Starting phenix.real_space_refine on Fri Jul 25 10:08:52 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dmk_27542/07_2025/8dmk_27542.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dmk_27542/07_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_27542/07_2025/8dmk_27542.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dmk_27542/07_2025/8dmk_27542.map" model { file = "/net/cci-nas-00/data/ceres_data/8dmk_27542/07_2025/8dmk_27542.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dmk_27542/07_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-5711/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: 4.81, per 1000 atoms: 0.65 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: 1.88 Conformation dependent library (CDL) restraints added in 1.3 seconds 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: 0.78 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: 1.65 Time building geometry restraints manager: 2.16 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: 0.000 Normalize map: mean=0, sd=1: 1.650 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: 0.000 Extract box with map and model: 0.270 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 20.260 Find NCS groups from input model: 0.120 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: 0.000 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: 25.430 ------------------------------------------------------------------------------- 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 7568 Z= 0.124 Angle : 0.585 8.688 10306 Z= 0.309 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 Details of bonding type rmsd link_NAG-ASN : bond 0.00663 ( 4) link_NAG-ASN : angle 2.98282 ( 12) hydrogen bonds : bond 0.30917 ( 104) hydrogen bonds : angle 10.51519 ( 237) SS BOND : bond 0.00245 ( 23) SS BOND : angle 1.42494 ( 46) covalent geometry : bond 0.00259 ( 7541) covalent geometry : angle 0.56987 (10248) *********************** 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 : 0.841 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: 0.1925 time to fit residues: 23.3897 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 : 1.161 ------------------------------------------------------------------------------- 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: 6.9990 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 = 41)----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.095676 restraints weight = 22689.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.098759 restraints weight = 13090.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.100846 restraints weight = 8929.908| |-----------------------------------------------------------------------------| 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 7568 Z= 0.189 Angle : 0.646 9.998 10306 Z= 0.327 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 Details of bonding type rmsd link_NAG-ASN : bond 0.00802 ( 4) link_NAG-ASN : angle 3.17058 ( 12) hydrogen bonds : bond 0.04934 ( 104) hydrogen bonds : angle 8.27194 ( 237) SS BOND : bond 0.00325 ( 23) SS BOND : angle 1.27012 ( 46) covalent geometry : bond 0.00424 ( 7541) covalent geometry : angle 0.63291 (10248) *********************** 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 : 0.851 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 230 ILE cc_start: 0.7084 (mm) cc_final: 0.6747 (mm) outliers start: 7 outliers final: 4 residues processed: 77 average time/residue: 0.1904 time to fit residues: 20.4119 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 : 0.806 ------------------------------------------------------------------------------- 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: 0.3980 chunk 76 optimal weight: 10.0000 chunk 77 optimal weight: 0.9980 chunk 43 optimal weight: 0.8980 chunk 15 optimal weight: 4.9990 chunk 44 optimal weight: 2.9990 chunk 2 optimal weight: 3.9990 chunk 69 optimal weight: 4.9990 chunk 17 optimal weight: 5.9990 chunk 29 optimal weight: 10.0000 chunk 53 optimal weight: 3.9990 overall best weight: 1.8584 ------------------------------------------------------------------------------- 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 = 0.4315 r_free = 0.4315 target = 0.115123 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.094640 restraints weight = 22810.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.097783 restraints weight = 13059.960| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4070 r_free = 0.4070 target = 0.099859 restraints weight = 8867.676| |-----------------------------------------------------------------------------| r_work (final): 0.4062 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7355 moved from start: 0.1931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 7568 Z= 0.161 Angle : 0.615 10.309 10306 Z= 0.309 Chirality : 0.045 0.350 1099 Planarity : 0.004 0.044 1342 Dihedral : 5.492 51.810 1114 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 14.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.59 % Favored : 93.41 % Rotamer: Outliers : 1.50 % Allowed : 11.72 % Favored : 86.78 % 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: -1.62 (0.27), residues: 911 helix: -2.78 (0.48), residues: 76 sheet: -1.15 (0.43), residues: 144 loop : -0.88 (0.24), residues: 691 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 111 HIS 0.007 0.001 HIS B 135 PHE 0.012 0.001 PHE B 237 TYR 0.023 0.002 TYR G 175 ARG 0.006 0.001 ARG A 262 Details of bonding type rmsd link_NAG-ASN : bond 0.00796 ( 4) link_NAG-ASN : angle 3.24278 ( 12) hydrogen bonds : bond 0.04086 ( 104) hydrogen bonds : angle 7.76366 ( 237) SS BOND : bond 0.00262 ( 23) SS BOND : angle 1.16646 ( 46) covalent geometry : bond 0.00365 ( 7541) covalent geometry : angle 0.60198 (10248) *********************** 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: 12 poor density : 75 time to evaluate : 0.832 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 56 PHE cc_start: 0.7524 (p90) cc_final: 0.7166 (p90) REVERT: A 290 GLU cc_start: 0.7921 (mm-30) cc_final: 0.7579 (mm-30) REVERT: B 135 HIS cc_start: 0.7968 (p-80) cc_final: 0.7444 (p90) REVERT: B 230 ILE cc_start: 0.7274 (mm) cc_final: 0.6999 (mm) outliers start: 12 outliers final: 8 residues processed: 83 average time/residue: 0.2040 time to fit residues: 23.4461 Evaluate side-chains 76 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 68 time to evaluate : 0.829 ------------------------------------------------------------------------------- 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: 0.8980 chunk 24 optimal weight: 0.9990 chunk 78 optimal weight: 4.9990 chunk 30 optimal weight: 0.2980 chunk 56 optimal weight: 8.9990 chunk 8 optimal weight: 5.9990 chunk 15 optimal weight: 5.9990 chunk 34 optimal weight: 0.5980 chunk 16 optimal weight: 6.9990 chunk 81 optimal weight: 5.9990 chunk 14 optimal weight: 2.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 112 HIS ** A 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4330 r_free = 0.4330 target = 0.116090 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.095686 restraints weight = 22585.058| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.098828 restraints weight = 12965.067| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.4087 r_free = 0.4087 target = 0.100923 restraints weight = 8822.216| |-----------------------------------------------------------------------------| r_work (final): 0.4079 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7325 moved from start: 0.2090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 7568 Z= 0.121 Angle : 0.582 10.073 10306 Z= 0.290 Chirality : 0.044 0.352 1099 Planarity : 0.004 0.045 1342 Dihedral : 5.136 46.939 1114 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 12.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.59 % Favored : 93.41 % Rotamer: Outliers : 1.62 % Allowed : 14.59 % Favored : 83.79 % 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: -1.56 (0.28), residues: 911 helix: -2.75 (0.48), residues: 76 sheet: -1.09 (0.45), residues: 138 loop : -0.85 (0.24), residues: 697 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 111 HIS 0.014 0.001 HIS A 301 PHE 0.012 0.001 PHE B 237 TYR 0.019 0.001 TYR G 175 ARG 0.003 0.000 ARG A 262 Details of bonding type rmsd link_NAG-ASN : bond 0.00702 ( 4) link_NAG-ASN : angle 3.21870 ( 12) hydrogen bonds : bond 0.03345 ( 104) hydrogen bonds : angle 7.32689 ( 237) SS BOND : bond 0.00208 ( 23) SS BOND : angle 1.12098 ( 46) covalent geometry : bond 0.00283 ( 7541) covalent geometry : angle 0.56865 (10248) *********************** 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 89 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 76 time to evaluate : 0.820 Fit side-chains revert: symmetry clash REVERT: A 56 PHE cc_start: 0.7417 (p90) cc_final: 0.7131 (p90) REVERT: A 257 ASP cc_start: 0.8770 (t0) cc_final: 0.8505 (t0) REVERT: B 230 ILE cc_start: 0.7428 (mm) cc_final: 0.7106 (mm) outliers start: 13 outliers final: 8 residues processed: 85 average time/residue: 0.1851 time to fit residues: 22.1063 Evaluate side-chains 73 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 65 time to evaluate : 0.812 ------------------------------------------------------------------------------- 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 99 VAL 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 312 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 52 optimal weight: 0.6980 chunk 73 optimal weight: 0.8980 chunk 48 optimal weight: 7.9990 chunk 55 optimal weight: 6.9990 chunk 32 optimal weight: 8.9990 chunk 46 optimal weight: 0.9980 chunk 81 optimal weight: 5.9990 chunk 78 optimal weight: 3.9990 chunk 61 optimal weight: 10.0000 chunk 85 optimal weight: 0.8980 chunk 63 optimal weight: 2.9990 overall best weight: 1.2982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 112 HIS ** A 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4314 r_free = 0.4314 target = 0.119554 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.097465 restraints weight = 23120.917| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.4073 r_free = 0.4073 target = 0.100681 restraints weight = 13390.626| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.4107 r_free = 0.4107 target = 0.102906 restraints weight = 9164.134| |-----------------------------------------------------------------------------| r_work (final): 0.4068 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7353 moved from start: 0.2330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 7568 Z= 0.128 Angle : 0.584 10.049 10306 Z= 0.292 Chirality : 0.045 0.355 1099 Planarity : 0.004 0.045 1342 Dihedral : 4.951 48.822 1114 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 12.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.48 % Favored : 93.52 % Rotamer: Outliers : 2.00 % Allowed : 16.96 % Favored : 81.05 % 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: -1.54 (0.28), residues: 911 helix: -2.67 (0.48), residues: 76 sheet: -0.86 (0.47), residues: 134 loop : -0.90 (0.24), residues: 701 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 320 HIS 0.010 0.001 HIS A 301 PHE 0.011 0.001 PHE B 237 TYR 0.028 0.001 TYR G 175 ARG 0.008 0.000 ARG A 69 Details of bonding type rmsd link_NAG-ASN : bond 0.00716 ( 4) link_NAG-ASN : angle 3.26223 ( 12) hydrogen bonds : bond 0.03380 ( 104) hydrogen bonds : angle 7.07167 ( 237) SS BOND : bond 0.00188 ( 23) SS BOND : angle 1.08957 ( 46) covalent geometry : bond 0.00299 ( 7541) covalent geometry : angle 0.57069 (10248) *********************** 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 85 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 69 time to evaluate : 0.770 Fit side-chains revert: symmetry clash REVERT: B 230 ILE cc_start: 0.7483 (mm) cc_final: 0.7175 (mm) outliers start: 16 outliers final: 12 residues processed: 81 average time/residue: 0.1674 time to fit residues: 19.6960 Evaluate side-chains 76 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 64 time to evaluate : 0.913 ------------------------------------------------------------------------------- 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 99 VAL Chi-restraints excluded: chain B residue 106 ASN Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 197 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 261 ASP 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: 0.8980 chunk 71 optimal weight: 0.6980 chunk 87 optimal weight: 6.9990 chunk 17 optimal weight: 3.9990 chunk 82 optimal weight: 6.9990 chunk 54 optimal weight: 0.8980 chunk 45 optimal weight: 8.9990 chunk 42 optimal weight: 10.0000 chunk 40 optimal weight: 2.9990 chunk 26 optimal weight: 5.9990 chunk 46 optimal weight: 7.9990 overall best weight: 1.8984 ------------------------------------------------------------------------------- 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 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 318 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** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4292 r_free = 0.4292 target = 0.117995 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.095718 restraints weight = 23502.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.098926 restraints weight = 13552.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4079 r_free = 0.4079 target = 0.101093 restraints weight = 9278.999| |-----------------------------------------------------------------------------| r_work (final): 0.4039 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7399 moved from start: 0.2545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 7568 Z= 0.163 Angle : 0.618 9.959 10306 Z= 0.311 Chirality : 0.045 0.361 1099 Planarity : 0.004 0.045 1342 Dihedral : 5.048 50.404 1114 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 14.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.35 % Favored : 92.65 % Rotamer: Outliers : 1.75 % Allowed : 18.95 % Favored : 79.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.76 (0.27), residues: 911 helix: -2.86 (0.43), residues: 87 sheet: -0.91 (0.47), residues: 134 loop : -1.04 (0.24), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 111 HIS 0.011 0.001 HIS A 301 PHE 0.009 0.001 PHE B 237 TYR 0.019 0.002 TYR G 175 ARG 0.007 0.000 ARG A 69 Details of bonding type rmsd link_NAG-ASN : bond 0.00750 ( 4) link_NAG-ASN : angle 3.39371 ( 12) hydrogen bonds : bond 0.03575 ( 104) hydrogen bonds : angle 7.02603 ( 237) SS BOND : bond 0.00232 ( 23) SS BOND : angle 1.10587 ( 46) covalent geometry : bond 0.00375 ( 7541) covalent geometry : angle 0.60432 (10248) *********************** 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 81 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 67 time to evaluate : 0.783 Fit side-chains revert: symmetry clash REVERT: B 163 TYR cc_start: 0.8787 (OUTLIER) cc_final: 0.8425 (m-10) REVERT: B 230 ILE cc_start: 0.7567 (mm) cc_final: 0.7279 (mm) outliers start: 14 outliers final: 11 residues processed: 79 average time/residue: 0.1649 time to fit residues: 18.8999 Evaluate side-chains 76 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 64 time to evaluate : 0.903 ------------------------------------------------------------------------------- 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 99 VAL Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 163 TYR Chi-restraints excluded: chain B residue 197 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 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: 0.9990 chunk 71 optimal weight: 0.9990 chunk 79 optimal weight: 2.9990 chunk 81 optimal weight: 6.9990 chunk 22 optimal weight: 9.9990 chunk 9 optimal weight: 4.9990 chunk 59 optimal weight: 5.9990 chunk 64 optimal weight: 5.9990 chunk 46 optimal weight: 0.8980 chunk 54 optimal weight: 6.9990 chunk 2 optimal weight: 4.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- 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 112 HIS A 301 HIS ** A 318 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** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4262 r_free = 0.4262 target = 0.116096 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.093870 restraints weight = 23391.233| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.097014 restraints weight = 13555.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.099149 restraints weight = 9313.256| |-----------------------------------------------------------------------------| r_work (final): 0.3997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7446 moved from start: 0.2903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 7568 Z= 0.184 Angle : 0.654 10.167 10306 Z= 0.329 Chirality : 0.045 0.367 1099 Planarity : 0.005 0.044 1342 Dihedral : 5.258 51.606 1114 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 16.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.90 % Favored : 92.10 % Rotamer: Outliers : 2.24 % Allowed : 19.83 % Favored : 77.93 % 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: -1.82 (0.27), residues: 911 helix: -2.76 (0.47), residues: 74 sheet: -1.01 (0.47), residues: 131 loop : -1.14 (0.23), residues: 706 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 113 HIS 0.008 0.001 HIS B 135 PHE 0.009 0.001 PHE B 237 TYR 0.042 0.002 TYR G 175 ARG 0.005 0.000 ARG A 69 Details of bonding type rmsd link_NAG-ASN : bond 0.00810 ( 4) link_NAG-ASN : angle 3.60350 ( 12) hydrogen bonds : bond 0.03697 ( 104) hydrogen bonds : angle 7.10268 ( 237) SS BOND : bond 0.00261 ( 23) SS BOND : angle 1.40514 ( 46) covalent geometry : bond 0.00423 ( 7541) covalent geometry : angle 0.63682 (10248) *********************** 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 80 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 62 time to evaluate : 0.823 Fit side-chains REVERT: B 163 TYR cc_start: 0.8776 (OUTLIER) cc_final: 0.8403 (m-10) REVERT: B 230 ILE cc_start: 0.7604 (mm) cc_final: 0.7329 (mm) outliers start: 18 outliers final: 11 residues processed: 77 average time/residue: 0.1660 time to fit residues: 18.6745 Evaluate side-chains 72 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 60 time to evaluate : 0.771 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 163 TYR Chi-restraints excluded: chain B residue 197 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 261 ASP 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: 0.0570 chunk 30 optimal weight: 9.9990 chunk 34 optimal weight: 0.0980 chunk 25 optimal weight: 8.9990 chunk 85 optimal weight: 3.9990 chunk 48 optimal weight: 6.9990 chunk 7 optimal weight: 0.6980 chunk 82 optimal weight: 0.9980 chunk 87 optimal weight: 5.9990 chunk 70 optimal weight: 1.9990 chunk 83 optimal weight: 2.9990 overall best weight: 0.7700 ------------------------------------------------------------------------------- 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 302 ASN ** B 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 79 GLN ** 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 = 0.4310 r_free = 0.4310 target = 0.119163 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.097225 restraints weight = 23054.481| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.4070 r_free = 0.4070 target = 0.100501 restraints weight = 13189.925| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.4105 r_free = 0.4105 target = 0.102742 restraints weight = 8954.020| |-----------------------------------------------------------------------------| r_work (final): 0.4068 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7352 moved from start: 0.2780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 7568 Z= 0.111 Angle : 0.616 10.534 10306 Z= 0.306 Chirality : 0.045 0.350 1099 Planarity : 0.004 0.045 1342 Dihedral : 4.869 45.814 1114 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 12.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.70 % Favored : 93.30 % Rotamer: Outliers : 1.37 % Allowed : 20.95 % Favored : 77.68 % 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: -1.74 (0.27), residues: 911 helix: -2.91 (0.44), residues: 81 sheet: -0.92 (0.48), residues: 134 loop : -1.03 (0.24), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 111 HIS 0.005 0.001 HIS B 135 PHE 0.009 0.001 PHE B 237 TYR 0.017 0.001 TYR B 259 ARG 0.003 0.000 ARG B 152 Details of bonding type rmsd link_NAG-ASN : bond 0.00677 ( 4) link_NAG-ASN : angle 3.27593 ( 12) hydrogen bonds : bond 0.03152 ( 104) hydrogen bonds : angle 6.75510 ( 237) SS BOND : bond 0.00172 ( 23) SS BOND : angle 1.31371 ( 46) covalent geometry : bond 0.00265 ( 7541) covalent geometry : angle 0.60077 (10248) *********************** 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 78 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 67 time to evaluate : 0.805 Fit side-chains revert: symmetry clash REVERT: B 163 TYR cc_start: 0.8777 (OUTLIER) cc_final: 0.8349 (m-10) REVERT: B 230 ILE cc_start: 0.7479 (mm) cc_final: 0.7225 (mm) outliers start: 11 outliers final: 7 residues processed: 76 average time/residue: 0.1654 time to fit residues: 18.3102 Evaluate side-chains 72 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 64 time to evaluate : 0.788 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 163 TYR 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 20 optimal weight: 5.9990 chunk 35 optimal weight: 0.0020 chunk 16 optimal weight: 8.9990 chunk 14 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 6 optimal weight: 0.0370 chunk 39 optimal weight: 1.9990 chunk 46 optimal weight: 0.8980 chunk 1 optimal weight: 1.9990 chunk 26 optimal weight: 0.0050 chunk 32 optimal weight: 0.6980 overall best weight: 0.3280 ------------------------------------------------------------------------------- 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** B 297 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4342 r_free = 0.4342 target = 0.117156 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.097162 restraints weight = 22597.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.100381 restraints weight = 12835.538| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4114 r_free = 0.4114 target = 0.102530 restraints weight = 8622.843| |-----------------------------------------------------------------------------| r_work (final): 0.4108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7283 moved from start: 0.2733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 7568 Z= 0.102 Angle : 0.614 10.179 10306 Z= 0.303 Chirality : 0.045 0.348 1099 Planarity : 0.004 0.045 1342 Dihedral : 4.689 44.062 1114 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.37 % Favored : 93.63 % Rotamer: Outliers : 1.62 % Allowed : 20.82 % 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: -1.56 (0.27), residues: 911 helix: -2.71 (0.47), residues: 76 sheet: -0.62 (0.49), residues: 124 loop : -0.97 (0.24), residues: 711 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 100 HIS 0.007 0.001 HIS B 135 PHE 0.009 0.001 PHE B 237 TYR 0.017 0.001 TYR B 259 ARG 0.003 0.000 ARG B 152 Details of bonding type rmsd link_NAG-ASN : bond 0.00679 ( 4) link_NAG-ASN : angle 3.16513 ( 12) hydrogen bonds : bond 0.02905 ( 104) hydrogen bonds : angle 6.43039 ( 237) SS BOND : bond 0.00194 ( 23) SS BOND : angle 1.25481 ( 46) covalent geometry : bond 0.00243 ( 7541) covalent geometry : angle 0.60065 (10248) *********************** 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 85 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 72 time to evaluate : 0.898 Fit side-chains revert: symmetry clash REVERT: B 230 ILE cc_start: 0.7486 (mm) cc_final: 0.7178 (mm) outliers start: 13 outliers final: 8 residues processed: 83 average time/residue: 0.1727 time to fit residues: 20.6058 Evaluate side-chains 72 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 64 time to evaluate : 0.861 ------------------------------------------------------------------------------- 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 99 VAL 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 27 optimal weight: 0.0060 chunk 11 optimal weight: 0.8980 chunk 53 optimal weight: 2.9990 chunk 49 optimal weight: 0.5980 chunk 13 optimal weight: 0.9990 chunk 88 optimal weight: 3.9990 chunk 8 optimal weight: 0.0970 chunk 30 optimal weight: 10.0000 chunk 51 optimal weight: 0.5980 chunk 46 optimal weight: 9.9990 chunk 70 optimal weight: 0.7980 overall best weight: 0.4194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 301 HIS ** B 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4350 r_free = 0.4350 target = 0.117733 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.097761 restraints weight = 22953.562| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4085 r_free = 0.4085 target = 0.100953 restraints weight = 13022.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4121 r_free = 0.4121 target = 0.103119 restraints weight = 8773.793| |-----------------------------------------------------------------------------| r_work (final): 0.4113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7277 moved from start: 0.2737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 7568 Z= 0.103 Angle : 0.631 10.456 10306 Z= 0.308 Chirality : 0.045 0.348 1099 Planarity : 0.004 0.046 1342 Dihedral : 4.630 44.157 1114 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 10.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.37 % Favored : 93.63 % Rotamer: Outliers : 1.00 % Allowed : 22.32 % Favored : 76.68 % 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: -1.57 (0.27), residues: 911 helix: -2.72 (0.47), residues: 76 sheet: -0.56 (0.49), residues: 124 loop : -0.99 (0.23), residues: 711 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP G 117 HIS 0.012 0.001 HIS A 301 PHE 0.011 0.001 PHE B 207 TYR 0.018 0.001 TYR B 259 ARG 0.005 0.000 ARG B 152 Details of bonding type rmsd link_NAG-ASN : bond 0.00679 ( 4) link_NAG-ASN : angle 3.14254 ( 12) hydrogen bonds : bond 0.02849 ( 104) hydrogen bonds : angle 6.29412 ( 237) SS BOND : bond 0.00219 ( 23) SS BOND : angle 1.45961 ( 46) covalent geometry : bond 0.00252 ( 7541) covalent geometry : angle 0.61608 (10248) ********************** 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 71 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 63 time to evaluate : 0.883 Fit side-chains revert: symmetry clash REVERT: B 230 ILE cc_start: 0.7555 (mm) cc_final: 0.7120 (mm) outliers start: 8 outliers final: 7 residues processed: 69 average time/residue: 0.1693 time to fit residues: 17.0078 Evaluate side-chains 70 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 63 time to evaluate : 0.795 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 HIS Chi-restraints excluded: chain B residue 65 CYS Chi-restraints excluded: chain B residue 99 VAL 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 54 optimal weight: 8.9990 chunk 78 optimal weight: 6.9990 chunk 67 optimal weight: 8.9990 chunk 89 optimal weight: 10.0000 chunk 6 optimal weight: 1.9990 chunk 68 optimal weight: 0.6980 chunk 38 optimal weight: 0.0070 chunk 7 optimal weight: 0.0070 chunk 36 optimal weight: 4.9990 chunk 10 optimal weight: 0.9980 chunk 18 optimal weight: 0.5980 overall best weight: 0.4616 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 301 HIS ** B 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4352 r_free = 0.4352 target = 0.117607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.097613 restraints weight = 22607.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4088 r_free = 0.4088 target = 0.100754 restraints weight = 12919.052| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.102903 restraints weight = 8746.616| |-----------------------------------------------------------------------------| r_work (final): 0.4124 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7265 moved from start: 0.2740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 7568 Z= 0.100 Angle : 0.623 10.097 10306 Z= 0.302 Chirality : 0.045 0.348 1099 Planarity : 0.004 0.045 1342 Dihedral : 4.546 44.140 1114 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 10.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.48 % Favored : 93.52 % Rotamer: Outliers : 0.87 % Allowed : 22.69 % Favored : 76.43 % 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: -1.43 (0.27), residues: 911 helix: -2.49 (0.51), residues: 69 sheet: -0.47 (0.49), residues: 124 loop : -0.93 (0.23), residues: 718 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP G 117 HIS 0.009 0.001 HIS A 301 PHE 0.010 0.001 PHE B 207 TYR 0.022 0.001 TYR G 175 ARG 0.005 0.000 ARG B 152 Details of bonding type rmsd link_NAG-ASN : bond 0.00680 ( 4) link_NAG-ASN : angle 3.13546 ( 12) hydrogen bonds : bond 0.02750 ( 104) hydrogen bonds : angle 6.18028 ( 237) SS BOND : bond 0.00169 ( 23) SS BOND : angle 1.30539 ( 46) covalent geometry : bond 0.00246 ( 7541) covalent geometry : angle 0.60880 (10248) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2597.36 seconds wall clock time: 45 minutes 56.96 seconds (2756.96 seconds total)