Starting phenix.real_space_refine on Wed May 14 14:23:02 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8unj_42406/05_2025/8unj_42406.cif Found real_map, /net/cci-nas-00/data/ceres_data/8unj_42406/05_2025/8unj_42406.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.35 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8unj_42406/05_2025/8unj_42406.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8unj_42406/05_2025/8unj_42406.map" model { file = "/net/cci-nas-00/data/ceres_data/8unj_42406/05_2025/8unj_42406.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8unj_42406/05_2025/8unj_42406.cif" } resolution = 3.35 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= -0.001 sd= 0.041 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: 6 Type Number sf(0) Gaussians P 11 5.49 5 Mg 3 5.21 5 S 75 5.16 5 C 7496 2.51 5 N 2087 2.21 5 O 2244 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 11916 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 1374 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1374 Classifications: {'peptide': 172} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 12, 'TRANS': 159} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 2514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 319, 2514 Classifications: {'peptide': 319} Link IDs: {'PTRANS': 13, 'TRANS': 305} Chain: "C" Number of atoms: 2591 Number of conformers: 1 Conformer: "" Number of residues, atoms: 325, 2591 Classifications: {'peptide': 325} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 312} Chain: "D" Number of atoms: 2541 Number of conformers: 1 Conformer: "" Number of residues, atoms: 329, 2541 Classifications: {'peptide': 329} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 13, 'TRANS': 315} Chain: "E" Number of atoms: 2773 Number of conformers: 1 Conformer: "" Number of residues, atoms: 348, 2773 Classifications: {'peptide': 348} Link IDs: {'PTRANS': 15, 'TRANS': 332} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 7.96, per 1000 atoms: 0.67 Number of scatterers: 11916 At special positions: 0 Unit cell: (94.392, 110.952, 124.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 75 16.00 P 11 15.00 Mg 3 11.99 O 2244 8.00 N 2087 7.00 C 7496 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: 2.76 Conformation dependent library (CDL) restraints added in 1.6 seconds 2962 Ramachandran restraints generated. 1481 Oldfield, 0 Emsley, 1481 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2852 Finding SS restraints... Secondary structure from input PDB file: 78 helices and 6 sheets defined 64.5% alpha, 6.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.12 Creating SS restraints... Processing helix chain 'A' and resid 722 through 743 Processing helix chain 'A' and resid 745 through 750 removed outlier: 3.789A pdb=" N SER A 750 " --> pdb=" O PRO A 746 " (cutoff:3.500A) Processing helix chain 'A' and resid 753 through 760 Processing helix chain 'A' and resid 762 through 769 Processing helix chain 'A' and resid 782 through 800 Processing helix chain 'A' and resid 837 through 863 Processing helix chain 'B' and resid 37 through 42 Processing helix chain 'B' and resid 46 through 50 Processing helix chain 'B' and resid 53 through 67 Processing helix chain 'B' and resid 81 through 95 Processing helix chain 'B' and resid 114 through 119 Processing helix chain 'B' and resid 119 through 125 Processing helix chain 'B' and resid 147 through 161 removed outlier: 3.708A pdb=" N ARG B 155 " --> pdb=" O GLN B 151 " (cutoff:3.500A) removed outlier: 4.783A pdb=" N ARG B 156 " --> pdb=" O GLN B 152 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N THR B 157 " --> pdb=" O ALA B 153 " (cutoff:3.500A) Processing helix chain 'B' and resid 178 through 184 Processing helix chain 'B' and resid 194 through 210 removed outlier: 3.649A pdb=" N ARG B 201 " --> pdb=" O GLN B 197 " (cutoff:3.500A) Processing helix chain 'B' and resid 214 through 226 removed outlier: 3.712A pdb=" N LEU B 218 " --> pdb=" O THR B 214 " (cutoff:3.500A) Processing helix chain 'B' and resid 228 through 243 Processing helix chain 'B' and resid 247 through 255 Processing helix chain 'B' and resid 259 through 272 removed outlier: 3.677A pdb=" N VAL B 263 " --> pdb=" O HIS B 259 " (cutoff:3.500A) Processing helix chain 'B' and resid 274 through 288 removed outlier: 3.645A pdb=" N LEU B 288 " --> pdb=" O HIS B 284 " (cutoff:3.500A) Processing helix chain 'B' and resid 291 through 305 removed outlier: 3.616A pdb=" N THR B 305 " --> pdb=" O ARG B 301 " (cutoff:3.500A) Processing helix chain 'B' and resid 309 through 329 Processing helix chain 'B' and resid 333 through 349 removed outlier: 3.548A pdb=" N MET B 337 " --> pdb=" O SER B 333 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N THR B 348 " --> pdb=" O LEU B 344 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N MET B 349 " --> pdb=" O CYS B 345 " (cutoff:3.500A) Processing helix chain 'C' and resid 21 through 26 Processing helix chain 'C' and resid 37 through 50 removed outlier: 3.591A pdb=" N GLU C 50 " --> pdb=" O LYS C 46 " (cutoff:3.500A) Processing helix chain 'C' and resid 65 through 78 Processing helix chain 'C' and resid 79 through 83 removed outlier: 3.915A pdb=" N PHE C 83 " --> pdb=" O ASP C 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 97 through 102 Processing helix chain 'C' and resid 103 through 110 Processing helix chain 'C' and resid 126 through 130 removed outlier: 3.820A pdb=" N ALA C 129 " --> pdb=" O GLU C 126 " (cutoff:3.500A) Processing helix chain 'C' and resid 131 through 145 removed outlier: 4.025A pdb=" N ARG C 139 " --> pdb=" O GLN C 135 " (cutoff:3.500A) removed outlier: 5.150A pdb=" N ARG C 140 " --> pdb=" O ASN C 136 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N VAL C 141 " --> pdb=" O ALA C 137 " (cutoff:3.500A) Processing helix chain 'C' and resid 157 through 161 removed outlier: 3.725A pdb=" N LYS C 160 " --> pdb=" O TYR C 157 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ILE C 161 " --> pdb=" O LEU C 158 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 157 through 161' Processing helix chain 'C' and resid 162 through 169 removed outlier: 3.527A pdb=" N CYS C 169 " --> pdb=" O LEU C 165 " (cutoff:3.500A) Processing helix chain 'C' and resid 182 through 194 removed outlier: 3.693A pdb=" N LEU C 186 " --> pdb=" O MET C 182 " (cutoff:3.500A) Processing helix chain 'C' and resid 198 through 208 removed outlier: 3.643A pdb=" N LEU C 208 " --> pdb=" O ALA C 204 " (cutoff:3.500A) Processing helix chain 'C' and resid 215 through 227 Processing helix chain 'C' and resid 231 through 237 Processing helix chain 'C' and resid 243 through 257 removed outlier: 3.970A pdb=" N MET C 254 " --> pdb=" O ILE C 250 " (cutoff:3.500A) Processing helix chain 'C' and resid 258 through 271 Processing helix chain 'C' and resid 276 through 291 removed outlier: 3.762A pdb=" N HIS C 289 " --> pdb=" O HIS C 285 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ARG C 290 " --> pdb=" O LEU C 286 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 313 Processing helix chain 'C' and resid 317 through 340 removed outlier: 3.634A pdb=" N PHE C 329 " --> pdb=" O LEU C 325 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N THR C 332 " --> pdb=" O ALA C 328 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N ASP C 334 " --> pdb=" O GLN C 330 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N LEU C 335 " --> pdb=" O VAL C 331 " (cutoff:3.500A) Processing helix chain 'D' and resid 48 through 52 removed outlier: 3.569A pdb=" N GLU D 51 " --> pdb=" O CYS D 48 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 68 Processing helix chain 'D' and resid 83 through 97 removed outlier: 3.568A pdb=" N THR D 87 " --> pdb=" O GLY D 83 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N ILE D 88 " --> pdb=" O LYS D 84 " (cutoff:3.500A) Processing helix chain 'D' and resid 100 through 104 removed outlier: 3.675A pdb=" N ARG D 104 " --> pdb=" O LEU D 100 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 100 through 104' Processing helix chain 'D' and resid 115 through 128 removed outlier: 4.208A pdb=" N VAL D 123 " --> pdb=" O VAL D 119 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N LYS D 124 " --> pdb=" O ARG D 120 " (cutoff:3.500A) Processing helix chain 'D' and resid 156 through 170 removed outlier: 3.851A pdb=" N LEU D 163 " --> pdb=" O ALA D 159 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N ARG D 164 " --> pdb=" O GLN D 160 " (cutoff:3.500A) removed outlier: 5.237A pdb=" N ARG D 165 " --> pdb=" O ALA D 161 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N THR D 166 " --> pdb=" O ALA D 162 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N GLU D 170 " --> pdb=" O THR D 166 " (cutoff:3.500A) Processing helix chain 'D' and resid 182 through 186 removed outlier: 3.750A pdb=" N ARG D 185 " --> pdb=" O TYR D 182 " (cutoff:3.500A) Processing helix chain 'D' and resid 187 through 193 Processing helix chain 'D' and resid 203 through 218 removed outlier: 3.557A pdb=" N GLN D 209 " --> pdb=" O LYS D 205 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ARG D 210 " --> pdb=" O ILE D 206 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LEU D 211 " --> pdb=" O GLN D 207 " (cutoff:3.500A) Processing helix chain 'D' and resid 223 through 235 removed outlier: 3.759A pdb=" N GLU D 235 " --> pdb=" O VAL D 231 " (cutoff:3.500A) Processing helix chain 'D' and resid 237 through 253 Processing helix chain 'D' and resid 258 through 266 removed outlier: 3.717A pdb=" N ALA D 266 " --> pdb=" O ILE D 262 " (cutoff:3.500A) Processing helix chain 'D' and resid 270 through 284 removed outlier: 3.544A pdb=" N GLN D 282 " --> pdb=" O PHE D 278 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLY D 284 " --> pdb=" O ALA D 280 " (cutoff:3.500A) Processing helix chain 'D' and resid 285 through 299 Processing helix chain 'D' and resid 302 through 316 Processing helix chain 'D' and resid 320 through 340 Processing helix chain 'D' and resid 343 through 360 Processing helix chain 'E' and resid 12 through 16 removed outlier: 3.654A pdb=" N LEU E 16 " --> pdb=" O LEU E 13 " (cutoff:3.500A) Processing helix chain 'E' and resid 19 through 32 removed outlier: 4.279A pdb=" N CYS E 32 " --> pdb=" O ASN E 28 " (cutoff:3.500A) Processing helix chain 'E' and resid 47 through 60 Processing helix chain 'E' and resid 97 through 102 removed outlier: 6.611A pdb=" N ASN E 102 " --> pdb=" O ASP E 99 " (cutoff:3.500A) Processing helix chain 'E' and resid 103 through 110 Processing helix chain 'E' and resid 110 through 117 Processing helix chain 'E' and resid 136 through 140 Processing helix chain 'E' and resid 141 through 147 Processing helix chain 'E' and resid 147 through 155 removed outlier: 3.905A pdb=" N THR E 151 " --> pdb=" O ALA E 147 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N TYR E 155 " --> pdb=" O THR E 151 " (cutoff:3.500A) Processing helix chain 'E' and resid 167 through 171 removed outlier: 3.586A pdb=" N LYS E 170 " --> pdb=" O SER E 167 " (cutoff:3.500A) Processing helix chain 'E' and resid 172 through 179 removed outlier: 3.886A pdb=" N ARG E 178 " --> pdb=" O PRO E 174 " (cutoff:3.500A) Processing helix chain 'E' and resid 188 through 203 Processing helix chain 'E' and resid 208 through 218 Processing helix chain 'E' and resid 222 through 237 Processing helix chain 'E' and resid 249 through 265 Processing helix chain 'E' and resid 267 through 284 Processing helix chain 'E' and resid 287 through 300 Processing helix chain 'E' and resid 307 through 325 Processing helix chain 'E' and resid 328 through 349 removed outlier: 3.593A pdb=" N ASP E 349 " --> pdb=" O LYS E 345 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 179 through 181 Processing sheet with id=AA2, first strand: chain 'A' and resid 803 through 807 Processing sheet with id=AA3, first strand: chain 'B' and resid 102 through 105 removed outlier: 6.115A pdb=" N LYS B 136 " --> pdb=" O ARG B 166 " (cutoff:3.500A) removed outlier: 7.098A pdb=" N ALA B 168 " --> pdb=" O LYS B 136 " (cutoff:3.500A) removed outlier: 5.997A pdb=" N ILE B 138 " --> pdb=" O ALA B 168 " (cutoff:3.500A) removed outlier: 7.673A pdb=" N ALA B 170 " --> pdb=" O ILE B 138 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N LEU B 140 " --> pdb=" O ALA B 170 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ILE B 73 " --> pdb=" O ALA B 186 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 87 through 90 removed outlier: 6.712A pdb=" N LYS C 120 " --> pdb=" O ARG C 150 " (cutoff:3.500A) removed outlier: 7.941A pdb=" N CYS C 152 " --> pdb=" O LYS C 120 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N VAL C 122 " --> pdb=" O CYS C 152 " (cutoff:3.500A) removed outlier: 7.505A pdb=" N ILE C 154 " --> pdb=" O VAL C 122 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N LEU C 124 " --> pdb=" O ILE C 154 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N LEU C 56 " --> pdb=" O LEU C 153 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N LEU C 57 " --> pdb=" O PHE C 172 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 105 through 108 removed outlier: 6.241A pdb=" N LYS D 145 " --> pdb=" O ARG D 175 " (cutoff:3.500A) removed outlier: 7.624A pdb=" N CYS D 177 " --> pdb=" O LYS D 145 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N VAL D 147 " --> pdb=" O CYS D 177 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N ILE D 179 " --> pdb=" O VAL D 147 " (cutoff:3.500A) removed outlier: 5.980A pdb=" N LEU D 149 " --> pdb=" O ILE D 179 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N LEU D 74 " --> pdb=" O LEU D 178 " (cutoff:3.500A) removed outlier: 7.903A pdb=" N CYS D 180 " --> pdb=" O LEU D 74 " (cutoff:3.500A) removed outlier: 6.053A pdb=" N PHE D 76 " --> pdb=" O CYS D 180 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N LEU D 75 " --> pdb=" O PHE D 197 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 68 through 75 removed outlier: 6.807A pdb=" N LEU E 93 " --> pdb=" O LEU E 133 " (cutoff:3.500A) removed outlier: 5.885A pdb=" N LYS E 130 " --> pdb=" O ARG E 160 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N ILE E 162 " --> pdb=" O LYS E 130 " (cutoff:3.500A) removed outlier: 6.041A pdb=" N VAL E 132 " --> pdb=" O ILE E 162 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N CYS E 164 " --> pdb=" O VAL E 132 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N LEU E 134 " --> pdb=" O CYS E 164 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N LEU E 38 " --> pdb=" O LEU E 163 " (cutoff:3.500A) removed outlier: 5.546A pdb=" N LEU E 39 " --> pdb=" O VAL E 182 " (cutoff:3.500A) 636 hydrogen bonds defined for protein. 1866 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: 3.55 Time building geometry restraints manager: 3.26 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.37: 4005 1.37 - 1.51: 3171 1.51 - 1.66: 4823 1.66 - 1.80: 76 1.80 - 1.95: 34 Bond restraints: 12109 Sorted by residual: bond pdb=" C GLN D 208 " pdb=" O GLN D 208 " ideal model delta sigma weight residual 1.236 1.286 -0.050 1.15e-02 7.56e+03 1.88e+01 bond pdb=" N ILE E 329 " pdb=" CA ILE E 329 " ideal model delta sigma weight residual 1.461 1.494 -0.034 1.19e-02 7.06e+03 8.08e+00 bond pdb=" N GLN D 208 " pdb=" CA GLN D 208 " ideal model delta sigma weight residual 1.459 1.489 -0.030 1.19e-02 7.06e+03 6.40e+00 bond pdb=" N ALA D 215 " pdb=" CA ALA D 215 " ideal model delta sigma weight residual 1.459 1.489 -0.030 1.23e-02 6.61e+03 6.09e+00 bond pdb=" N LEU D 211 " pdb=" CA LEU D 211 " ideal model delta sigma weight residual 1.459 1.490 -0.032 1.28e-02 6.10e+03 6.07e+00 ... (remaining 12104 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.01: 16031 2.01 - 4.03: 315 4.03 - 6.04: 37 6.04 - 8.06: 9 8.06 - 10.07: 2 Bond angle restraints: 16394 Sorted by residual: angle pdb=" N ASN D 181 " pdb=" CA ASN D 181 " pdb=" C ASN D 181 " ideal model delta sigma weight residual 113.16 105.52 7.64 1.24e+00 6.50e-01 3.79e+01 angle pdb=" C GLN D 207 " pdb=" N GLN D 208 " pdb=" CA GLN D 208 " ideal model delta sigma weight residual 120.44 113.54 6.90 1.30e+00 5.92e-01 2.82e+01 angle pdb=" N GLU D 218 " pdb=" CA GLU D 218 " pdb=" C GLU D 218 " ideal model delta sigma weight residual 113.19 107.56 5.63 1.19e+00 7.06e-01 2.24e+01 angle pdb=" N ILE D 214 " pdb=" CA ILE D 214 " pdb=" C ILE D 214 " ideal model delta sigma weight residual 110.42 106.01 4.41 9.60e-01 1.09e+00 2.11e+01 angle pdb=" N LEU D 211 " pdb=" CA LEU D 211 " pdb=" C LEU D 211 " ideal model delta sigma weight residual 111.82 106.82 5.00 1.16e+00 7.43e-01 1.86e+01 ... (remaining 16389 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.71: 7045 23.71 - 47.42: 400 47.42 - 71.13: 68 71.13 - 94.84: 8 94.84 - 118.54: 3 Dihedral angle restraints: 7524 sinusoidal: 3144 harmonic: 4380 Sorted by residual: dihedral pdb=" C5' ADP E2000 " pdb=" O5' ADP E2000 " pdb=" PA ADP E2000 " pdb=" O2A ADP E2000 " ideal model delta sinusoidal sigma weight residual -60.00 -178.54 118.54 1 2.00e+01 2.50e-03 3.55e+01 dihedral pdb=" O1B ADP E2000 " pdb=" O3A ADP E2000 " pdb=" PB ADP E2000 " pdb=" PA ADP E2000 " ideal model delta sinusoidal sigma weight residual -60.00 52.99 -112.99 1 2.00e+01 2.50e-03 3.34e+01 dihedral pdb=" CA HIS C 241 " pdb=" C HIS C 241 " pdb=" N PRO C 242 " pdb=" CA PRO C 242 " ideal model delta harmonic sigma weight residual -180.00 -157.71 -22.29 0 5.00e+00 4.00e-02 1.99e+01 ... (remaining 7521 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 1388 0.043 - 0.086: 391 0.086 - 0.129: 112 0.129 - 0.172: 18 0.172 - 0.215: 6 Chirality restraints: 1915 Sorted by residual: chirality pdb=" CA LEU D 212 " pdb=" N LEU D 212 " pdb=" C LEU D 212 " pdb=" CB LEU D 212 " both_signs ideal model delta sigma weight residual False 2.51 2.73 -0.21 2.00e-01 2.50e+01 1.15e+00 chirality pdb=" CA ILE D 214 " pdb=" N ILE D 214 " pdb=" C ILE D 214 " pdb=" CB ILE D 214 " both_signs ideal model delta sigma weight residual False 2.43 2.64 -0.20 2.00e-01 2.50e+01 1.02e+00 chirality pdb=" CA LEU E 67 " pdb=" N LEU E 67 " pdb=" C LEU E 67 " pdb=" CB LEU E 67 " both_signs ideal model delta sigma weight residual False 2.51 2.70 -0.19 2.00e-01 2.50e+01 8.72e-01 ... (remaining 1912 not shown) Planarity restraints: 2080 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO E 173 " 0.067 5.00e-02 4.00e+02 1.01e-01 1.63e+01 pdb=" N PRO E 174 " -0.174 5.00e-02 4.00e+02 pdb=" CA PRO E 174 " 0.051 5.00e-02 4.00e+02 pdb=" CD PRO E 174 " 0.056 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU B 257 " 0.048 5.00e-02 4.00e+02 7.25e-02 8.40e+00 pdb=" N PRO B 258 " -0.125 5.00e-02 4.00e+02 pdb=" CA PRO B 258 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO B 258 " 0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR E 267 " 0.037 5.00e-02 4.00e+02 5.66e-02 5.12e+00 pdb=" N PRO E 268 " -0.098 5.00e-02 4.00e+02 pdb=" CA PRO E 268 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO E 268 " 0.031 5.00e-02 4.00e+02 ... (remaining 2077 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.65: 167 2.65 - 3.21: 10342 3.21 - 3.77: 19485 3.77 - 4.34: 25332 4.34 - 4.90: 41544 Nonbonded interactions: 96870 Sorted by model distance: nonbonded pdb="MG MG D 401 " pdb=" O2B AGS D 402 " model vdw 2.083 2.170 nonbonded pdb="MG MG C 401 " pdb=" O3G AGS C 402 " model vdw 2.087 2.170 nonbonded pdb="MG MG B 401 " pdb=" O2G AGS B 402 " model vdw 2.116 2.170 nonbonded pdb=" OG1 THR B 83 " pdb="MG MG B 401 " model vdw 2.119 2.170 nonbonded pdb="MG MG D 401 " pdb=" O2G AGS D 402 " model vdw 2.197 2.170 ... (remaining 96865 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: 0.010 Normalize map: mean=0, sd=1: 2.010 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: 0.020 Extract box with map and model: 0.530 Check model and map are aligned: 0.090 Set scattering table: 0.130 Process input model: 28.860 Find NCS groups from input model: 0.490 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5760 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 0.050 12109 Z= 0.198 Angle : 0.700 10.070 16394 Z= 0.411 Chirality : 0.045 0.215 1915 Planarity : 0.007 0.101 2080 Dihedral : 14.943 118.544 4672 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 3.51 % Allowed : 9.39 % Favored : 87.10 % 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: -1.77 (0.19), residues: 1481 helix: -1.30 (0.15), residues: 879 sheet: -0.63 (0.41), residues: 143 loop : -0.63 (0.28), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP C 253 HIS 0.005 0.001 HIS E 19 PHE 0.014 0.001 PHE E 339 TYR 0.020 0.001 TYR E 41 ARG 0.004 0.000 ARG C 215 Details of bonding type rmsd hydrogen bonds : bond 0.14496 ( 636) hydrogen bonds : angle 6.23379 ( 1866) covalent geometry : bond 0.00344 (12109) covalent geometry : angle 0.70027 (16394) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2962 Ramachandran restraints generated. 1481 Oldfield, 0 Emsley, 1481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2962 Ramachandran restraints generated. 1481 Oldfield, 0 Emsley, 1481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 1311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 246 time to evaluate : 1.308 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 158 MET cc_start: -0.2409 (ttm) cc_final: -0.3480 (ptm) REVERT: B 185 CYS cc_start: 0.2644 (m) cc_final: 0.2287 (m) REVERT: C 202 MET cc_start: 0.5514 (tmm) cc_final: 0.5016 (tmm) REVERT: C 206 VAL cc_start: 0.7070 (OUTLIER) cc_final: 0.6861 (p) REVERT: D 77 TYR cc_start: 0.3767 (p90) cc_final: 0.3194 (p90) REVERT: D 227 ILE cc_start: 0.7255 (tt) cc_final: 0.7054 (tt) REVERT: D 304 THR cc_start: 0.7812 (OUTLIER) cc_final: 0.7581 (p) outliers start: 46 outliers final: 12 residues processed: 278 average time/residue: 0.2351 time to fit residues: 93.0373 Evaluate side-chains 179 residues out of total 1311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 165 time to evaluate : 1.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 830 LEU Chi-restraints excluded: chain A residue 855 ARG Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 331 VAL Chi-restraints excluded: chain C residue 162 ILE Chi-restraints excluded: chain C residue 206 VAL Chi-restraints excluded: chain D residue 49 VAL Chi-restraints excluded: chain D residue 181 ASN Chi-restraints excluded: chain D residue 232 LYS Chi-restraints excluded: chain D residue 304 THR Chi-restraints excluded: chain D residue 328 THR Chi-restraints excluded: chain E residue 254 TYR Chi-restraints excluded: chain E residue 314 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 123 optimal weight: 0.0970 chunk 110 optimal weight: 5.9990 chunk 61 optimal weight: 9.9990 chunk 37 optimal weight: 10.0000 chunk 74 optimal weight: 2.9990 chunk 59 optimal weight: 9.9990 chunk 114 optimal weight: 2.9990 chunk 44 optimal weight: 1.9990 chunk 69 optimal weight: 0.7980 chunk 85 optimal weight: 0.6980 chunk 132 optimal weight: 6.9990 overall best weight: 1.3182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 735 ASN A 788 GLN A 820 ASN B 126 GLN B 237 GLN B 268 GLN C 32 ASN C 38 GLN C 135 GLN C 300 HIS D 73 ASN ** D 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 22 GLN E 92 HIS E 126 GLN E 206 ASN E 265 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4786 r_free = 0.4786 target = 0.220800 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4420 r_free = 0.4420 target = 0.184399 restraints weight = 20081.338| |-----------------------------------------------------------------------------| r_work (start): 0.4398 rms_B_bonded: 3.42 r_work: 0.4182 rms_B_bonded: 4.17 restraints_weight: 0.5000 r_work (final): 0.4182 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6401 moved from start: 0.1764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 12109 Z= 0.158 Angle : 0.622 10.731 16394 Z= 0.310 Chirality : 0.041 0.145 1915 Planarity : 0.005 0.082 2080 Dihedral : 10.072 111.921 1722 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 11.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 2.82 % Allowed : 14.73 % Favored : 82.44 % 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: -0.45 (0.21), residues: 1481 helix: -0.13 (0.17), residues: 884 sheet: -0.79 (0.41), residues: 143 loop : -0.07 (0.30), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 40 HIS 0.006 0.001 HIS D 345 PHE 0.014 0.001 PHE E 339 TYR 0.024 0.002 TYR B 279 ARG 0.005 0.001 ARG A 854 Details of bonding type rmsd hydrogen bonds : bond 0.03959 ( 636) hydrogen bonds : angle 4.44758 ( 1866) covalent geometry : bond 0.00351 (12109) covalent geometry : angle 0.62177 (16394) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2962 Ramachandran restraints generated. 1481 Oldfield, 0 Emsley, 1481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2962 Ramachandran restraints generated. 1481 Oldfield, 0 Emsley, 1481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 178 time to evaluate : 1.551 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 738 GLN cc_start: 0.7792 (mm110) cc_final: 0.7561 (tp40) REVERT: A 762 LEU cc_start: 0.6515 (OUTLIER) cc_final: 0.6080 (tp) REVERT: A 820 ASN cc_start: 0.7132 (OUTLIER) cc_final: 0.6838 (p0) REVERT: B 158 MET cc_start: -0.3406 (ttm) cc_final: -0.3935 (ptm) REVERT: B 185 CYS cc_start: 0.2730 (m) cc_final: 0.2204 (m) REVERT: B 229 MET cc_start: 0.5149 (tpp) cc_final: 0.4579 (tpp) REVERT: B 231 GLN cc_start: 0.8042 (tt0) cc_final: 0.7818 (tt0) REVERT: B 246 ILE cc_start: 0.4496 (mm) cc_final: 0.4222 (mm) REVERT: C 22 TRP cc_start: 0.4228 (m-10) cc_final: 0.4016 (m-10) REVERT: C 202 MET cc_start: 0.5145 (tmm) cc_final: 0.4801 (tmm) REVERT: D 77 TYR cc_start: 0.4481 (p90) cc_final: 0.3796 (p90) REVERT: D 304 THR cc_start: 0.8011 (OUTLIER) cc_final: 0.7799 (p) REVERT: D 356 MET cc_start: 0.7949 (ttp) cc_final: 0.7661 (mtp) REVERT: E 214 ARG cc_start: 0.6129 (mtm110) cc_final: 0.5442 (mtt90) outliers start: 37 outliers final: 22 residues processed: 203 average time/residue: 0.2446 time to fit residues: 72.4769 Evaluate side-chains 182 residues out of total 1311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 157 time to evaluate : 1.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 762 LEU Chi-restraints excluded: chain A residue 820 ASN Chi-restraints excluded: chain A residue 830 LEU Chi-restraints excluded: chain A residue 855 ARG Chi-restraints excluded: chain B residue 87 LEU Chi-restraints excluded: chain B residue 194 THR Chi-restraints excluded: chain B residue 197 GLN Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 276 ASP Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 153 LEU Chi-restraints excluded: chain C residue 161 ILE Chi-restraints excluded: chain C residue 162 ILE Chi-restraints excluded: chain D residue 49 VAL Chi-restraints excluded: chain D residue 304 THR Chi-restraints excluded: chain E residue 30 VAL Chi-restraints excluded: chain E residue 102 ASN Chi-restraints excluded: chain E residue 143 ASP Chi-restraints excluded: chain E residue 206 ASN Chi-restraints excluded: chain E residue 241 THR Chi-restraints excluded: chain E residue 254 TYR Chi-restraints excluded: chain E residue 279 TYR Chi-restraints excluded: chain E residue 302 ASN Chi-restraints excluded: chain E residue 303 CYS Chi-restraints excluded: chain E residue 329 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 115 optimal weight: 2.9990 chunk 81 optimal weight: 7.9990 chunk 79 optimal weight: 2.9990 chunk 95 optimal weight: 5.9990 chunk 107 optimal weight: 0.9990 chunk 80 optimal weight: 4.9990 chunk 114 optimal weight: 0.7980 chunk 104 optimal weight: 0.6980 chunk 98 optimal weight: 0.3980 chunk 133 optimal weight: 4.9990 chunk 119 optimal weight: 0.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 165 ASN ** A 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 237 GLN C 135 GLN ** D 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 236 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4809 r_free = 0.4809 target = 0.222109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4437 r_free = 0.4437 target = 0.185316 restraints weight = 20276.180| |-----------------------------------------------------------------------------| r_work (start): 0.4404 rms_B_bonded: 3.24 r_work: 0.4211 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.4211 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6356 moved from start: 0.2003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 12109 Z= 0.121 Angle : 0.564 11.415 16394 Z= 0.279 Chirality : 0.039 0.143 1915 Planarity : 0.005 0.074 2080 Dihedral : 9.656 111.446 1707 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 11.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 2.98 % Allowed : 15.65 % Favored : 81.37 % 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: 0.17 (0.22), residues: 1481 helix: 0.45 (0.17), residues: 874 sheet: -0.98 (0.39), residues: 156 loop : 0.19 (0.31), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 40 HIS 0.004 0.001 HIS D 311 PHE 0.015 0.001 PHE E 339 TYR 0.022 0.002 TYR B 279 ARG 0.004 0.000 ARG C 150 Details of bonding type rmsd hydrogen bonds : bond 0.03541 ( 636) hydrogen bonds : angle 4.20996 ( 1866) covalent geometry : bond 0.00266 (12109) covalent geometry : angle 0.56448 (16394) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2962 Ramachandran restraints generated. 1481 Oldfield, 0 Emsley, 1481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2962 Ramachandran restraints generated. 1481 Oldfield, 0 Emsley, 1481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 177 time to evaluate : 1.239 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 727 GLN cc_start: 0.8435 (tp-100) cc_final: 0.7825 (pp30) REVERT: A 762 LEU cc_start: 0.6482 (OUTLIER) cc_final: 0.5789 (tp) REVERT: A 815 TYR cc_start: 0.3938 (m-80) cc_final: 0.3095 (m-80) REVERT: B 146 MET cc_start: 0.1986 (ttt) cc_final: 0.1682 (ttp) REVERT: B 158 MET cc_start: -0.3329 (ttm) cc_final: -0.3924 (ptm) REVERT: B 229 MET cc_start: 0.5093 (tpp) cc_final: 0.4590 (tpp) REVERT: B 231 GLN cc_start: 0.8023 (tt0) cc_final: 0.7712 (tt0) REVERT: C 202 MET cc_start: 0.5002 (tmm) cc_final: 0.4691 (tmm) REVERT: C 275 LEU cc_start: 0.6828 (OUTLIER) cc_final: 0.6429 (tt) REVERT: D 77 TYR cc_start: 0.4443 (p90) cc_final: 0.3730 (p90) REVERT: D 304 THR cc_start: 0.8031 (OUTLIER) cc_final: 0.7809 (p) REVERT: D 356 MET cc_start: 0.7949 (ttp) cc_final: 0.7628 (mtp) REVERT: E 4 TRP cc_start: 0.4821 (OUTLIER) cc_final: 0.4593 (m-10) REVERT: E 108 ILE cc_start: 0.7900 (mm) cc_final: 0.7622 (mt) REVERT: E 110 GLU cc_start: 0.6425 (tp30) cc_final: 0.6205 (mm-30) outliers start: 39 outliers final: 20 residues processed: 201 average time/residue: 0.2098 time to fit residues: 62.6710 Evaluate side-chains 184 residues out of total 1311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 160 time to evaluate : 1.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 762 LEU Chi-restraints excluded: chain B residue 171 CYS Chi-restraints excluded: chain B residue 194 THR Chi-restraints excluded: chain B residue 197 GLN Chi-restraints excluded: chain B residue 236 LEU Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 276 ASP Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 119 PHE Chi-restraints excluded: chain C residue 161 ILE Chi-restraints excluded: chain C residue 162 ILE Chi-restraints excluded: chain C residue 178 THR Chi-restraints excluded: chain C residue 275 LEU Chi-restraints excluded: chain D residue 304 THR Chi-restraints excluded: chain E residue 4 TRP Chi-restraints excluded: chain E residue 102 ASN Chi-restraints excluded: chain E residue 143 ASP Chi-restraints excluded: chain E residue 149 ARG Chi-restraints excluded: chain E residue 168 THR Chi-restraints excluded: chain E residue 206 ASN Chi-restraints excluded: chain E residue 254 TYR Chi-restraints excluded: chain E residue 282 LEU Chi-restraints excluded: chain E residue 302 ASN Chi-restraints excluded: chain E residue 329 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 91 optimal weight: 4.9990 chunk 125 optimal weight: 0.8980 chunk 81 optimal weight: 9.9990 chunk 136 optimal weight: 6.9990 chunk 10 optimal weight: 10.0000 chunk 144 optimal weight: 4.9990 chunk 28 optimal weight: 30.0000 chunk 103 optimal weight: 0.0370 chunk 116 optimal weight: 1.9990 chunk 45 optimal weight: 4.9990 chunk 120 optimal weight: 1.9990 overall best weight: 1.9864 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 237 GLN C 156 ASN C 224 ASN D 128 GLN ** D 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 301 HIS ** E 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 206 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4755 r_free = 0.4755 target = 0.217016 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4368 r_free = 0.4368 target = 0.179202 restraints weight = 20176.098| |-----------------------------------------------------------------------------| r_work (start): 0.4349 rms_B_bonded: 3.27 r_work: 0.4144 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.4144 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6527 moved from start: 0.2576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 12109 Z= 0.204 Angle : 0.665 9.995 16394 Z= 0.331 Chirality : 0.043 0.146 1915 Planarity : 0.005 0.074 2080 Dihedral : 9.415 116.718 1700 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 13.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 3.51 % Allowed : 16.03 % Favored : 80.46 % 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: -0.03 (0.22), residues: 1481 helix: 0.32 (0.17), residues: 879 sheet: -0.95 (0.44), residues: 125 loop : -0.10 (0.29), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.003 TRP D 40 HIS 0.006 0.002 HIS C 241 PHE 0.019 0.002 PHE E 339 TYR 0.021 0.002 TYR E 279 ARG 0.005 0.001 ARG D 114 Details of bonding type rmsd hydrogen bonds : bond 0.04062 ( 636) hydrogen bonds : angle 4.46683 ( 1866) covalent geometry : bond 0.00467 (12109) covalent geometry : angle 0.66521 (16394) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2962 Ramachandran restraints generated. 1481 Oldfield, 0 Emsley, 1481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2962 Ramachandran restraints generated. 1481 Oldfield, 0 Emsley, 1481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 172 time to evaluate : 1.353 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 762 LEU cc_start: 0.6576 (OUTLIER) cc_final: 0.6253 (tp) REVERT: A 815 TYR cc_start: 0.4170 (m-80) cc_final: 0.3281 (m-80) REVERT: B 146 MET cc_start: 0.2251 (ttt) cc_final: 0.1892 (tmm) REVERT: B 158 MET cc_start: -0.3531 (ttm) cc_final: -0.4019 (ptm) REVERT: B 229 MET cc_start: 0.5131 (tpp) cc_final: 0.4654 (tpp) REVERT: B 231 GLN cc_start: 0.8254 (tt0) cc_final: 0.7847 (tt0) REVERT: C 122 VAL cc_start: 0.7145 (t) cc_final: 0.6651 (m) REVERT: C 202 MET cc_start: 0.5340 (tmm) cc_final: 0.4869 (tmm) REVERT: C 275 LEU cc_start: 0.6860 (OUTLIER) cc_final: 0.6505 (tt) REVERT: C 292 ASP cc_start: 0.6742 (t0) cc_final: 0.6387 (t0) REVERT: D 77 TYR cc_start: 0.4759 (p90) cc_final: 0.4045 (p90) REVERT: E 4 TRP cc_start: 0.5320 (OUTLIER) cc_final: 0.4582 (m-10) REVERT: E 108 ILE cc_start: 0.7739 (mm) cc_final: 0.7466 (mt) REVERT: E 214 ARG cc_start: 0.6154 (mtm110) cc_final: 0.5474 (mtt90) outliers start: 46 outliers final: 28 residues processed: 203 average time/residue: 0.2250 time to fit residues: 67.4097 Evaluate side-chains 190 residues out of total 1311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 159 time to evaluate : 1.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 733 MET Chi-restraints excluded: chain A residue 762 LEU Chi-restraints excluded: chain A residue 830 LEU Chi-restraints excluded: chain B residue 171 CYS Chi-restraints excluded: chain B residue 197 GLN Chi-restraints excluded: chain B residue 236 LEU Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 276 ASP Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 329 GLU Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 119 PHE Chi-restraints excluded: chain C residue 161 ILE Chi-restraints excluded: chain C residue 162 ILE Chi-restraints excluded: chain C residue 178 THR Chi-restraints excluded: chain C residue 275 LEU Chi-restraints excluded: chain C residue 314 VAL Chi-restraints excluded: chain C residue 334 ASP Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain E residue 4 TRP Chi-restraints excluded: chain E residue 30 VAL Chi-restraints excluded: chain E residue 102 ASN Chi-restraints excluded: chain E residue 143 ASP Chi-restraints excluded: chain E residue 149 ARG Chi-restraints excluded: chain E residue 168 THR Chi-restraints excluded: chain E residue 206 ASN Chi-restraints excluded: chain E residue 207 LEU Chi-restraints excluded: chain E residue 241 THR Chi-restraints excluded: chain E residue 254 TYR Chi-restraints excluded: chain E residue 282 LEU Chi-restraints excluded: chain E residue 302 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 28 optimal weight: 0.9990 chunk 119 optimal weight: 2.9990 chunk 33 optimal weight: 20.0000 chunk 41 optimal weight: 2.9990 chunk 54 optimal weight: 7.9990 chunk 63 optimal weight: 0.0470 chunk 85 optimal weight: 0.6980 chunk 139 optimal weight: 3.9990 chunk 26 optimal weight: 9.9990 chunk 131 optimal weight: 2.9990 chunk 81 optimal weight: 6.9990 overall best weight: 1.5484 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 207 GLN ** D 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 109 GLN E 302 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4752 r_free = 0.4752 target = 0.216719 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4377 r_free = 0.4377 target = 0.180309 restraints weight = 20225.756| |-----------------------------------------------------------------------------| r_work (start): 0.4355 rms_B_bonded: 3.03 r_work: 0.4137 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.4137 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6496 moved from start: 0.2822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 12109 Z= 0.167 Angle : 0.618 10.740 16394 Z= 0.307 Chirality : 0.041 0.145 1915 Planarity : 0.005 0.070 2080 Dihedral : 9.227 118.354 1699 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 12.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 3.51 % Allowed : 18.02 % Favored : 78.47 % 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: 0.05 (0.22), residues: 1481 helix: 0.44 (0.17), residues: 878 sheet: -1.20 (0.40), residues: 147 loop : -0.04 (0.30), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP D 40 HIS 0.004 0.001 HIS C 241 PHE 0.015 0.002 PHE E 339 TYR 0.021 0.002 TYR E 279 ARG 0.004 0.000 ARG E 224 Details of bonding type rmsd hydrogen bonds : bond 0.03761 ( 636) hydrogen bonds : angle 4.39332 ( 1866) covalent geometry : bond 0.00381 (12109) covalent geometry : angle 0.61837 (16394) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2962 Ramachandran restraints generated. 1481 Oldfield, 0 Emsley, 1481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2962 Ramachandran restraints generated. 1481 Oldfield, 0 Emsley, 1481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 174 time to evaluate : 1.227 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 762 LEU cc_start: 0.6626 (OUTLIER) cc_final: 0.6328 (tp) REVERT: A 815 TYR cc_start: 0.4073 (m-80) cc_final: 0.3281 (m-80) REVERT: A 820 ASN cc_start: 0.7145 (p0) cc_final: 0.6711 (p0) REVERT: B 158 MET cc_start: -0.3489 (ttm) cc_final: -0.4010 (ptm) REVERT: B 229 MET cc_start: 0.4946 (tpp) cc_final: 0.4494 (tpp) REVERT: B 231 GLN cc_start: 0.8213 (tt0) cc_final: 0.7789 (tt0) REVERT: C 122 VAL cc_start: 0.7167 (t) cc_final: 0.6726 (m) REVERT: C 202 MET cc_start: 0.5320 (tmm) cc_final: 0.4803 (tmm) REVERT: C 275 LEU cc_start: 0.6632 (OUTLIER) cc_final: 0.6276 (tt) REVERT: C 292 ASP cc_start: 0.6732 (t0) cc_final: 0.6398 (t0) REVERT: D 43 LYS cc_start: 0.5973 (OUTLIER) cc_final: 0.5505 (mtmm) REVERT: D 77 TYR cc_start: 0.4726 (p90) cc_final: 0.4035 (p90) REVERT: D 304 THR cc_start: 0.8082 (OUTLIER) cc_final: 0.7855 (p) REVERT: E 108 ILE cc_start: 0.7772 (mm) cc_final: 0.7496 (mt) REVERT: E 214 ARG cc_start: 0.6139 (mtm110) cc_final: 0.5369 (mtt90) REVERT: E 281 LEU cc_start: 0.7757 (OUTLIER) cc_final: 0.7331 (tt) outliers start: 46 outliers final: 29 residues processed: 208 average time/residue: 0.2180 time to fit residues: 67.0116 Evaluate side-chains 199 residues out of total 1311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 165 time to evaluate : 1.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 733 MET Chi-restraints excluded: chain A residue 762 LEU Chi-restraints excluded: chain A residue 830 LEU Chi-restraints excluded: chain B residue 171 CYS Chi-restraints excluded: chain B residue 197 GLN Chi-restraints excluded: chain B residue 204 ASN Chi-restraints excluded: chain B residue 236 LEU Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 276 ASP Chi-restraints excluded: chain B residue 329 GLU Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 119 PHE Chi-restraints excluded: chain C residue 161 ILE Chi-restraints excluded: chain C residue 162 ILE Chi-restraints excluded: chain C residue 178 THR Chi-restraints excluded: chain C residue 275 LEU Chi-restraints excluded: chain C residue 314 VAL Chi-restraints excluded: chain C residue 334 ASP Chi-restraints excluded: chain D residue 43 LYS Chi-restraints excluded: chain D residue 74 LEU Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain D residue 221 LYS Chi-restraints excluded: chain D residue 304 THR Chi-restraints excluded: chain E residue 30 VAL Chi-restraints excluded: chain E residue 143 ASP Chi-restraints excluded: chain E residue 149 ARG Chi-restraints excluded: chain E residue 168 THR Chi-restraints excluded: chain E residue 207 LEU Chi-restraints excluded: chain E residue 254 TYR Chi-restraints excluded: chain E residue 281 LEU Chi-restraints excluded: chain E residue 282 LEU Chi-restraints excluded: chain E residue 296 LEU Chi-restraints excluded: chain E residue 302 ASN Chi-restraints excluded: chain E residue 303 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 133 optimal weight: 7.9990 chunk 141 optimal weight: 3.9990 chunk 92 optimal weight: 0.8980 chunk 42 optimal weight: 2.9990 chunk 41 optimal weight: 2.9990 chunk 105 optimal weight: 3.9990 chunk 40 optimal weight: 1.9990 chunk 53 optimal weight: 3.9990 chunk 71 optimal weight: 0.5980 chunk 144 optimal weight: 3.9990 chunk 124 optimal weight: 9.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 120 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4745 r_free = 0.4745 target = 0.215370 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4417 r_free = 0.4417 target = 0.181662 restraints weight = 20375.270| |-----------------------------------------------------------------------------| r_work (start): 0.4354 rms_B_bonded: 2.73 r_work: 0.4160 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.4160 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6507 moved from start: 0.3097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 12109 Z= 0.195 Angle : 0.659 11.309 16394 Z= 0.327 Chirality : 0.042 0.144 1915 Planarity : 0.005 0.072 2080 Dihedral : 9.237 123.353 1699 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 14.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 4.20 % Allowed : 18.24 % Favored : 77.56 % 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: -0.08 (0.22), residues: 1481 helix: 0.34 (0.17), residues: 880 sheet: -1.28 (0.42), residues: 137 loop : -0.09 (0.30), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP D 40 HIS 0.005 0.001 HIS C 37 PHE 0.016 0.002 PHE E 339 TYR 0.023 0.002 TYR B 279 ARG 0.004 0.001 ARG D 114 Details of bonding type rmsd hydrogen bonds : bond 0.03910 ( 636) hydrogen bonds : angle 4.53370 ( 1866) covalent geometry : bond 0.00446 (12109) covalent geometry : angle 0.65881 (16394) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2962 Ramachandran restraints generated. 1481 Oldfield, 0 Emsley, 1481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2962 Ramachandran restraints generated. 1481 Oldfield, 0 Emsley, 1481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 166 time to evaluate : 1.405 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 762 LEU cc_start: 0.6643 (OUTLIER) cc_final: 0.6364 (tp) REVERT: A 815 TYR cc_start: 0.4173 (m-80) cc_final: 0.3353 (m-80) REVERT: B 158 MET cc_start: -0.3588 (ttm) cc_final: -0.4086 (ptm) REVERT: B 229 MET cc_start: 0.4957 (tpp) cc_final: 0.4481 (tpp) REVERT: C 122 VAL cc_start: 0.7288 (t) cc_final: 0.6893 (m) REVERT: C 202 MET cc_start: 0.5695 (tmm) cc_final: 0.5200 (tmm) REVERT: C 213 MET cc_start: 0.7075 (mmp) cc_final: 0.6266 (mmp) REVERT: C 275 LEU cc_start: 0.6653 (OUTLIER) cc_final: 0.6329 (tt) REVERT: C 292 ASP cc_start: 0.6719 (t0) cc_final: 0.6408 (t0) REVERT: D 77 TYR cc_start: 0.4657 (p90) cc_final: 0.4044 (p90) REVERT: D 257 ILE cc_start: 0.8157 (OUTLIER) cc_final: 0.7787 (mp) REVERT: D 304 THR cc_start: 0.8064 (OUTLIER) cc_final: 0.7849 (p) REVERT: E 214 ARG cc_start: 0.6318 (mtm110) cc_final: 0.5625 (mtt90) REVERT: E 281 LEU cc_start: 0.7898 (OUTLIER) cc_final: 0.7473 (tt) REVERT: E 332 LEU cc_start: 0.7678 (OUTLIER) cc_final: 0.7369 (mp) outliers start: 55 outliers final: 36 residues processed: 211 average time/residue: 0.2171 time to fit residues: 67.2767 Evaluate side-chains 204 residues out of total 1311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 162 time to evaluate : 1.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 762 LEU Chi-restraints excluded: chain A residue 830 LEU Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 171 CYS Chi-restraints excluded: chain B residue 197 GLN Chi-restraints excluded: chain B residue 204 ASN Chi-restraints excluded: chain B residue 236 LEU Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 263 VAL Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 329 GLU Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 119 PHE Chi-restraints excluded: chain C residue 161 ILE Chi-restraints excluded: chain C residue 162 ILE Chi-restraints excluded: chain C residue 178 THR Chi-restraints excluded: chain C residue 275 LEU Chi-restraints excluded: chain C residue 314 VAL Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain C residue 334 ASP Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 74 LEU Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain D residue 147 VAL Chi-restraints excluded: chain D residue 221 LYS Chi-restraints excluded: chain D residue 232 LYS Chi-restraints excluded: chain D residue 257 ILE Chi-restraints excluded: chain D residue 304 THR Chi-restraints excluded: chain E residue 4 TRP Chi-restraints excluded: chain E residue 30 VAL Chi-restraints excluded: chain E residue 143 ASP Chi-restraints excluded: chain E residue 168 THR Chi-restraints excluded: chain E residue 199 VAL Chi-restraints excluded: chain E residue 241 THR Chi-restraints excluded: chain E residue 254 TYR Chi-restraints excluded: chain E residue 281 LEU Chi-restraints excluded: chain E residue 282 LEU Chi-restraints excluded: chain E residue 296 LEU Chi-restraints excluded: chain E residue 303 CYS Chi-restraints excluded: chain E residue 329 ILE Chi-restraints excluded: chain E residue 332 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 121 optimal weight: 1.9990 chunk 61 optimal weight: 5.9990 chunk 16 optimal weight: 5.9990 chunk 35 optimal weight: 6.9990 chunk 66 optimal weight: 6.9990 chunk 94 optimal weight: 0.3980 chunk 69 optimal weight: 3.9990 chunk 51 optimal weight: 8.9990 chunk 28 optimal weight: 40.0000 chunk 21 optimal weight: 4.9990 chunk 83 optimal weight: 9.9990 overall best weight: 3.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 132 GLN C 135 GLN C 136 ASN C 156 ASN ** D 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 209 GLN ** E 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4770 r_free = 0.4770 target = 0.212630 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4460 r_free = 0.4460 target = 0.179704 restraints weight = 20533.432| |-----------------------------------------------------------------------------| r_work (start): 0.4410 rms_B_bonded: 2.86 r_work: 0.4202 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.4202 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6702 moved from start: 0.4028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.096 12109 Z= 0.326 Angle : 0.886 12.819 16394 Z= 0.439 Chirality : 0.050 0.230 1915 Planarity : 0.006 0.075 2080 Dihedral : 9.714 132.126 1699 Min Nonbonded Distance : 1.842 Molprobity Statistics. All-atom Clashscore : 20.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer: Outliers : 3.82 % Allowed : 20.00 % Favored : 76.18 % 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: -0.89 (0.21), residues: 1481 helix: -0.28 (0.17), residues: 873 sheet: -1.68 (0.43), residues: 127 loop : -0.52 (0.29), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.006 TRP D 40 HIS 0.008 0.002 HIS A 179 PHE 0.023 0.003 PHE E 339 TYR 0.031 0.003 TYR B 279 ARG 0.011 0.001 ARG A 855 Details of bonding type rmsd hydrogen bonds : bond 0.05329 ( 636) hydrogen bonds : angle 5.30799 ( 1866) covalent geometry : bond 0.00751 (12109) covalent geometry : angle 0.88573 (16394) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2962 Ramachandran restraints generated. 1481 Oldfield, 0 Emsley, 1481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2962 Ramachandran restraints generated. 1481 Oldfield, 0 Emsley, 1481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 175 time to evaluate : 1.311 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 815 TYR cc_start: 0.4441 (m-80) cc_final: 0.3544 (m-80) REVERT: B 51 VAL cc_start: 0.7007 (m) cc_final: 0.6787 (p) REVERT: B 146 MET cc_start: 0.2170 (ttt) cc_final: 0.1903 (tmm) REVERT: B 158 MET cc_start: -0.3385 (ttm) cc_final: -0.3908 (ptm) REVERT: B 229 MET cc_start: 0.4903 (tpp) cc_final: 0.4669 (tpp) REVERT: B 246 ILE cc_start: 0.4928 (mm) cc_final: 0.4707 (mm) REVERT: C 122 VAL cc_start: 0.7718 (t) cc_final: 0.7439 (m) REVERT: C 202 MET cc_start: 0.6060 (tmm) cc_final: 0.5268 (tmm) REVERT: C 214 ARG cc_start: 0.7186 (OUTLIER) cc_final: 0.6769 (tpt90) REVERT: D 77 TYR cc_start: 0.4725 (p90) cc_final: 0.3965 (p90) REVERT: D 257 ILE cc_start: 0.8160 (OUTLIER) cc_final: 0.7757 (mp) REVERT: D 304 THR cc_start: 0.8091 (OUTLIER) cc_final: 0.7891 (p) REVERT: E 281 LEU cc_start: 0.8008 (OUTLIER) cc_final: 0.7775 (tt) REVERT: E 332 LEU cc_start: 0.7966 (OUTLIER) cc_final: 0.7549 (mp) outliers start: 50 outliers final: 34 residues processed: 216 average time/residue: 0.2265 time to fit residues: 71.3265 Evaluate side-chains 193 residues out of total 1311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 154 time to evaluate : 1.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 830 LEU Chi-restraints excluded: chain B residue 171 CYS Chi-restraints excluded: chain B residue 204 ASN Chi-restraints excluded: chain B residue 236 LEU Chi-restraints excluded: chain B residue 257 GLU Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 263 VAL Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 311 TYR Chi-restraints excluded: chain B residue 329 GLU Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 119 PHE Chi-restraints excluded: chain C residue 161 ILE Chi-restraints excluded: chain C residue 162 ILE Chi-restraints excluded: chain C residue 178 THR Chi-restraints excluded: chain C residue 214 ARG Chi-restraints excluded: chain C residue 314 VAL Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain C residue 334 ASP Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 74 LEU Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain D residue 147 VAL Chi-restraints excluded: chain D residue 221 LYS Chi-restraints excluded: chain D residue 257 ILE Chi-restraints excluded: chain D residue 304 THR Chi-restraints excluded: chain E residue 30 VAL Chi-restraints excluded: chain E residue 106 VAL Chi-restraints excluded: chain E residue 143 ASP Chi-restraints excluded: chain E residue 168 THR Chi-restraints excluded: chain E residue 199 VAL Chi-restraints excluded: chain E residue 206 ASN Chi-restraints excluded: chain E residue 241 THR Chi-restraints excluded: chain E residue 281 LEU Chi-restraints excluded: chain E residue 282 LEU Chi-restraints excluded: chain E residue 296 LEU Chi-restraints excluded: chain E residue 302 ASN Chi-restraints excluded: chain E residue 332 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 104 optimal weight: 0.6980 chunk 75 optimal weight: 1.9990 chunk 88 optimal weight: 4.9990 chunk 134 optimal weight: 0.8980 chunk 27 optimal weight: 8.9990 chunk 14 optimal weight: 5.9990 chunk 142 optimal weight: 0.0070 chunk 72 optimal weight: 0.8980 chunk 94 optimal weight: 2.9990 chunk 132 optimal weight: 0.7980 chunk 138 optimal weight: 0.6980 overall best weight: 0.6198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 210 GLN E 302 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4777 r_free = 0.4777 target = 0.215581 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4426 r_free = 0.4426 target = 0.179625 restraints weight = 20546.285| |-----------------------------------------------------------------------------| r_work (start): 0.4387 rms_B_bonded: 3.00 r_work: 0.4191 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.4191 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6522 moved from start: 0.3914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 12109 Z= 0.139 Angle : 0.670 12.546 16394 Z= 0.331 Chirality : 0.042 0.219 1915 Planarity : 0.005 0.066 2080 Dihedral : 9.046 123.541 1697 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 14.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 2.44 % Allowed : 21.45 % Favored : 76.11 % 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: -0.33 (0.22), residues: 1481 helix: 0.14 (0.17), residues: 875 sheet: -1.55 (0.43), residues: 132 loop : -0.17 (0.30), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.065 0.004 TRP D 40 HIS 0.010 0.001 HIS C 55 PHE 0.013 0.001 PHE E 346 TYR 0.027 0.002 TYR B 322 ARG 0.006 0.001 ARG E 234 Details of bonding type rmsd hydrogen bonds : bond 0.03701 ( 636) hydrogen bonds : angle 4.69826 ( 1866) covalent geometry : bond 0.00308 (12109) covalent geometry : angle 0.66991 (16394) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2962 Ramachandran restraints generated. 1481 Oldfield, 0 Emsley, 1481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2962 Ramachandran restraints generated. 1481 Oldfield, 0 Emsley, 1481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 172 time to evaluate : 1.296 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 815 TYR cc_start: 0.4239 (m-80) cc_final: 0.3514 (m-80) REVERT: A 827 PHE cc_start: 0.5298 (m-10) cc_final: 0.4342 (m-10) REVERT: B 146 MET cc_start: 0.2282 (ttt) cc_final: 0.1952 (tmm) REVERT: B 158 MET cc_start: -0.3336 (ttm) cc_final: -0.3841 (ptm) REVERT: B 229 MET cc_start: 0.4780 (tpp) cc_final: 0.4346 (tpp) REVERT: B 246 ILE cc_start: 0.4771 (mm) cc_final: 0.4515 (mm) REVERT: B 341 LEU cc_start: 0.8152 (mp) cc_final: 0.7618 (mt) REVERT: C 122 VAL cc_start: 0.7336 (t) cc_final: 0.7041 (m) REVERT: C 191 GLU cc_start: 0.8104 (OUTLIER) cc_final: 0.7604 (mm-30) REVERT: C 202 MET cc_start: 0.5699 (tmm) cc_final: 0.5176 (tmm) REVERT: C 212 ASP cc_start: 0.7531 (p0) cc_final: 0.7260 (p0) REVERT: D 77 TYR cc_start: 0.4558 (p90) cc_final: 0.3832 (p90) REVERT: E 281 LEU cc_start: 0.7858 (OUTLIER) cc_final: 0.7536 (tt) outliers start: 32 outliers final: 27 residues processed: 199 average time/residue: 0.2275 time to fit residues: 66.0151 Evaluate side-chains 187 residues out of total 1311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 158 time to evaluate : 1.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 830 LEU Chi-restraints excluded: chain B residue 171 CYS Chi-restraints excluded: chain B residue 204 ASN Chi-restraints excluded: chain B residue 236 LEU Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 263 VAL Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 123 ILE Chi-restraints excluded: chain C residue 161 ILE Chi-restraints excluded: chain C residue 162 ILE Chi-restraints excluded: chain C residue 178 THR Chi-restraints excluded: chain C residue 191 GLU Chi-restraints excluded: chain C residue 314 VAL Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 74 LEU Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain D residue 188 GLU Chi-restraints excluded: chain D residue 221 LYS Chi-restraints excluded: chain D residue 232 LYS Chi-restraints excluded: chain D residue 295 ASP Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain E residue 143 ASP Chi-restraints excluded: chain E residue 168 THR Chi-restraints excluded: chain E residue 241 THR Chi-restraints excluded: chain E residue 281 LEU Chi-restraints excluded: chain E residue 282 LEU Chi-restraints excluded: chain E residue 296 LEU Chi-restraints excluded: chain E residue 303 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 132 optimal weight: 2.9990 chunk 110 optimal weight: 5.9990 chunk 144 optimal weight: 0.9980 chunk 60 optimal weight: 6.9990 chunk 24 optimal weight: 3.9990 chunk 53 optimal weight: 9.9990 chunk 54 optimal weight: 6.9990 chunk 120 optimal weight: 0.8980 chunk 95 optimal weight: 0.7980 chunk 59 optimal weight: 5.9990 chunk 107 optimal weight: 0.7980 overall best weight: 1.2982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 206 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4768 r_free = 0.4768 target = 0.214190 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4411 r_free = 0.4411 target = 0.178237 restraints weight = 20407.413| |-----------------------------------------------------------------------------| r_work (start): 0.4376 rms_B_bonded: 2.79 r_work: 0.4185 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.4185 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6553 moved from start: 0.4060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 12109 Z= 0.166 Angle : 0.681 12.078 16394 Z= 0.336 Chirality : 0.042 0.227 1915 Planarity : 0.005 0.065 2080 Dihedral : 8.968 125.739 1697 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 15.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 2.82 % Allowed : 21.68 % Favored : 75.50 % 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: -0.18 (0.22), residues: 1481 helix: 0.28 (0.17), residues: 878 sheet: -1.48 (0.43), residues: 132 loop : -0.16 (0.30), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.063 0.004 TRP D 40 HIS 0.005 0.001 HIS C 55 PHE 0.014 0.002 PHE D 176 TYR 0.022 0.002 TYR D 44 ARG 0.007 0.000 ARG E 234 Details of bonding type rmsd hydrogen bonds : bond 0.03816 ( 636) hydrogen bonds : angle 4.61516 ( 1866) covalent geometry : bond 0.00379 (12109) covalent geometry : angle 0.68118 (16394) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2962 Ramachandran restraints generated. 1481 Oldfield, 0 Emsley, 1481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2962 Ramachandran restraints generated. 1481 Oldfield, 0 Emsley, 1481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 166 time to evaluate : 1.320 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 806 GLU cc_start: 0.4093 (mp0) cc_final: 0.3847 (mp0) REVERT: A 815 TYR cc_start: 0.4268 (m-80) cc_final: 0.3561 (m-80) REVERT: B 146 MET cc_start: 0.2284 (ttt) cc_final: 0.2014 (tmm) REVERT: B 158 MET cc_start: -0.3528 (ttm) cc_final: -0.3993 (ptm) REVERT: B 229 MET cc_start: 0.4800 (tpp) cc_final: 0.4531 (tpp) REVERT: B 246 ILE cc_start: 0.4801 (mm) cc_final: 0.4560 (mm) REVERT: B 308 MET cc_start: 0.7490 (mmm) cc_final: 0.6877 (mmt) REVERT: C 122 VAL cc_start: 0.7381 (t) cc_final: 0.7085 (m) REVERT: C 202 MET cc_start: 0.5820 (tmm) cc_final: 0.5424 (tmm) REVERT: C 212 ASP cc_start: 0.7602 (p0) cc_final: 0.7271 (p0) REVERT: C 213 MET cc_start: 0.7098 (mmp) cc_final: 0.6430 (mmp) REVERT: D 77 TYR cc_start: 0.4568 (p90) cc_final: 0.3931 (p90) REVERT: D 257 ILE cc_start: 0.8115 (OUTLIER) cc_final: 0.7742 (mp) REVERT: D 304 THR cc_start: 0.8145 (OUTLIER) cc_final: 0.7938 (p) REVERT: D 356 MET cc_start: 0.7836 (mtp) cc_final: 0.7630 (mtp) REVERT: E 108 ILE cc_start: 0.7507 (mm) cc_final: 0.7287 (mt) REVERT: E 281 LEU cc_start: 0.7907 (OUTLIER) cc_final: 0.7605 (tt) outliers start: 37 outliers final: 28 residues processed: 192 average time/residue: 0.2206 time to fit residues: 62.4589 Evaluate side-chains 189 residues out of total 1311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 158 time to evaluate : 1.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 830 LEU Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 171 CYS Chi-restraints excluded: chain B residue 204 ASN Chi-restraints excluded: chain B residue 236 LEU Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 263 VAL Chi-restraints excluded: chain B residue 311 TYR Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 123 ILE Chi-restraints excluded: chain C residue 161 ILE Chi-restraints excluded: chain C residue 162 ILE Chi-restraints excluded: chain C residue 219 ILE Chi-restraints excluded: chain C residue 314 VAL Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 74 LEU Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain D residue 167 MET Chi-restraints excluded: chain D residue 221 LYS Chi-restraints excluded: chain D residue 232 LYS Chi-restraints excluded: chain D residue 257 ILE Chi-restraints excluded: chain D residue 295 ASP Chi-restraints excluded: chain D residue 304 THR Chi-restraints excluded: chain E residue 143 ASP Chi-restraints excluded: chain E residue 206 ASN Chi-restraints excluded: chain E residue 241 THR Chi-restraints excluded: chain E residue 281 LEU Chi-restraints excluded: chain E residue 282 LEU Chi-restraints excluded: chain E residue 296 LEU Chi-restraints excluded: chain E residue 302 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 36 optimal weight: 10.0000 chunk 77 optimal weight: 2.9990 chunk 5 optimal weight: 0.2980 chunk 18 optimal weight: 4.9990 chunk 1 optimal weight: 3.9990 chunk 22 optimal weight: 7.9990 chunk 135 optimal weight: 0.9980 chunk 31 optimal weight: 8.9990 chunk 9 optimal weight: 2.9990 chunk 44 optimal weight: 4.9990 chunk 27 optimal weight: 9.9990 overall best weight: 2.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 31 GLN ** E 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 206 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4754 r_free = 0.4754 target = 0.213176 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4421 r_free = 0.4421 target = 0.178438 restraints weight = 20252.846| |-----------------------------------------------------------------------------| r_work (start): 0.4374 rms_B_bonded: 3.19 r_work: 0.4167 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.4167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6635 moved from start: 0.4330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 12109 Z= 0.233 Angle : 0.771 11.829 16394 Z= 0.383 Chirality : 0.045 0.208 1915 Planarity : 0.006 0.069 2080 Dihedral : 9.070 129.734 1697 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 16.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 2.37 % Allowed : 22.52 % Favored : 75.11 % 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: -0.44 (0.22), residues: 1481 helix: 0.10 (0.17), residues: 876 sheet: -1.49 (0.43), residues: 132 loop : -0.35 (0.30), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.065 0.004 TRP D 40 HIS 0.005 0.001 HIS C 37 PHE 0.035 0.002 PHE E 339 TYR 0.047 0.003 TYR B 322 ARG 0.008 0.001 ARG E 51 Details of bonding type rmsd hydrogen bonds : bond 0.04398 ( 636) hydrogen bonds : angle 4.87529 ( 1866) covalent geometry : bond 0.00541 (12109) covalent geometry : angle 0.77118 (16394) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2962 Ramachandran restraints generated. 1481 Oldfield, 0 Emsley, 1481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2962 Ramachandran restraints generated. 1481 Oldfield, 0 Emsley, 1481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 157 time to evaluate : 1.298 Fit side-chains revert: symmetry clash REVERT: A 806 GLU cc_start: 0.4001 (mp0) cc_final: 0.3769 (mp0) REVERT: A 815 TYR cc_start: 0.4322 (m-80) cc_final: 0.3629 (m-80) REVERT: B 146 MET cc_start: 0.2416 (ttt) cc_final: 0.2102 (tmm) REVERT: B 158 MET cc_start: -0.3619 (ttm) cc_final: -0.4036 (ptm) REVERT: B 229 MET cc_start: 0.4862 (tpp) cc_final: 0.4425 (tpp) REVERT: B 246 ILE cc_start: 0.4915 (mm) cc_final: 0.4675 (mm) REVERT: C 122 VAL cc_start: 0.7468 (t) cc_final: 0.7222 (m) REVERT: C 202 MET cc_start: 0.6009 (tmm) cc_final: 0.5478 (tmm) REVERT: C 214 ARG cc_start: 0.7028 (OUTLIER) cc_final: 0.6480 (tpt90) REVERT: D 77 TYR cc_start: 0.4558 (p90) cc_final: 0.3913 (p90) REVERT: D 120 ARG cc_start: 0.4995 (mtm180) cc_final: 0.4576 (mmm-85) REVERT: D 257 ILE cc_start: 0.8082 (OUTLIER) cc_final: 0.7702 (mp) REVERT: D 304 THR cc_start: 0.8107 (OUTLIER) cc_final: 0.7895 (p) REVERT: E 108 ILE cc_start: 0.7474 (mm) cc_final: 0.7268 (mt) REVERT: E 281 LEU cc_start: 0.7984 (OUTLIER) cc_final: 0.7713 (tt) outliers start: 31 outliers final: 25 residues processed: 182 average time/residue: 0.2223 time to fit residues: 59.8918 Evaluate side-chains 185 residues out of total 1311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 156 time to evaluate : 1.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 830 LEU Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 171 CYS Chi-restraints excluded: chain B residue 204 ASN Chi-restraints excluded: chain B residue 236 LEU Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 263 VAL Chi-restraints excluded: chain B residue 311 TYR Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 123 ILE Chi-restraints excluded: chain C residue 161 ILE Chi-restraints excluded: chain C residue 162 ILE Chi-restraints excluded: chain C residue 214 ARG Chi-restraints excluded: chain C residue 314 VAL Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 74 LEU Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain D residue 221 LYS Chi-restraints excluded: chain D residue 257 ILE Chi-restraints excluded: chain D residue 295 ASP Chi-restraints excluded: chain D residue 304 THR Chi-restraints excluded: chain E residue 30 VAL Chi-restraints excluded: chain E residue 143 ASP Chi-restraints excluded: chain E residue 241 THR Chi-restraints excluded: chain E residue 281 LEU Chi-restraints excluded: chain E residue 282 LEU Chi-restraints excluded: chain E residue 296 LEU Chi-restraints excluded: chain E residue 302 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 55 optimal weight: 0.0370 chunk 17 optimal weight: 0.3980 chunk 7 optimal weight: 0.7980 chunk 30 optimal weight: 30.0000 chunk 39 optimal weight: 0.0050 chunk 122 optimal weight: 2.9990 chunk 50 optimal weight: 10.0000 chunk 131 optimal weight: 0.6980 chunk 102 optimal weight: 0.5980 chunk 73 optimal weight: 0.9980 chunk 89 optimal weight: 0.9990 overall best weight: 0.3472 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 820 ASN ** C 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 289 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 128 GLN ** D 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 37 HIS ** 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 = 0.4792 r_free = 0.4792 target = 0.217229 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4469 r_free = 0.4469 target = 0.183422 restraints weight = 20425.674| |-----------------------------------------------------------------------------| r_work (start): 0.4434 rms_B_bonded: 3.05 r_work: 0.4223 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.4223 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6453 moved from start: 0.4198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 12109 Z= 0.130 Angle : 0.657 12.007 16394 Z= 0.327 Chirality : 0.041 0.174 1915 Planarity : 0.005 0.063 2080 Dihedral : 8.617 120.058 1697 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 13.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 2.21 % Allowed : 22.75 % Favored : 75.04 % 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: 0.05 (0.22), residues: 1481 helix: 0.43 (0.17), residues: 877 sheet: -1.32 (0.43), residues: 135 loop : -0.02 (0.31), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.004 TRP D 40 HIS 0.005 0.001 HIS B 324 PHE 0.029 0.001 PHE E 339 TYR 0.030 0.002 TYR B 322 ARG 0.007 0.001 ARG E 51 Details of bonding type rmsd hydrogen bonds : bond 0.03546 ( 636) hydrogen bonds : angle 4.49801 ( 1866) covalent geometry : bond 0.00289 (12109) covalent geometry : angle 0.65701 (16394) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5853.75 seconds wall clock time: 102 minutes 25.38 seconds (6145.38 seconds total)