e+01 4.44e-03 1.06e+01 dihedral pdb=" CG ARG S 98 " pdb=" CD ARG S 98 " pdb=" NE ARG S 98 " pdb=" CZ ARG S 98 " ideal model delta sinusoidal sigma weight residual 180.00 139.00 41.00 2 1.50e+01 4.44e-03 9.18e+00 dihedral pdb=" CB LYS R 117 " pdb=" CG LYS R 117 " pdb=" CD LYS R 117 " pdb=" CE LYS R 117 " ideal model delta sinusoidal sigma weight residual -60.00 -112.40 52.40 3 1.50e+01 4.44e-03 9.11e+00 ... (remaining 5586 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 905 0.029 - 0.059: 372 0.059 - 0.088: 93 0.088 - 0.118: 66 0.118 - 0.147: 10 Chirality restraints: 1446 Sorted by residual: chirality pdb=" CA ILE R 195 " pdb=" N ILE R 195 " pdb=" C ILE R 195 " pdb=" CB ILE R 195 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.40e-01 chirality pdb=" CB VAL A 201 " pdb=" CA VAL A 201 " pdb=" CG1 VAL A 201 " pdb=" CG2 VAL A 201 " both_signs ideal model delta sigma weight residual False -2.63 -2.50 -0.13 2.00e-01 2.50e+01 4.32e-01 chirality pdb=" CA VAL B 327 " pdb=" N VAL B 327 " pdb=" C VAL B 327 " pdb=" CB VAL B 327 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.01e-01 ... (remaining 1443 not shown) Planarity restraints: 1598 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR A 287 " -0.053 5.00e-02 4.00e+02 8.01e-02 1.03e+01 pdb=" N PRO A 288 " 0.139 5.00e-02 4.00e+02 pdb=" CA PRO A 288 " -0.042 5.00e-02 4.00e+02 pdb=" CD PRO A 288 " -0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB ASP A 193 " -0.008 2.00e-02 2.50e+03 1.57e-02 2.45e+00 pdb=" CG ASP A 193 " 0.027 2.00e-02 2.50e+03 pdb=" OD1 ASP A 193 " -0.010 2.00e-02 2.50e+03 pdb=" OD2 ASP A 193 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE R 195 " -0.024 5.00e-02 4.00e+02 3.72e-02 2.21e+00 pdb=" N PRO R 196 " 0.064 5.00e-02 4.00e+02 pdb=" CA PRO R 196 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO R 196 " -0.021 5.00e-02 4.00e+02 ... (remaining 1595 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 175 2.70 - 3.25: 8642 3.25 - 3.80: 13260 3.80 - 4.35: 17677 4.35 - 4.90: 30775 Nonbonded interactions: 70529 Sorted by model distance: nonbonded pdb=" O ASP B 333 " pdb=" OD1 ASP B 333 " model vdw 2.153 3.040 nonbonded pdb=" O GLY A 40 " pdb=" OG SER A 44 " model vdw 2.283 3.040 nonbonded pdb=" NH2 ARG S 67 " pdb=" OD2 ASP S 90 " model vdw 2.286 3.120 nonbonded pdb=" OG SER S 17 " pdb=" O MET S 83 " model vdw 2.319 3.040 nonbonded pdb=" OG SER B 108 " pdb=" OD1 ASP B 154 " model vdw 2.334 3.040 ... (remaining 70524 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.010 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: 0.350 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 23.780 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.170 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7737 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.110 9379 Z= 0.177 Angle : 0.436 5.675 12702 Z= 0.229 Chirality : 0.039 0.147 1446 Planarity : 0.003 0.080 1598 Dihedral : 13.434 88.762 3385 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: -0.16 (0.25), residues: 1148 helix: -0.06 (0.27), residues: 370 sheet: 0.37 (0.34), residues: 251 loop : -0.23 (0.27), residues: 527 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP S 47 HIS 0.004 0.001 HIS B 62 PHE 0.008 0.001 PHE B 199 TYR 0.009 0.001 TYR S 190 ARG 0.002 0.000 ARG B 150 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 152 time to evaluate : 0.879 Fit side-chains REVERT: A 246 SER cc_start: 0.7112 (p) cc_final: 0.6875 (p) REVERT: A 305 CYS cc_start: 0.7607 (m) cc_final: 0.7299 (m) REVERT: R 315 MET cc_start: 0.7175 (mmt) cc_final: 0.6875 (mmt) outliers start: 0 outliers final: 0 residues processed: 152 average time/residue: 0.2889 time to fit residues: 57.0168 Evaluate side-chains 128 residues out of total 1007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 128 time to evaluate : 1.050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 96 optimal weight: 1.9990 chunk 86 optimal weight: 3.9990 chunk 47 optimal weight: 0.4980 chunk 29 optimal weight: 0.0770 chunk 58 optimal weight: 5.9990 chunk 46 optimal weight: 0.0070 chunk 89 optimal weight: 1.9990 chunk 34 optimal weight: 4.9990 chunk 54 optimal weight: 10.0000 chunk 66 optimal weight: 0.6980 chunk 103 optimal weight: 0.5980 overall best weight: 0.3756 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 331 ASN ** R 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 100 ASN S 186 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.120958 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.092735 restraints weight = 16009.989| |-----------------------------------------------------------------------------| r_work (start): 0.3300 rms_B_bonded: 2.65 r_work: 0.3131 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3131 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8019 moved from start: 0.1423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 9379 Z= 0.155 Angle : 0.495 6.206 12702 Z= 0.266 Chirality : 0.041 0.165 1446 Planarity : 0.004 0.055 1598 Dihedral : 4.845 58.966 1273 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 0.99 % Allowed : 7.85 % Favored : 91.16 % 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: 0.43 (0.25), residues: 1148 helix: 0.96 (0.27), residues: 379 sheet: 0.45 (0.31), residues: 274 loop : -0.22 (0.29), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP S 47 HIS 0.003 0.001 HIS B 62 PHE 0.012 0.001 PHE R 319 TYR 0.015 0.001 TYR S 190 ARG 0.005 0.000 ARG R 241 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 145 time to evaluate : 1.027 Fit side-chains REVERT: A 246 SER cc_start: 0.7595 (p) cc_final: 0.7392 (p) REVERT: A 305 CYS cc_start: 0.7573 (m) cc_final: 0.7194 (m) REVERT: B 13 GLN cc_start: 0.8425 (tm-30) cc_final: 0.8151 (tm-30) REVERT: B 17 GLN cc_start: 0.6970 (tm-30) cc_final: 0.6586 (tm-30) REVERT: B 18 ILE cc_start: 0.7183 (mm) cc_final: 0.6968 (mt) REVERT: B 258 ASP cc_start: 0.6852 (t0) cc_final: 0.6167 (t70) REVERT: B 335 PHE cc_start: 0.8684 (m-80) cc_final: 0.8464 (m-80) REVERT: R 188 GLU cc_start: 0.7537 (pp20) cc_final: 0.7140 (tm-30) outliers start: 10 outliers final: 6 residues processed: 150 average time/residue: 0.2771 time to fit residues: 54.8926 Evaluate side-chains 138 residues out of total 1007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 132 time to evaluate : 1.022 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 206 SER Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain R residue 178 LEU Chi-restraints excluded: chain S residue 186 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 82 optimal weight: 2.9990 chunk 4 optimal weight: 3.9990 chunk 2 optimal weight: 0.9980 chunk 90 optimal weight: 2.9990 chunk 54 optimal weight: 9.9990 chunk 78 optimal weight: 0.4980 chunk 110 optimal weight: 0.9990 chunk 25 optimal weight: 0.9990 chunk 81 optimal weight: 0.9980 chunk 42 optimal weight: 1.9990 chunk 47 optimal weight: 0.0270 overall best weight: 0.7040 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 HIS A 306 GLN ** R 86 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 = 0.3755 r_free = 0.3755 target = 0.120065 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.091869 restraints weight = 16263.656| |-----------------------------------------------------------------------------| r_work (start): 0.3271 rms_B_bonded: 2.58 r_work: 0.3119 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3119 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 moved from start: 0.1621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 9379 Z= 0.208 Angle : 0.495 5.964 12702 Z= 0.263 Chirality : 0.041 0.165 1446 Planarity : 0.003 0.047 1598 Dihedral : 4.610 51.364 1273 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 1.29 % Allowed : 9.14 % Favored : 89.57 % 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: 0.53 (0.25), residues: 1148 helix: 1.28 (0.27), residues: 380 sheet: 0.29 (0.31), residues: 287 loop : -0.25 (0.29), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 211 HIS 0.004 0.001 HIS S 35 PHE 0.027 0.001 PHE R 319 TYR 0.013 0.001 TYR S 190 ARG 0.003 0.000 ARG R 241 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 135 time to evaluate : 0.977 Fit side-chains REVERT: A 53 MET cc_start: 0.7431 (mmt) cc_final: 0.7160 (mmt) REVERT: A 305 CYS cc_start: 0.7543 (m) cc_final: 0.7175 (m) REVERT: B 18 ILE cc_start: 0.7227 (mm) cc_final: 0.6963 (mt) REVERT: B 258 ASP cc_start: 0.7058 (t0) cc_final: 0.6450 (t70) REVERT: R 135 GLN cc_start: 0.8291 (OUTLIER) cc_final: 0.8006 (mt0) REVERT: R 291 VAL cc_start: 0.8050 (t) cc_final: 0.7734 (p) outliers start: 13 outliers final: 10 residues processed: 139 average time/residue: 0.2835 time to fit residues: 51.4007 Evaluate side-chains 139 residues out of total 1007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 128 time to evaluate : 1.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 199 PHE Chi-restraints excluded: chain A residue 206 SER Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain R residue 135 GLN Chi-restraints excluded: chain R residue 178 LEU Chi-restraints excluded: chain R residue 214 ILE Chi-restraints excluded: chain S residue 109 ASP Chi-restraints excluded: chain S residue 168 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 30 optimal weight: 0.4980 chunk 38 optimal weight: 0.9990 chunk 104 optimal weight: 0.0050 chunk 72 optimal weight: 0.0980 chunk 113 optimal weight: 0.9990 chunk 87 optimal weight: 0.7980 chunk 110 optimal weight: 1.9990 chunk 84 optimal weight: 0.6980 chunk 70 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 99 optimal weight: 2.9990 overall best weight: 0.4194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 HIS A 306 GLN ** R 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 258 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.120736 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.090865 restraints weight = 16145.137| |-----------------------------------------------------------------------------| r_work (start): 0.3262 rms_B_bonded: 2.81 r_work: 0.3095 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3095 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.1880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 9379 Z= 0.147 Angle : 0.452 5.160 12702 Z= 0.242 Chirality : 0.040 0.168 1446 Planarity : 0.003 0.044 1598 Dihedral : 4.224 42.726 1273 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 1.49 % Allowed : 10.82 % Favored : 87.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.65 (0.25), residues: 1148 helix: 1.52 (0.27), residues: 384 sheet: 0.23 (0.31), residues: 279 loop : -0.23 (0.29), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP S 47 HIS 0.003 0.001 HIS S 35 PHE 0.034 0.001 PHE R 319 TYR 0.015 0.001 TYR S 190 ARG 0.003 0.000 ARG R 150 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 136 time to evaluate : 1.044 Fit side-chains REVERT: A 51 LYS cc_start: 0.7846 (pttp) cc_final: 0.7432 (ptmm) REVERT: B 258 ASP cc_start: 0.7125 (t0) cc_final: 0.6585 (t70) REVERT: R 135 GLN cc_start: 0.8365 (OUTLIER) cc_final: 0.8055 (mt0) REVERT: R 291 VAL cc_start: 0.7841 (t) cc_final: 0.7557 (p) outliers start: 15 outliers final: 11 residues processed: 142 average time/residue: 0.2671 time to fit residues: 49.7750 Evaluate side-chains 142 residues out of total 1007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 130 time to evaluate : 1.065 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 206 SER Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain R residue 135 GLN Chi-restraints excluded: chain R residue 178 LEU Chi-restraints excluded: chain R residue 269 MET Chi-restraints excluded: chain S residue 109 ASP Chi-restraints excluded: chain S residue 168 SER Chi-restraints excluded: chain S residue 183 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 67 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 73 optimal weight: 0.9980 chunk 15 optimal weight: 2.9990 chunk 72 optimal weight: 0.0870 chunk 63 optimal weight: 2.9990 chunk 14 optimal weight: 3.9990 chunk 89 optimal weight: 0.8980 chunk 68 optimal weight: 0.9980 chunk 62 optimal weight: 0.7980 chunk 37 optimal weight: 0.7980 overall best weight: 0.7158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 HIS A 306 GLN ** R 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 258 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.120104 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.090650 restraints weight = 16129.110| |-----------------------------------------------------------------------------| r_work (start): 0.3245 rms_B_bonded: 2.72 r_work: 0.3075 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3075 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8048 moved from start: 0.1948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 9379 Z= 0.206 Angle : 0.487 5.922 12702 Z= 0.258 Chirality : 0.041 0.170 1446 Planarity : 0.003 0.045 1598 Dihedral : 4.034 31.932 1273 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 1.99 % Allowed : 12.31 % Favored : 85.70 % 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: 0.61 (0.25), residues: 1148 helix: 1.52 (0.27), residues: 387 sheet: 0.17 (0.30), residues: 291 loop : -0.27 (0.29), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 211 HIS 0.005 0.001 HIS S 35 PHE 0.031 0.001 PHE R 319 TYR 0.012 0.001 TYR S 190 ARG 0.003 0.000 ARG R 150 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 136 time to evaluate : 1.010 Fit side-chains REVERT: B 150 ARG cc_start: 0.8074 (ttm-80) cc_final: 0.7868 (ttm-80) REVERT: B 258 ASP cc_start: 0.7111 (t0) cc_final: 0.6600 (t70) REVERT: R 135 GLN cc_start: 0.8297 (OUTLIER) cc_final: 0.7994 (mt0) REVERT: R 291 VAL cc_start: 0.7988 (t) cc_final: 0.7709 (p) outliers start: 20 outliers final: 15 residues processed: 146 average time/residue: 0.2745 time to fit residues: 52.8791 Evaluate side-chains 148 residues out of total 1007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 132 time to evaluate : 1.024 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 199 PHE Chi-restraints excluded: chain A residue 206 SER Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain R residue 135 GLN Chi-restraints excluded: chain R residue 178 LEU Chi-restraints excluded: chain R residue 214 ILE Chi-restraints excluded: chain S residue 80 PHE Chi-restraints excluded: chain S residue 109 ASP Chi-restraints excluded: chain S residue 168 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 103 optimal weight: 0.8980 chunk 28 optimal weight: 0.5980 chunk 11 optimal weight: 2.9990 chunk 75 optimal weight: 0.0980 chunk 81 optimal weight: 0.8980 chunk 59 optimal weight: 4.9990 chunk 6 optimal weight: 2.9990 chunk 5 optimal weight: 0.9980 chunk 68 optimal weight: 2.9990 chunk 3 optimal weight: 0.8980 chunk 105 optimal weight: 3.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 HIS A 306 GLN ** R 86 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 = 0.3735 r_free = 0.3735 target = 0.119339 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.089871 restraints weight = 16147.191| |-----------------------------------------------------------------------------| r_work (start): 0.3241 rms_B_bonded: 2.74 r_work: 0.3074 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 moved from start: 0.2048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 9379 Z= 0.197 Angle : 0.484 5.797 12702 Z= 0.256 Chirality : 0.041 0.171 1446 Planarity : 0.003 0.046 1598 Dihedral : 3.862 22.203 1273 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 2.18 % Allowed : 12.71 % Favored : 85.10 % 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 (0.25), residues: 1148 helix: 1.55 (0.27), residues: 387 sheet: 0.18 (0.30), residues: 285 loop : -0.30 (0.29), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 211 HIS 0.004 0.001 HIS S 35 PHE 0.028 0.001 PHE R 319 TYR 0.013 0.001 TYR S 190 ARG 0.003 0.000 ARG R 150 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 136 time to evaluate : 0.998 Fit side-chains REVERT: B 150 ARG cc_start: 0.8118 (ttm-80) cc_final: 0.7909 (ttm-80) REVERT: B 258 ASP cc_start: 0.7086 (t0) cc_final: 0.6592 (t70) REVERT: B 266 HIS cc_start: 0.7834 (OUTLIER) cc_final: 0.7389 (t-90) REVERT: R 135 GLN cc_start: 0.8306 (OUTLIER) cc_final: 0.8006 (mt0) REVERT: R 291 VAL cc_start: 0.7992 (t) cc_final: 0.7719 (p) outliers start: 22 outliers final: 16 residues processed: 147 average time/residue: 0.2904 time to fit residues: 55.6447 Evaluate side-chains 152 residues out of total 1007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 134 time to evaluate : 1.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 199 PHE Chi-restraints excluded: chain A residue 206 SER Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 266 HIS Chi-restraints excluded: chain R residue 61 ILE Chi-restraints excluded: chain R residue 135 GLN Chi-restraints excluded: chain R residue 178 LEU Chi-restraints excluded: chain R residue 214 ILE Chi-restraints excluded: chain S residue 80 PHE Chi-restraints excluded: chain S residue 109 ASP Chi-restraints excluded: chain S residue 168 SER Chi-restraints excluded: chain S residue 183 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 0 optimal weight: 3.9990 chunk 34 optimal weight: 0.6980 chunk 12 optimal weight: 0.9990 chunk 43 optimal weight: 0.9990 chunk 46 optimal weight: 0.4980 chunk 66 optimal weight: 0.7980 chunk 47 optimal weight: 2.9990 chunk 16 optimal weight: 0.6980 chunk 92 optimal weight: 0.6980 chunk 2 optimal weight: 3.9990 chunk 65 optimal weight: 0.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 HIS A 306 GLN ** R 86 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 = 0.3737 r_free = 0.3737 target = 0.119512 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.089997 restraints weight = 16192.484| |-----------------------------------------------------------------------------| r_work (start): 0.3244 rms_B_bonded: 2.75 r_work: 0.3072 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3072 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 moved from start: 0.2079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 9379 Z= 0.199 Angle : 0.491 7.347 12702 Z= 0.260 Chirality : 0.041 0.171 1446 Planarity : 0.003 0.047 1598 Dihedral : 3.787 18.317 1273 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 3.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 2.09 % Allowed : 13.31 % Favored : 84.61 % 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: 0.66 (0.25), residues: 1148 helix: 1.62 (0.27), residues: 387 sheet: 0.18 (0.30), residues: 285 loop : -0.30 (0.29), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 211 HIS 0.005 0.001 HIS S 35 PHE 0.037 0.001 PHE R 319 TYR 0.013 0.001 TYR S 190 ARG 0.006 0.000 ARG R 241 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 136 time to evaluate : 1.059 Fit side-chains REVERT: A 51 LYS cc_start: 0.7893 (pttp) cc_final: 0.7494 (ptmm) REVERT: B 258 ASP cc_start: 0.7069 (t0) cc_final: 0.6598 (t70) REVERT: B 266 HIS cc_start: 0.7875 (OUTLIER) cc_final: 0.7403 (t-90) REVERT: R 135 GLN cc_start: 0.8371 (OUTLIER) cc_final: 0.8074 (mt0) REVERT: R 291 VAL cc_start: 0.8022 (t) cc_final: 0.7746 (p) outliers start: 21 outliers final: 17 residues processed: 147 average time/residue: 0.2947 time to fit residues: 56.1394 Evaluate side-chains 151 residues out of total 1007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 132 time to evaluate : 1.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 199 PHE Chi-restraints excluded: chain A residue 206 SER Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 266 HIS Chi-restraints excluded: chain R residue 61 ILE Chi-restraints excluded: chain R residue 83 THR Chi-restraints excluded: chain R residue 135 GLN Chi-restraints excluded: chain R residue 178 LEU Chi-restraints excluded: chain R residue 214 ILE Chi-restraints excluded: chain S residue 80 PHE Chi-restraints excluded: chain S residue 109 ASP Chi-restraints excluded: chain S residue 168 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 31 optimal weight: 0.9990 chunk 90 optimal weight: 0.9980 chunk 43 optimal weight: 0.8980 chunk 93 optimal weight: 2.9990 chunk 30 optimal weight: 0.8980 chunk 6 optimal weight: 2.9990 chunk 40 optimal weight: 0.0770 chunk 44 optimal weight: 0.9990 chunk 2 optimal weight: 4.9990 chunk 92 optimal weight: 1.9990 chunk 5 optimal weight: 0.8980 overall best weight: 0.7538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 HIS A 306 GLN S 82 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.119389 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.089472 restraints weight = 16398.407| |-----------------------------------------------------------------------------| r_work (start): 0.3232 rms_B_bonded: 2.82 r_work: 0.3065 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3065 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 moved from start: 0.2137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 9379 Z= 0.216 Angle : 0.502 7.165 12702 Z= 0.265 Chirality : 0.041 0.171 1446 Planarity : 0.003 0.047 1598 Dihedral : 3.794 18.722 1273 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 2.28 % Allowed : 13.80 % Favored : 83.91 % 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: 0.66 (0.25), residues: 1148 helix: 1.65 (0.27), residues: 387 sheet: 0.16 (0.30), residues: 285 loop : -0.31 (0.29), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 211 HIS 0.004 0.001 HIS S 35 PHE 0.034 0.001 PHE R 319 TYR 0.013 0.001 TYR S 190 ARG 0.006 0.000 ARG B 150 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 134 time to evaluate : 1.020 Fit side-chains REVERT: A 51 LYS cc_start: 0.7887 (pttp) cc_final: 0.7505 (ptmm) REVERT: B 258 ASP cc_start: 0.7075 (t0) cc_final: 0.6553 (t70) REVERT: B 266 HIS cc_start: 0.7854 (OUTLIER) cc_final: 0.7311 (t-90) REVERT: R 135 GLN cc_start: 0.8402 (OUTLIER) cc_final: 0.8066 (mt0) REVERT: R 291 VAL cc_start: 0.7935 (t) cc_final: 0.7657 (p) outliers start: 23 outliers final: 20 residues processed: 147 average time/residue: 0.2961 time to fit residues: 56.5866 Evaluate side-chains 152 residues out of total 1007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 130 time to evaluate : 1.032 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 199 PHE Chi-restraints excluded: chain A residue 206 SER Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain A residue 295 THR Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 266 HIS Chi-restraints excluded: chain R residue 61 ILE Chi-restraints excluded: chain R residue 83 THR Chi-restraints excluded: chain R residue 135 GLN Chi-restraints excluded: chain R residue 178 LEU Chi-restraints excluded: chain R residue 214 ILE Chi-restraints excluded: chain R residue 266 THR Chi-restraints excluded: chain S residue 80 PHE Chi-restraints excluded: chain S residue 109 ASP Chi-restraints excluded: chain S residue 168 SER Chi-restraints excluded: chain S residue 183 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 54 optimal weight: 5.9990 chunk 98 optimal weight: 0.0470 chunk 78 optimal weight: 2.9990 chunk 15 optimal weight: 0.8980 chunk 93 optimal weight: 0.7980 chunk 30 optimal weight: 0.7980 chunk 58 optimal weight: 0.0270 chunk 109 optimal weight: 0.0470 chunk 113 optimal weight: 2.9990 chunk 102 optimal weight: 0.6980 chunk 42 optimal weight: 1.9990 overall best weight: 0.3234 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.121937 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.092473 restraints weight = 16198.612| |-----------------------------------------------------------------------------| r_work (start): 0.3275 rms_B_bonded: 2.74 r_work: 0.3110 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3110 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8010 moved from start: 0.2240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 9379 Z= 0.132 Angle : 0.454 6.383 12702 Z= 0.242 Chirality : 0.040 0.171 1446 Planarity : 0.003 0.048 1598 Dihedral : 3.566 17.997 1273 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 3.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 1.49 % Allowed : 14.90 % Favored : 83.61 % 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: 0.76 (0.25), residues: 1148 helix: 1.75 (0.27), residues: 393 sheet: 0.23 (0.31), residues: 277 loop : -0.29 (0.29), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP S 47 HIS 0.003 0.001 HIS S 35 PHE 0.032 0.001 PHE R 319 TYR 0.016 0.001 TYR S 190 ARG 0.007 0.000 ARG R 241 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 142 time to evaluate : 1.011 Fit side-chains REVERT: A 51 LYS cc_start: 0.7827 (pttp) cc_final: 0.7459 (ptmm) REVERT: B 258 ASP cc_start: 0.7027 (t0) cc_final: 0.6528 (t70) REVERT: B 266 HIS cc_start: 0.7904 (OUTLIER) cc_final: 0.7334 (t-90) REVERT: R 135 GLN cc_start: 0.8385 (OUTLIER) cc_final: 0.8068 (mt0) REVERT: R 188 GLU cc_start: 0.7297 (pp20) cc_final: 0.6988 (tm-30) REVERT: R 291 VAL cc_start: 0.7995 (t) cc_final: 0.7727 (p) outliers start: 15 outliers final: 13 residues processed: 151 average time/residue: 0.2909 time to fit residues: 56.6696 Evaluate side-chains 150 residues out of total 1007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 135 time to evaluate : 1.032 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 199 PHE Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 266 HIS Chi-restraints excluded: chain R residue 61 ILE Chi-restraints excluded: chain R residue 83 THR Chi-restraints excluded: chain R residue 135 GLN Chi-restraints excluded: chain R residue 178 LEU Chi-restraints excluded: chain R residue 266 THR Chi-restraints excluded: chain S residue 80 PHE Chi-restraints excluded: chain S residue 109 ASP Chi-restraints excluded: chain S residue 168 SER Chi-restraints excluded: chain S residue 231 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 89 optimal weight: 0.8980 chunk 19 optimal weight: 0.5980 chunk 71 optimal weight: 0.7980 chunk 57 optimal weight: 0.9980 chunk 15 optimal weight: 0.7980 chunk 41 optimal weight: 0.9990 chunk 77 optimal weight: 3.9990 chunk 2 optimal weight: 4.9990 chunk 34 optimal weight: 0.9990 chunk 20 optimal weight: 0.5980 chunk 5 optimal weight: 4.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.119988 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.090558 restraints weight = 16354.575| |-----------------------------------------------------------------------------| r_work (start): 0.3242 rms_B_bonded: 2.73 r_work: 0.3077 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8035 moved from start: 0.2206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9379 Z= 0.213 Angle : 0.505 6.922 12702 Z= 0.267 Chirality : 0.041 0.175 1446 Planarity : 0.003 0.047 1598 Dihedral : 3.710 18.000 1273 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 3.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 1.89 % Allowed : 14.50 % Favored : 83.61 % 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: 0.71 (0.25), residues: 1148 helix: 1.73 (0.27), residues: 393 sheet: 0.18 (0.30), residues: 285 loop : -0.35 (0.29), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 211 HIS 0.004 0.001 HIS S 35 PHE 0.033 0.001 PHE R 319 TYR 0.014 0.001 TYR B 59 ARG 0.007 0.000 ARG R 241 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 136 time to evaluate : 1.116 Fit side-chains REVERT: A 51 LYS cc_start: 0.7852 (pttp) cc_final: 0.7486 (ptmm) REVERT: B 153 ASP cc_start: 0.7860 (t0) cc_final: 0.7611 (t0) REVERT: B 258 ASP cc_start: 0.7044 (t0) cc_final: 0.6536 (t70) REVERT: B 266 HIS cc_start: 0.7887 (OUTLIER) cc_final: 0.7471 (t-90) REVERT: R 135 GLN cc_start: 0.8390 (OUTLIER) cc_final: 0.8063 (mt0) REVERT: R 291 VAL cc_start: 0.7982 (t) cc_final: 0.7708 (p) REVERT: S 116 THR cc_start: 0.8673 (p) cc_final: 0.8419 (t) outliers start: 19 outliers final: 15 residues processed: 148 average time/residue: 0.2884 time to fit residues: 55.5477 Evaluate side-chains 151 residues out of total 1007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 134 time to evaluate : 1.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 199 PHE Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain A residue 295 THR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 266 HIS Chi-restraints excluded: chain R residue 61 ILE Chi-restraints excluded: chain R residue 83 THR Chi-restraints excluded: chain R residue 135 GLN Chi-restraints excluded: chain R residue 178 LEU Chi-restraints excluded: chain R residue 266 THR Chi-restraints excluded: chain S residue 80 PHE Chi-restraints excluded: chain S residue 109 ASP Chi-restraints excluded: chain S residue 168 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 60 optimal weight: 3.9990 chunk 103 optimal weight: 3.9990 chunk 110 optimal weight: 1.9990 chunk 85 optimal weight: 2.9990 chunk 17 optimal weight: 0.9980 chunk 105 optimal weight: 5.9990 chunk 80 optimal weight: 0.9980 chunk 50 optimal weight: 0.3980 chunk 90 optimal weight: 0.7980 chunk 113 optimal weight: 0.5980 chunk 61 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.119647 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.090318 restraints weight = 16279.944| |-----------------------------------------------------------------------------| r_work (start): 0.3238 rms_B_bonded: 2.72 r_work: 0.3072 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3072 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 moved from start: 0.2240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 9379 Z= 0.217 Angle : 0.508 6.932 12702 Z= 0.268 Chirality : 0.041 0.172 1446 Planarity : 0.003 0.048 1598 Dihedral : 3.774 18.104 1273 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 3.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 1.99 % Allowed : 14.40 % Favored : 83.61 % 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: 0.66 (0.25), residues: 1148 helix: 1.71 (0.27), residues: 390 sheet: 0.16 (0.30), residues: 285 loop : -0.38 (0.29), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 82 HIS 0.004 0.001 HIS S 35 PHE 0.033 0.001 PHE R 319 TYR 0.014 0.001 TYR B 59 ARG 0.007 0.000 ARG R 241 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5276.21 seconds wall clock time: 94 minutes 36.73 seconds (5676.73 seconds total)