Starting phenix.real_space_refine on Wed Feb 12 06:29:17 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dmk_27542/02_2025/8dmk_27542.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dmk_27542/02_2025/8dmk_27542.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8dmk_27542/02_2025/8dmk_27542.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dmk_27542/02_2025/8dmk_27542.map" model { file = "/net/cci-nas-00/data/ceres_data/8dmk_27542/02_2025/8dmk_27542.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dmk_27542/02_2025/8dmk_27542.cif" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.027 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Ca 1 9.91 5 S 64 5.16 5 C 4601 2.51 5 N 1278 2.21 5 O 1404 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 53 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 7348 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2432 Number of conformers: 1 Conformer: "" Number of residues, atoms: 305, 2432 Classifications: {'peptide': 305} Link IDs: {'PTRANS': 22, 'TRANS': 282} Chain: "B" Number of atoms: 2454 Number of conformers: 1 Conformer: "" Number of residues, atoms: 307, 2454 Classifications: {'peptide': 307} Link IDs: {'PTRANS': 16, 'TRANS': 290} Chain: "G" Number of atoms: 2391 Number of conformers: 1 Conformer: "" Number of residues, atoms: 305, 2391 Classifications: {'peptide': 305} Link IDs: {'PTRANS': 16, 'TRANS': 288} Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "G" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Unusual residues: {' CA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 5.16, per 1000 atoms: 0.70 Number of scatterers: 7348 At special positions: 0 Unit cell: (69.012, 122.472, 110.808, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ca 1 19.99 S 64 16.00 O 1404 8.00 N 1278 7.00 C 4601 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=23, symmetry=0 Simple disulfide: pdb=" SG CYS A 48 " - pdb=" SG CYS A 76 " distance=2.03 Simple disulfide: pdb=" SG CYS A 57 " - pdb=" SG CYS A 73 " distance=2.02 Simple disulfide: pdb=" SG CYS A 166 " - pdb=" SG CYS A 189 " distance=2.03 Simple disulfide: pdb=" SG CYS A 277 " - pdb=" SG CYS A 286 " distance=2.03 Simple disulfide: pdb=" SG CYS A 279 " - pdb=" SG CYS A 297 " distance=2.03 Simple disulfide: pdb=" SG CYS A 299 " - pdb=" SG CYS A 308 " distance=2.03 Simple disulfide: pdb=" SG CYS A 304 " - pdb=" SG CYS A 312 " distance=2.03 Simple disulfide: pdb=" SG CYS A 311 " - pdb=" SG CYS A 331 " distance=2.03 Simple disulfide: pdb=" SG CYS B 30 " - pdb=" SG CYS B 35 " distance=2.03 Simple disulfide: pdb=" SG CYS B 56 " - pdb=" SG CYS B 79 " distance=2.03 Simple disulfide: pdb=" SG CYS B 65 " - pdb=" SG CYS B 76 " distance=2.03 Simple disulfide: pdb=" SG CYS B 170 " - pdb=" SG CYS B 190 " distance=2.03 Simple disulfide: pdb=" SG CYS B 271 " - pdb=" SG CYS B 280 " distance=2.03 Simple disulfide: pdb=" SG CYS B 273 " - pdb=" SG CYS B 298 " distance=2.03 Simple disulfide: pdb=" SG CYS B 300 " - pdb=" SG CYS B 309 " distance=2.03 Simple disulfide: pdb=" SG CYS B 312 " - pdb=" SG CYS B 332 " distance=2.03 Simple disulfide: pdb=" SG CYS G 69 " - pdb=" SG CYS G 92 " distance=2.03 Simple disulfide: pdb=" SG CYS G 77 " - pdb=" SG CYS G 89 " distance=2.03 Simple disulfide: pdb=" SG CYS G 182 " - pdb=" SG CYS G 205 " distance=2.03 Simple disulfide: pdb=" SG CYS G 286 " - pdb=" SG CYS G 295 " distance=2.03 Simple disulfide: pdb=" SG CYS G 288 " - pdb=" SG CYS G 305 " distance=2.03 Simple disulfide: pdb=" SG CYS G 307 " - pdb=" SG CYS G 316 " distance=2.03 Simple disulfide: pdb=" SG CYS G 319 " - pdb=" SG CYS G 339 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A 401 " - " ASN A 45 " " NAG A 402 " - " ASN A 79 " " NAG B 401 " - " ASN B 120 " " NAG G 401 " - " ASN G 60 " Time building additional restraints: 1.50 Conformation dependent library (CDL) restraints added in 998.7 milliseconds 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1714 Finding SS restraints... Secondary structure from input PDB file: 19 helices and 14 sheets defined 12.2% alpha, 21.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.04 Creating SS restraints... Processing helix chain 'A' and resid 88 through 92 Processing helix chain 'A' and resid 108 through 113 Processing helix chain 'A' and resid 162 through 169 removed outlier: 3.881A pdb=" N LEU A 167 " --> pdb=" O ASP A 163 " (cutoff:3.500A) Processing helix chain 'A' and resid 219 through 226 removed outlier: 3.951A pdb=" N GLU A 224 " --> pdb=" O PRO A 220 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 247 removed outlier: 3.794A pdb=" N THR A 247 " --> pdb=" O ALA A 243 " (cutoff:3.500A) Processing helix chain 'A' and resid 257 through 262 Processing helix chain 'B' and resid 104 through 110 removed outlier: 4.484A pdb=" N LEU B 108 " --> pdb=" O PRO B 105 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ILE B 110 " --> pdb=" O ARG B 107 " (cutoff:3.500A) Processing helix chain 'B' and resid 169 through 174 Processing helix chain 'B' and resid 221 through 226 Processing helix chain 'B' and resid 254 through 258 Processing helix chain 'G' and resid 79 through 83 removed outlier: 4.108A pdb=" N VAL G 82 " --> pdb=" O GLN G 79 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N THR G 83 " --> pdb=" O THR G 80 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 79 through 83' Processing helix chain 'G' and resid 102 through 106 Processing helix chain 'G' and resid 122 through 126 Processing helix chain 'G' and resid 181 through 186 Processing helix chain 'G' and resid 233 through 236 Processing helix chain 'G' and resid 237 through 245 removed outlier: 3.721A pdb=" N THR G 245 " --> pdb=" O GLN G 241 " (cutoff:3.500A) Processing helix chain 'G' and resid 260 through 264 removed outlier: 4.178A pdb=" N VAL G 263 " --> pdb=" O GLY G 260 " (cutoff:3.500A) Processing helix chain 'G' and resid 266 through 271 Processing helix chain 'G' and resid 321 through 324 removed outlier: 3.971A pdb=" N ASN G 324 " --> pdb=" O PRO G 321 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 321 through 324' Processing sheet with id=AA1, first strand: chain 'A' and resid 34 through 35 removed outlier: 4.452A pdb=" N LEU A 34 " --> pdb=" O GLY A 275 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N GLY A 275 " --> pdb=" O LEU A 34 " (cutoff:3.500A) removed outlier: 7.577A pdb=" N GLY A 274 " --> pdb=" O ALA A 127 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ILE A 231 " --> pdb=" O LEU A 118 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LEU A 120 " --> pdb=" O ARG A 229 " (cutoff:3.500A) removed outlier: 8.167A pdb=" N ARG A 229 " --> pdb=" O LEU A 120 " (cutoff:3.500A) removed outlier: 11.066A pdb=" N GLN A 122 " --> pdb=" O SER A 227 " (cutoff:3.500A) removed outlier: 9.860A pdb=" N SER A 227 " --> pdb=" O GLN A 122 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N SER A 147 " --> pdb=" O ARG A 229 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N ILE A 231 " --> pdb=" O GLU A 145 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N GLU A 145 " --> pdb=" O ILE A 231 " (cutoff:3.500A) removed outlier: 4.780A pdb=" N LEU A 233 " --> pdb=" O ILE A 143 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N ILE A 143 " --> pdb=" O LEU A 233 " (cutoff:3.500A) removed outlier: 5.347A pdb=" N LEU A 235 " --> pdb=" O ASN A 141 " (cutoff:3.500A) removed outlier: 8.094A pdb=" N ASN A 141 " --> pdb=" O LEU A 235 " (cutoff:3.500A) removed outlier: 7.089A pdb=" N TRP A 142 " --> pdb=" O TYR A 158 " (cutoff:3.500A) removed outlier: 5.457A pdb=" N TYR A 158 " --> pdb=" O TRP A 142 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N LEU A 144 " --> pdb=" O TRP A 156 " (cutoff:3.500A) removed outlier: 8.423A pdb=" N THR A 190 " --> pdb=" O TRP A 156 " (cutoff:3.500A) removed outlier: 6.067A pdb=" N TYR A 158 " --> pdb=" O THR A 190 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 41 through 44 Processing sheet with id=AA3, first strand: chain 'A' and resid 54 through 57 Processing sheet with id=AA4, first strand: chain 'A' and resid 100 through 101 removed outlier: 3.559A pdb=" N TRP A 100 " --> pdb=" O ILE A 268 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 288 through 289 removed outlier: 3.644A pdb=" N GLN A 294 " --> pdb=" O ASP A 289 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 40 through 41 removed outlier: 3.725A pdb=" N VAL B 262 " --> pdb=" O TRP B 112 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N TRP B 112 " --> pdb=" O VAL B 262 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 40 through 41 removed outlier: 6.669A pdb=" N THR B 139 " --> pdb=" O TYR B 263 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N MET B 265 " --> pdb=" O ILE B 137 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N ILE B 137 " --> pdb=" O MET B 265 " (cutoff:3.500A) removed outlier: 5.053A pdb=" N VAL B 267 " --> pdb=" O HIS B 135 " (cutoff:3.500A) removed outlier: 7.669A pdb=" N HIS B 135 " --> pdb=" O VAL B 267 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N MET B 138 " --> pdb=" O VAL B 205 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 50 through 52 removed outlier: 4.167A pdb=" N SER B 51 " --> pdb=" O GLN B 124 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLN B 124 " --> pdb=" O SER B 51 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LEU B 149 " --> pdb=" O LYS B 236 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N VAL B 238 " --> pdb=" O ALA B 147 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N ALA B 147 " --> pdb=" O VAL B 238 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N MET B 148 " --> pdb=" O TYR B 165 " (cutoff:3.500A) removed outlier: 4.707A pdb=" N TYR B 165 " --> pdb=" O MET B 148 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N ILE B 150 " --> pdb=" O TYR B 163 " (cutoff:3.500A) removed outlier: 9.253A pdb=" N ASP B 191 " --> pdb=" O TYR B 163 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N TYR B 165 " --> pdb=" O ASP B 191 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 131 through 132 Processing sheet with id=AB1, first strand: chain 'G' and resid 63 through 65 removed outlier: 11.634A pdb=" N LEU G 135 " --> pdb=" O ASN G 254 " (cutoff:3.500A) removed outlier: 10.910A pdb=" N ASN G 254 " --> pdb=" O LEU G 135 " (cutoff:3.500A) removed outlier: 12.939A pdb=" N LEU G 137 " --> pdb=" O THR G 252 " (cutoff:3.500A) removed outlier: 11.869A pdb=" N THR G 252 " --> pdb=" O LEU G 137 " (cutoff:3.500A) removed outlier: 12.403A pdb=" N LEU G 139 " --> pdb=" O SER G 250 " (cutoff:3.500A) removed outlier: 13.058A pdb=" N SER G 250 " --> pdb=" O LEU G 139 " (cutoff:3.500A) removed outlier: 9.733A pdb=" N LYS G 141 " --> pdb=" O ASP G 248 " (cutoff:3.500A) removed outlier: 5.699A pdb=" N ASP G 248 " --> pdb=" O LYS G 141 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N SER G 159 " --> pdb=" O ASN G 254 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N PHE G 160 " --> pdb=" O TYR G 177 " (cutoff:3.500A) removed outlier: 5.121A pdb=" N TYR G 177 " --> pdb=" O PHE G 160 " (cutoff:3.500A) removed outlier: 7.214A pdb=" N ILE G 162 " --> pdb=" O TYR G 175 " (cutoff:3.500A) removed outlier: 7.103A pdb=" N TYR G 175 " --> pdb=" O LEU G 204 " (cutoff:3.500A) removed outlier: 8.765A pdb=" N THR G 206 " --> pdb=" O TYR G 175 " (cutoff:3.500A) removed outlier: 5.926A pdb=" N TYR G 177 " --> pdb=" O THR G 206 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'G' and resid 74 through 75 removed outlier: 4.380A pdb=" N GLU G 74 " --> pdb=" O CYS G 92 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'G' and resid 118 through 119 removed outlier: 3.823A pdb=" N ASP G 279 " --> pdb=" O LYS G 151 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N TYR G 147 " --> pdb=" O GLY G 283 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'G' and resid 292 through 297 removed outlier: 5.243A pdb=" N GLU G 294 " --> pdb=" O ASN G 306 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N VAL G 304 " --> pdb=" O MET G 296 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'G' and resid 311 through 312 removed outlier: 4.199A pdb=" N LYS G 318 " --> pdb=" O TYR G 312 " (cutoff:3.500A) 106 hydrogen bonds defined for protein. 237 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: 1.63 Time building geometry restraints manager: 1.82 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2440 1.34 - 1.46: 1818 1.46 - 1.58: 3204 1.58 - 1.70: 0 1.70 - 1.82: 79 Bond restraints: 7541 Sorted by residual: bond pdb=" C1 NAG A 402 " pdb=" O5 NAG A 402 " ideal model delta sigma weight residual 1.406 1.441 -0.035 2.00e-02 2.50e+03 3.14e+00 bond pdb=" C1 NAG B 401 " pdb=" O5 NAG B 401 " ideal model delta sigma weight residual 1.406 1.434 -0.028 2.00e-02 2.50e+03 1.90e+00 bond pdb=" C1 NAG G 401 " pdb=" O5 NAG G 401 " ideal model delta sigma weight residual 1.406 1.433 -0.027 2.00e-02 2.50e+03 1.88e+00 bond pdb=" C SER G 213 " pdb=" N PRO G 214 " ideal model delta sigma weight residual 1.336 1.351 -0.015 1.20e-02 6.94e+03 1.60e+00 bond pdb=" CD2 HIS B 135 " pdb=" NE2 HIS B 135 " ideal model delta sigma weight residual 1.374 1.361 0.013 1.10e-02 8.26e+03 1.47e+00 ... (remaining 7536 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.69: 10029 1.69 - 3.38: 194 3.38 - 5.08: 18 5.08 - 6.77: 5 6.77 - 8.46: 2 Bond angle restraints: 10248 Sorted by residual: angle pdb=" CA CYS A 73 " pdb=" CB CYS A 73 " pdb=" SG CYS A 73 " ideal model delta sigma weight residual 114.40 122.86 -8.46 2.30e+00 1.89e-01 1.35e+01 angle pdb=" CB MET B 148 " pdb=" CG MET B 148 " pdb=" SD MET B 148 " ideal model delta sigma weight residual 112.70 120.80 -8.10 3.00e+00 1.11e-01 7.29e+00 angle pdb=" CA GLU B 128 " pdb=" CB GLU B 128 " pdb=" CG GLU B 128 " ideal model delta sigma weight residual 114.10 109.19 4.91 2.00e+00 2.50e-01 6.04e+00 angle pdb=" N VAL G 78 " pdb=" CA VAL G 78 " pdb=" C VAL G 78 " ideal model delta sigma weight residual 108.82 106.11 2.71 1.22e+00 6.72e-01 4.93e+00 angle pdb=" CG1 ILE A 271 " pdb=" CB ILE A 271 " pdb=" CG2 ILE A 271 " ideal model delta sigma weight residual 110.70 104.30 6.40 3.00e+00 1.11e-01 4.55e+00 ... (remaining 10243 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.47: 4091 17.47 - 34.94: 411 34.94 - 52.41: 94 52.41 - 69.88: 14 69.88 - 87.35: 13 Dihedral angle restraints: 4623 sinusoidal: 1953 harmonic: 2670 Sorted by residual: dihedral pdb=" CB CYS B 65 " pdb=" SG CYS B 65 " pdb=" SG CYS B 76 " pdb=" CB CYS B 76 " ideal model delta sinusoidal sigma weight residual -86.00 -2.33 -83.67 1 1.00e+01 1.00e-02 8.54e+01 dihedral pdb=" CB CYS A 277 " pdb=" SG CYS A 277 " pdb=" SG CYS A 286 " pdb=" CB CYS A 286 " ideal model delta sinusoidal sigma weight residual 93.00 166.70 -73.70 1 1.00e+01 1.00e-02 6.90e+01 dihedral pdb=" CB CYS A 279 " pdb=" SG CYS A 279 " pdb=" SG CYS A 297 " pdb=" CB CYS A 297 " ideal model delta sinusoidal sigma weight residual 93.00 152.87 -59.87 1 1.00e+01 1.00e-02 4.78e+01 ... (remaining 4620 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 954 0.060 - 0.121: 133 0.121 - 0.181: 10 0.181 - 0.241: 1 0.241 - 0.301: 1 Chirality restraints: 1099 Sorted by residual: chirality pdb=" C1 NAG A 402 " pdb=" ND2 ASN A 79 " pdb=" C2 NAG A 402 " pdb=" O5 NAG A 402 " both_signs ideal model delta sigma weight residual False -2.40 -2.10 -0.30 2.00e-01 2.50e+01 2.27e+00 chirality pdb=" CB ILE A 271 " pdb=" CA ILE A 271 " pdb=" CG1 ILE A 271 " pdb=" CG2 ILE A 271 " both_signs ideal model delta sigma weight residual False 2.64 2.83 -0.18 2.00e-01 2.50e+01 8.24e-01 chirality pdb=" CA VAL G 78 " pdb=" N VAL G 78 " pdb=" C VAL G 78 " pdb=" CB VAL G 78 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 5.15e-01 ... (remaining 1096 not shown) Planarity restraints: 1346 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR G 71 " 0.040 5.00e-02 4.00e+02 5.94e-02 5.65e+00 pdb=" N PRO G 72 " -0.103 5.00e-02 4.00e+02 pdb=" CA PRO G 72 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO G 72 " 0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 60 " -0.009 2.00e-02 2.50e+03 1.72e-02 2.95e+00 pdb=" C VAL A 60 " 0.030 2.00e-02 2.50e+03 pdb=" O VAL A 60 " -0.011 2.00e-02 2.50e+03 pdb=" N GLU A 61 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ARG A 66 " -0.026 5.00e-02 4.00e+02 3.94e-02 2.48e+00 pdb=" N PRO A 67 " 0.068 5.00e-02 4.00e+02 pdb=" CA PRO A 67 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 67 " -0.022 5.00e-02 4.00e+02 ... (remaining 1343 not shown) Histogram of nonbonded interaction distances: 1.43 - 2.12: 1 2.12 - 2.81: 2296 2.81 - 3.51: 10254 3.51 - 4.20: 17825 4.20 - 4.90: 29420 Nonbonded interactions: 59796 Sorted by model distance: nonbonded pdb=" OD2 ASP G 108 " pdb=" OG1 THR G 116 " model vdw 1.425 3.040 nonbonded pdb=" O ARG A 69 " pdb=" OH TYR G 109 " model vdw 2.154 3.040 nonbonded pdb=" OE2 GLU A 203 " pdb=" OG SER B 200 " model vdw 2.195 3.040 nonbonded pdb=" OG1 THR B 102 " pdb=" OG1 THR G 80 " model vdw 2.196 3.040 nonbonded pdb=" NH1 ARG A 263 " pdb=" OH TYR G 147 " model vdw 2.217 3.120 ... (remaining 59791 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 group one per residue 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: 1.720 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.280 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 19.570 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6574 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 0.039 7541 Z= 0.175 Angle : 0.570 8.462 10248 Z= 0.305 Chirality : 0.044 0.301 1099 Planarity : 0.004 0.059 1342 Dihedral : 14.545 87.345 2840 Min Nonbonded Distance : 1.425 Molprobity Statistics. All-atom Clashscore : 12.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.37 % Favored : 93.63 % Rotamer: Outliers : 0.00 % Allowed : 0.12 % Favored : 99.88 % 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: -1.18 (0.28), residues: 911 helix: -2.84 (0.52), residues: 59 sheet: -0.45 (0.48), residues: 135 loop : -0.69 (0.24), residues: 717 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP G 172 HIS 0.005 0.001 HIS A 62 PHE 0.025 0.001 PHE A 56 TYR 0.019 0.001 TYR B 263 ARG 0.009 0.000 ARG A 262 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 88 time to evaluate : 0.791 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 56 PHE cc_start: 0.7276 (p90) cc_final: 0.6993 (p90) REVERT: B 259 TYR cc_start: 0.7935 (p90) cc_final: 0.7723 (p90) outliers start: 0 outliers final: 0 residues processed: 88 average time/residue: 0.1973 time to fit residues: 23.8795 Evaluate side-chains 69 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 69 time to evaluate : 0.782 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 75 optimal weight: 6.9990 chunk 68 optimal weight: 0.9980 chunk 37 optimal weight: 0.9990 chunk 23 optimal weight: 3.9990 chunk 46 optimal weight: 9.9990 chunk 36 optimal weight: 0.7980 chunk 70 optimal weight: 7.9990 chunk 27 optimal weight: 7.9990 chunk 42 optimal weight: 9.9990 chunk 52 optimal weight: 3.9990 chunk 81 optimal weight: 3.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4332 r_free = 0.4332 target = 0.115966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.095682 restraints weight = 22689.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.098762 restraints weight = 13078.331| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.100852 restraints weight = 8926.775| |-----------------------------------------------------------------------------| r_work (final): 0.4085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7321 moved from start: 0.1452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 7541 Z= 0.281 Angle : 0.633 9.998 10248 Z= 0.323 Chirality : 0.045 0.344 1099 Planarity : 0.005 0.054 1342 Dihedral : 5.646 57.860 1114 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 14.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.81 % Favored : 93.19 % Rotamer: Outliers : 0.87 % Allowed : 8.48 % Favored : 90.65 % 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: -1.47 (0.28), residues: 911 helix: -2.78 (0.47), residues: 77 sheet: -1.08 (0.43), residues: 151 loop : -0.74 (0.24), residues: 683 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP G 117 HIS 0.011 0.001 HIS B 135 PHE 0.017 0.002 PHE A 56 TYR 0.025 0.002 TYR G 175 ARG 0.010 0.001 ARG A 262 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 74 time to evaluate : 0.823 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 230 ILE cc_start: 0.7083 (mm) cc_final: 0.6744 (mm) outliers start: 7 outliers final: 4 residues processed: 77 average time/residue: 0.2075 time to fit residues: 22.0929 Evaluate side-chains 73 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 69 time to evaluate : 0.988 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 316 HIS Chi-restraints excluded: chain B residue 106 ASN Chi-restraints excluded: chain G residue 71 THR Chi-restraints excluded: chain G residue 249 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 9 optimal weight: 1.9990 chunk 76 optimal weight: 10.0000 chunk 77 optimal weight: 0.9980 chunk 43 optimal weight: 0.7980 chunk 15 optimal weight: 4.9990 chunk 44 optimal weight: 5.9990 chunk 2 optimal weight: 4.9990 chunk 69 optimal weight: 4.9990 chunk 17 optimal weight: 5.9990 chunk 29 optimal weight: 0.9990 chunk 53 optimal weight: 3.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 112 HIS B 225 GLN ** B 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 310 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4319 r_free = 0.4319 target = 0.115376 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.094907 restraints weight = 22936.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.098046 restraints weight = 13144.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.100129 restraints weight = 8939.045| |-----------------------------------------------------------------------------| r_work (final): 0.4064 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7348 moved from start: 0.1937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 7541 Z= 0.233 Angle : 0.596 10.196 10248 Z= 0.303 Chirality : 0.045 0.349 1099 Planarity : 0.004 0.043 1342 Dihedral : 5.454 51.105 1114 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 13.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.15 % Favored : 93.85 % Rotamer: Outliers : 1.62 % Allowed : 11.47 % Favored : 86.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.61 (0.27), residues: 911 helix: -2.78 (0.47), residues: 76 sheet: -1.13 (0.43), residues: 144 loop : -0.87 (0.24), residues: 691 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 111 HIS 0.007 0.001 HIS B 135 PHE 0.011 0.001 PHE B 237 TYR 0.023 0.002 TYR G 175 ARG 0.004 0.000 ARG A 262 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 74 time to evaluate : 0.890 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 56 PHE cc_start: 0.7529 (p90) cc_final: 0.7204 (p90) REVERT: A 290 GLU cc_start: 0.7949 (mm-30) cc_final: 0.7604 (mm-30) REVERT: B 135 HIS cc_start: 0.7963 (p-80) cc_final: 0.7433 (p90) REVERT: B 230 ILE cc_start: 0.7290 (mm) cc_final: 0.7015 (mm) outliers start: 13 outliers final: 8 residues processed: 82 average time/residue: 0.1947 time to fit residues: 21.9967 Evaluate side-chains 74 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 66 time to evaluate : 0.784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 HIS Chi-restraints excluded: chain A residue 316 HIS Chi-restraints excluded: chain B residue 65 CYS Chi-restraints excluded: chain B residue 106 ASN Chi-restraints excluded: chain G residue 71 THR Chi-restraints excluded: chain G residue 129 TYR Chi-restraints excluded: chain G residue 261 ASP Chi-restraints excluded: chain G residue 312 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 43 optimal weight: 2.9990 chunk 24 optimal weight: 5.9990 chunk 78 optimal weight: 7.9990 chunk 30 optimal weight: 8.9990 chunk 56 optimal weight: 8.9990 chunk 8 optimal weight: 5.9990 chunk 15 optimal weight: 7.9990 chunk 34 optimal weight: 6.9990 chunk 16 optimal weight: 6.9990 chunk 81 optimal weight: 5.9990 chunk 14 optimal weight: 5.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 70 HIS A 101 GLN A 112 HIS A 242 ASN ** A 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4178 r_free = 0.4178 target = 0.106701 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.086083 restraints weight = 24048.563| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.088878 restraints weight = 14120.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.090804 restraints weight = 9865.078| |-----------------------------------------------------------------------------| r_work (final): 0.3896 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7579 moved from start: 0.3280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.074 7541 Z= 0.574 Angle : 0.832 10.772 10248 Z= 0.439 Chirality : 0.051 0.397 1099 Planarity : 0.006 0.058 1342 Dihedral : 6.652 59.635 1114 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 24.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.99 % Favored : 90.01 % Rotamer: Outliers : 2.12 % Allowed : 17.58 % Favored : 80.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.18 (0.27), residues: 911 helix: -2.66 (0.49), residues: 69 sheet: -1.43 (0.45), residues: 131 loop : -1.42 (0.23), residues: 711 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.003 TRP A 113 HIS 0.015 0.002 HIS B 135 PHE 0.018 0.003 PHE G 209 TYR 0.035 0.003 TYR G 175 ARG 0.005 0.001 ARG A 234 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 60 time to evaluate : 0.827 Fit side-chains revert: symmetry clash REVERT: A 246 MET cc_start: 0.6267 (tmm) cc_final: 0.5841 (tmm) REVERT: A 301 HIS cc_start: 0.7171 (t70) cc_final: 0.6892 (t-90) REVERT: B 230 ILE cc_start: 0.7504 (mm) cc_final: 0.7217 (mm) outliers start: 17 outliers final: 10 residues processed: 73 average time/residue: 0.1669 time to fit residues: 17.7349 Evaluate side-chains 65 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 55 time to evaluate : 0.873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 HIS Chi-restraints excluded: chain A residue 316 HIS Chi-restraints excluded: chain B residue 65 CYS Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 106 ASN Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain G residue 71 THR Chi-restraints excluded: chain G residue 129 TYR Chi-restraints excluded: chain G residue 249 ILE Chi-restraints excluded: chain G residue 312 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 52 optimal weight: 0.1980 chunk 73 optimal weight: 0.0000 chunk 48 optimal weight: 2.9990 chunk 55 optimal weight: 3.9990 chunk 32 optimal weight: 4.9990 chunk 46 optimal weight: 6.9990 chunk 81 optimal weight: 3.9990 chunk 78 optimal weight: 0.6980 chunk 61 optimal weight: 3.9990 chunk 85 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 overall best weight: 0.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 70 HIS A 101 GLN A 112 HIS A 301 HIS A 302 ASN ** B 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 98 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 = 0.4274 r_free = 0.4274 target = 0.112642 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.092286 restraints weight = 23185.638| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.095306 restraints weight = 13385.572| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.097324 restraints weight = 9200.352| |-----------------------------------------------------------------------------| r_work (final): 0.4015 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7411 moved from start: 0.2927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 7541 Z= 0.195 Angle : 0.607 10.637 10248 Z= 0.310 Chirality : 0.045 0.350 1099 Planarity : 0.005 0.046 1342 Dihedral : 5.587 47.981 1114 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 13.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.71 % Favored : 94.29 % Rotamer: Outliers : 1.87 % Allowed : 19.20 % Favored : 78.93 % 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: -1.93 (0.27), residues: 911 helix: -2.73 (0.47), residues: 75 sheet: -1.42 (0.45), residues: 138 loop : -1.14 (0.24), residues: 698 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 100 HIS 0.008 0.001 HIS A 301 PHE 0.012 0.001 PHE B 237 TYR 0.028 0.002 TYR G 175 ARG 0.006 0.000 ARG A 69 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 72 time to evaluate : 0.829 Fit side-chains REVERT: A 246 MET cc_start: 0.6066 (tmm) cc_final: 0.5738 (tmm) REVERT: B 230 ILE cc_start: 0.7576 (mm) cc_final: 0.7297 (mm) outliers start: 15 outliers final: 8 residues processed: 84 average time/residue: 0.1735 time to fit residues: 20.7847 Evaluate side-chains 68 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 60 time to evaluate : 0.821 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 HIS Chi-restraints excluded: chain A residue 316 HIS Chi-restraints excluded: chain B residue 65 CYS Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 254 ILE Chi-restraints excluded: chain G residue 71 THR Chi-restraints excluded: chain G residue 129 TYR Chi-restraints excluded: chain G residue 312 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 8 optimal weight: 6.9990 chunk 71 optimal weight: 3.9990 chunk 87 optimal weight: 9.9990 chunk 17 optimal weight: 4.9990 chunk 82 optimal weight: 1.9990 chunk 54 optimal weight: 2.9990 chunk 45 optimal weight: 10.0000 chunk 42 optimal weight: 9.9990 chunk 40 optimal weight: 2.9990 chunk 26 optimal weight: 6.9990 chunk 46 optimal weight: 5.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 70 HIS A 101 GLN A 112 HIS ** A 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 90 ASN ** B 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4211 r_free = 0.4211 target = 0.110197 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.088596 restraints weight = 23800.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.091559 restraints weight = 13761.840| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.093627 restraints weight = 9520.413| |-----------------------------------------------------------------------------| r_work (final): 0.3921 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7537 moved from start: 0.3379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 7541 Z= 0.399 Angle : 0.698 10.520 10248 Z= 0.363 Chirality : 0.047 0.377 1099 Planarity : 0.005 0.046 1342 Dihedral : 5.912 56.168 1114 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 19.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.66 % Favored : 90.34 % Rotamer: Outliers : 2.74 % Allowed : 19.95 % Favored : 77.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.12 (0.27), residues: 911 helix: -2.50 (0.49), residues: 68 sheet: -1.36 (0.49), residues: 121 loop : -1.40 (0.23), residues: 722 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 113 HIS 0.011 0.002 HIS A 301 PHE 0.013 0.002 PHE G 209 TYR 0.030 0.002 TYR G 175 ARG 0.004 0.001 ARG B 152 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 58 time to evaluate : 0.880 Fit side-chains revert: symmetry clash REVERT: A 301 HIS cc_start: 0.7453 (t70) cc_final: 0.6987 (t-90) REVERT: B 230 ILE cc_start: 0.7639 (mm) cc_final: 0.7350 (mm) REVERT: B 258 TYR cc_start: 0.6500 (m-10) cc_final: 0.6133 (m-10) outliers start: 22 outliers final: 13 residues processed: 76 average time/residue: 0.1627 time to fit residues: 18.1942 Evaluate side-chains 71 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 58 time to evaluate : 0.867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 HIS Chi-restraints excluded: chain A residue 316 HIS Chi-restraints excluded: chain B residue 65 CYS Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 106 ASN Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 254 ILE Chi-restraints excluded: chain G residue 71 THR Chi-restraints excluded: chain G residue 129 TYR Chi-restraints excluded: chain G residue 155 SER Chi-restraints excluded: chain G residue 249 ILE Chi-restraints excluded: chain G residue 261 ASP Chi-restraints excluded: chain G residue 312 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 4 optimal weight: 5.9990 chunk 71 optimal weight: 0.7980 chunk 79 optimal weight: 10.0000 chunk 81 optimal weight: 5.9990 chunk 22 optimal weight: 0.9990 chunk 9 optimal weight: 2.9990 chunk 59 optimal weight: 0.0020 chunk 64 optimal weight: 4.9990 chunk 46 optimal weight: 0.9990 chunk 54 optimal weight: 4.9990 chunk 2 optimal weight: 0.8980 overall best weight: 0.7392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 70 HIS A 101 GLN A 112 HIS A 301 HIS ** B 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4280 r_free = 0.4280 target = 0.114551 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.093055 restraints weight = 23231.881| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.096119 restraints weight = 13546.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.098263 restraints weight = 9378.596| |-----------------------------------------------------------------------------| r_work (final): 0.4023 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7416 moved from start: 0.3140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 7541 Z= 0.183 Angle : 0.610 10.684 10248 Z= 0.310 Chirality : 0.045 0.353 1099 Planarity : 0.005 0.044 1342 Dihedral : 5.312 46.344 1114 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 13.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.37 % Favored : 93.63 % Rotamer: Outliers : 2.00 % Allowed : 20.45 % 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: -1.95 (0.27), residues: 911 helix: -2.98 (0.45), residues: 73 sheet: -1.23 (0.46), residues: 134 loop : -1.18 (0.24), residues: 704 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 100 HIS 0.006 0.001 HIS B 135 PHE 0.010 0.001 PHE B 237 TYR 0.031 0.001 TYR G 175 ARG 0.004 0.000 ARG B 152 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 67 time to evaluate : 0.770 Fit side-chains REVERT: A 246 MET cc_start: 0.6126 (tmm) cc_final: 0.5868 (tmm) REVERT: A 301 HIS cc_start: 0.7450 (t-90) cc_final: 0.7169 (t-90) REVERT: B 230 ILE cc_start: 0.7601 (OUTLIER) cc_final: 0.7226 (mm) outliers start: 16 outliers final: 9 residues processed: 79 average time/residue: 0.1701 time to fit residues: 19.4992 Evaluate side-chains 73 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 63 time to evaluate : 0.852 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 HIS Chi-restraints excluded: chain A residue 316 HIS Chi-restraints excluded: chain B residue 65 CYS Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 230 ILE Chi-restraints excluded: chain B residue 254 ILE Chi-restraints excluded: chain G residue 71 THR Chi-restraints excluded: chain G residue 129 TYR Chi-restraints excluded: chain G residue 249 ILE Chi-restraints excluded: chain G residue 312 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 29 optimal weight: 3.9990 chunk 30 optimal weight: 0.5980 chunk 34 optimal weight: 6.9990 chunk 25 optimal weight: 5.9990 chunk 85 optimal weight: 7.9990 chunk 48 optimal weight: 0.4980 chunk 7 optimal weight: 0.0870 chunk 82 optimal weight: 0.9990 chunk 87 optimal weight: 10.0000 chunk 70 optimal weight: 0.9990 chunk 83 optimal weight: 0.9980 overall best weight: 0.6360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 62 HIS A 70 HIS A 101 GLN A 112 HIS B 225 GLN ** B 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 98 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 = 0.4296 r_free = 0.4296 target = 0.115456 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.094109 restraints weight = 23321.406| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.097245 restraints weight = 13569.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.099358 restraints weight = 9358.995| |-----------------------------------------------------------------------------| r_work (final): 0.4034 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7391 moved from start: 0.3121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 7541 Z= 0.177 Angle : 0.610 10.444 10248 Z= 0.307 Chirality : 0.045 0.356 1099 Planarity : 0.005 0.085 1342 Dihedral : 5.146 46.488 1114 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 12.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.24 % Favored : 92.76 % Rotamer: Outliers : 1.87 % Allowed : 21.32 % Favored : 76.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.86 (0.28), residues: 911 helix: -2.94 (0.45), residues: 74 sheet: -1.11 (0.47), residues: 134 loop : -1.12 (0.24), residues: 703 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 100 HIS 0.010 0.001 HIS A 70 PHE 0.030 0.001 PHE A 56 TYR 0.016 0.001 TYR G 175 ARG 0.007 0.000 ARG A 321 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 68 time to evaluate : 0.697 Fit side-chains REVERT: A 100 TRP cc_start: 0.6579 (p-90) cc_final: 0.6123 (p-90) REVERT: A 246 MET cc_start: 0.6046 (tmm) cc_final: 0.5843 (tmm) REVERT: A 301 HIS cc_start: 0.7346 (t-90) cc_final: 0.7116 (t70) REVERT: B 230 ILE cc_start: 0.7553 (OUTLIER) cc_final: 0.7124 (mm) outliers start: 15 outliers final: 11 residues processed: 79 average time/residue: 0.1691 time to fit residues: 19.0999 Evaluate side-chains 74 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 62 time to evaluate : 0.816 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 HIS Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 316 HIS Chi-restraints excluded: chain B residue 65 CYS Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 230 ILE Chi-restraints excluded: chain B residue 254 ILE Chi-restraints excluded: chain G residue 71 THR Chi-restraints excluded: chain G residue 129 TYR Chi-restraints excluded: chain G residue 247 THR Chi-restraints excluded: chain G residue 249 ILE Chi-restraints excluded: chain G residue 312 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 20 optimal weight: 6.9990 chunk 35 optimal weight: 10.0000 chunk 16 optimal weight: 9.9990 chunk 14 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 6 optimal weight: 6.9990 chunk 39 optimal weight: 1.9990 chunk 46 optimal weight: 0.8980 chunk 1 optimal weight: 2.9990 chunk 26 optimal weight: 0.1980 chunk 32 optimal weight: 0.7980 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 101 GLN A 112 HIS A 318 GLN ** B 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4285 r_free = 0.4285 target = 0.114737 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.093476 restraints weight = 23611.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.096592 restraints weight = 13717.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.098723 restraints weight = 9432.910| |-----------------------------------------------------------------------------| r_work (final): 0.4020 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7406 moved from start: 0.3178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 7541 Z= 0.202 Angle : 0.619 10.552 10248 Z= 0.312 Chirality : 0.045 0.359 1099 Planarity : 0.004 0.044 1342 Dihedral : 5.143 48.762 1114 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 13.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.70 % Favored : 93.30 % Rotamer: Outliers : 1.87 % Allowed : 22.19 % Favored : 75.94 % 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: -1.87 (0.28), residues: 911 helix: -2.91 (0.47), residues: 74 sheet: -1.15 (0.47), residues: 134 loop : -1.13 (0.24), residues: 703 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 100 HIS 0.007 0.001 HIS B 276 PHE 0.027 0.001 PHE A 56 TYR 0.019 0.001 TYR G 175 ARG 0.006 0.000 ARG B 152 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 64 time to evaluate : 0.873 Fit side-chains REVERT: A 100 TRP cc_start: 0.6605 (p-90) cc_final: 0.6180 (p-90) REVERT: A 246 MET cc_start: 0.6015 (tmm) cc_final: 0.5796 (tmm) REVERT: A 301 HIS cc_start: 0.7414 (t-90) cc_final: 0.6980 (t-90) REVERT: B 230 ILE cc_start: 0.7552 (OUTLIER) cc_final: 0.7119 (mm) outliers start: 15 outliers final: 11 residues processed: 75 average time/residue: 0.1744 time to fit residues: 18.9709 Evaluate side-chains 73 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 61 time to evaluate : 0.773 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 HIS Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 316 HIS Chi-restraints excluded: chain B residue 65 CYS Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 230 ILE Chi-restraints excluded: chain B residue 254 ILE Chi-restraints excluded: chain G residue 71 THR Chi-restraints excluded: chain G residue 129 TYR Chi-restraints excluded: chain G residue 247 THR Chi-restraints excluded: chain G residue 249 ILE Chi-restraints excluded: chain G residue 312 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 27 optimal weight: 7.9990 chunk 11 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 chunk 49 optimal weight: 4.9990 chunk 13 optimal weight: 3.9990 chunk 88 optimal weight: 5.9990 chunk 8 optimal weight: 5.9990 chunk 30 optimal weight: 0.5980 chunk 51 optimal weight: 0.9990 chunk 46 optimal weight: 6.9990 chunk 70 optimal weight: 4.9990 overall best weight: 2.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 101 GLN A 112 HIS ** B 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 98 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 = 0.4246 r_free = 0.4246 target = 0.112092 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.090453 restraints weight = 23996.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.093591 restraints weight = 13782.696| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.095706 restraints weight = 9451.070| |-----------------------------------------------------------------------------| r_work (final): 0.3969 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7473 moved from start: 0.3435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 7541 Z= 0.278 Angle : 0.662 10.683 10248 Z= 0.335 Chirality : 0.046 0.371 1099 Planarity : 0.005 0.043 1342 Dihedral : 5.437 51.981 1114 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 16.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.45 % Favored : 91.55 % Rotamer: Outliers : 1.87 % Allowed : 22.69 % Favored : 75.44 % 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: -1.90 (0.27), residues: 911 helix: -2.63 (0.50), residues: 66 sheet: -1.23 (0.47), residues: 131 loop : -1.21 (0.24), residues: 714 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 113 HIS 0.007 0.001 HIS B 135 PHE 0.027 0.002 PHE A 56 TYR 0.025 0.002 TYR G 175 ARG 0.005 0.000 ARG B 152 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 57 time to evaluate : 0.863 Fit side-chains REVERT: A 100 TRP cc_start: 0.6766 (p-90) cc_final: 0.6259 (p-90) REVERT: A 301 HIS cc_start: 0.7503 (t-90) cc_final: 0.7127 (t70) REVERT: B 230 ILE cc_start: 0.7555 (OUTLIER) cc_final: 0.7200 (mm) outliers start: 15 outliers final: 11 residues processed: 69 average time/residue: 0.1485 time to fit residues: 15.5991 Evaluate side-chains 69 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 57 time to evaluate : 0.858 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 HIS Chi-restraints excluded: chain A residue 316 HIS Chi-restraints excluded: chain B residue 65 CYS Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 230 ILE Chi-restraints excluded: chain B residue 254 ILE Chi-restraints excluded: chain G residue 71 THR Chi-restraints excluded: chain G residue 85 VAL Chi-restraints excluded: chain G residue 129 TYR Chi-restraints excluded: chain G residue 247 THR Chi-restraints excluded: chain G residue 249 ILE Chi-restraints excluded: chain G residue 312 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 54 optimal weight: 0.0870 chunk 78 optimal weight: 5.9990 chunk 67 optimal weight: 4.9990 chunk 89 optimal weight: 2.9990 chunk 6 optimal weight: 7.9990 chunk 68 optimal weight: 0.9980 chunk 38 optimal weight: 0.7980 chunk 7 optimal weight: 0.0670 chunk 36 optimal weight: 0.9980 chunk 10 optimal weight: 6.9990 chunk 18 optimal weight: 0.9980 overall best weight: 0.5896 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 101 GLN A 112 HIS ** B 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 96 GLN G 98 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4306 r_free = 0.4306 target = 0.115571 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.094587 restraints weight = 22494.511| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.097761 restraints weight = 12941.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.099917 restraints weight = 8852.421| |-----------------------------------------------------------------------------| r_work (final): 0.4063 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7359 moved from start: 0.3263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 7541 Z= 0.173 Angle : 0.622 10.511 10248 Z= 0.309 Chirality : 0.045 0.348 1099 Planarity : 0.004 0.045 1342 Dihedral : 5.006 44.499 1114 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 11.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.82 % Favored : 94.18 % Rotamer: Outliers : 1.62 % Allowed : 23.07 % Favored : 75.31 % 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: -1.89 (0.28), residues: 911 helix: -3.03 (0.48), residues: 68 sheet: -1.25 (0.45), residues: 145 loop : -1.13 (0.24), residues: 698 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 100 HIS 0.006 0.001 HIS B 135 PHE 0.019 0.001 PHE A 56 TYR 0.016 0.001 TYR B 259 ARG 0.006 0.000 ARG B 152 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2331.17 seconds wall clock time: 42 minutes 57.28 seconds (2577.28 seconds total)