Starting phenix.real_space_refine on Fri Feb 14 02:02:10 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bhm_44550/02_2025/9bhm_44550.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bhm_44550/02_2025/9bhm_44550.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9bhm_44550/02_2025/9bhm_44550.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bhm_44550/02_2025/9bhm_44550.map" model { file = "/net/cci-nas-00/data/ceres_data/9bhm_44550/02_2025/9bhm_44550.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bhm_44550/02_2025/9bhm_44550.cif" } resolution = 2.9 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= -0.009 sd= 0.774 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 3038 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 47 5.16 5 C 4567 2.51 5 N 1237 2.21 5 O 1299 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 7150 Number of models: 1 Model: "" Number of chains: 5 Chain: "R" Number of atoms: 2297 Number of conformers: 1 Conformer: "" Number of residues, atoms: 282, 2297 Classifications: {'peptide': 282} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 273} Chain: "A" Number of atoms: 1763 Number of conformers: 1 Conformer: "" Number of residues, atoms: 210, 1763 Classifications: {'peptide': 210} Link IDs: {'PTRANS': 3, 'TRANS': 206} Chain breaks: 3 Chain: "B" Number of atoms: 2211 Number of conformers: 1 Conformer: "" Number of residues, atoms: 289, 2211 Classifications: {'peptide': 289} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 284} Chain breaks: 2 Chain: "N" Number of atoms: 844 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 844 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 2, 'TRANS': 106} Chain breaks: 4 Chain: "R" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 35 Unusual residues: {'Y01': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.54, per 1000 atoms: 0.63 Number of scatterers: 7150 At special positions: 0 Unit cell: (71.38, 87.98, 126.99, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 47 16.00 O 1299 8.00 N 1237 7.00 C 4567 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS R 13 " - pdb=" SG CYS R 258 " distance=2.03 Simple disulfide: pdb=" SG CYS R 94 " - pdb=" SG CYS R 172 " distance=2.03 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.03 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.49 Conformation dependent library (CDL) restraints added in 902.4 milliseconds 1728 Ramachandran restraints generated. 864 Oldfield, 0 Emsley, 864 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1672 Finding SS restraints... Secondary structure from input PDB file: 19 helices and 12 sheets defined 40.7% alpha, 20.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.80 Creating SS restraints... Processing helix chain 'R' and resid 17 through 52 removed outlier: 4.007A pdb=" N GLN R 21 " --> pdb=" O HIS R 17 " (cutoff:3.500A) Proline residue: R 25 - end of helix Proline residue: R 37 - end of helix Processing helix chain 'R' and resid 54 through 82 removed outlier: 4.244A pdb=" N VAL R 58 " --> pdb=" O ASN R 54 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N TYR R 59 " --> pdb=" O GLU R 55 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N SER R 73 " --> pdb=" O PHE R 69 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N LEU R 74 " --> pdb=" O TYR R 70 " (cutoff:3.500A) Proline residue: R 75 - end of helix Processing helix chain 'R' and resid 90 through 124 removed outlier: 5.178A pdb=" N ILE R 105 " --> pdb=" O LEU R 101 " (cutoff:3.500A) removed outlier: 5.591A pdb=" N TYR R 106 " --> pdb=" O TYR R 102 " (cutoff:3.500A) Processing helix chain 'R' and resid 134 through 158 Processing helix chain 'R' and resid 159 through 161 No H-bonds generated for 'chain 'R' and resid 159 through 161' Processing helix chain 'R' and resid 179 through 215 removed outlier: 3.686A pdb=" N TYR R 187 " --> pdb=" O ARG R 183 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N TYR R 188 " --> pdb=" O ALA R 184 " (cutoff:3.500A) removed outlier: 4.827A pdb=" N PHE R 196 " --> pdb=" O VAL R 192 " (cutoff:3.500A) Proline residue: R 197 - end of helix removed outlier: 3.548A pdb=" N GLY R 207 " --> pdb=" O ALA R 203 " (cutoff:3.500A) Processing helix chain 'R' and resid 219 through 254 Proline residue: R 243 - end of helix Processing helix chain 'R' and resid 257 through 288 removed outlier: 4.774A pdb=" N ASN R 266 " --> pdb=" O LYS R 262 " (cutoff:3.500A) removed outlier: 5.271A pdb=" N ALA R 267 " --> pdb=" O GLY R 263 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N CYS R 279 " --> pdb=" O THR R 275 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N VAL R 280 " --> pdb=" O SER R 276 " (cutoff:3.500A) Proline residue: R 283 - end of helix Processing helix chain 'A' and resid 17 through 39 Processing helix chain 'A' and resid 52 through 58 Processing helix chain 'A' and resid 233 through 239 removed outlier: 3.657A pdb=" N ASN A 239 " --> pdb=" O GLN A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 279 removed outlier: 3.714A pdb=" N GLN A 267 " --> pdb=" O TYR A 253 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N GLU A 268 " --> pdb=" O ASN A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 285 removed outlier: 3.748A pdb=" N THR A 284 " --> pdb=" O TRP A 281 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 304 Processing helix chain 'A' and resid 307 through 312 removed outlier: 3.531A pdb=" N TYR A 311 " --> pdb=" O LYS A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 317 Processing helix chain 'A' and resid 332 through 351 removed outlier: 3.637A pdb=" N PHE A 345 " --> pdb=" O ILE A 341 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 391 Processing helix chain 'N' and resid 62 through 65 Processing sheet with id=AA1, first strand: chain 'R' and resid 163 through 166 Processing sheet with id=AA2, first strand: chain 'A' and resid 210 through 214 removed outlier: 6.492A pdb=" N HIS A 41 " --> pdb=" O HIS A 220 " (cutoff:3.500A) removed outlier: 7.397A pdb=" N PHE A 222 " --> pdb=" O HIS A 41 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N LEU A 43 " --> pdb=" O PHE A 222 " (cutoff:3.500A) removed outlier: 10.331A pdb=" N ALA A 243 " --> pdb=" O THR A 40 " (cutoff:3.500A) removed outlier: 7.310A pdb=" N ARG A 42 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 8.099A pdb=" N ILE A 245 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N LEU A 44 " --> pdb=" O ILE A 245 " (cutoff:3.500A) removed outlier: 7.427A pdb=" N VAL A 247 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N LEU A 46 " --> pdb=" O VAL A 247 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 47 through 50 removed outlier: 6.701A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.804A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N LYS B 337 " --> pdb=" O THR B 329 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N ALA B 328 " --> pdb=" O LEU B 318 " (cutoff:3.500A) removed outlier: 4.723A pdb=" N LEU B 318 " --> pdb=" O ALA B 328 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N GLY B 330 " --> pdb=" O SER B 316 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 58 through 63 removed outlier: 4.360A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 102 through 105 removed outlier: 3.548A pdb=" N SER B 122 " --> pdb=" O CYS B 114 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N LEU B 139 " --> pdb=" O CYS B 121 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 149 through 151 removed outlier: 7.031A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 187 through 192 removed outlier: 7.023A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.185A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 8.051A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N LYS B 209 " --> pdb=" O SER B 201 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 229 through 234 removed outlier: 3.714A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.450A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 7.173A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 4.916A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 7.076A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ASN B 295 " --> pdb=" O ALA B 287 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 7.334A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'N' and resid 3 through 7 removed outlier: 3.921A pdb=" N GLN N 3 " --> pdb=" O SER N 25 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N SER N 25 " --> pdb=" O GLN N 3 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N LEU N 79 " --> pdb=" O CYS N 22 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N THR N 69 " --> pdb=" O GLN N 82 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'N' and resid 10 through 11 removed outlier: 7.832A pdb=" N GLY N 10 " --> pdb=" O THR N 125 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'N' and resid 59 through 60 removed outlier: 3.829A pdb=" N SER N 59 " --> pdb=" O ASP N 50 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N ASP N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N MET N 34 " --> pdb=" O ASP N 50 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N VAL N 37 " --> pdb=" O TYR N 95 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N TYR N 95 " --> pdb=" O VAL N 37 " (cutoff:3.500A) 351 hydrogen bonds defined for protein. 990 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.13 Time building geometry restraints manager: 1.78 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 1138 1.30 - 1.43: 2063 1.43 - 1.56: 4034 1.56 - 1.69: 14 1.69 - 1.82: 60 Bond restraints: 7309 Sorted by residual: bond pdb=" CAI Y01 R1000 " pdb=" CAK Y01 R1000 " ideal model delta sigma weight residual 1.492 1.235 0.257 2.00e-02 2.50e+03 1.65e+02 bond pdb=" CAS Y01 R1000 " pdb=" CBF Y01 R1000 " ideal model delta sigma weight residual 1.533 1.277 0.256 2.00e-02 2.50e+03 1.64e+02 bond pdb=" CAZ Y01 R1000 " pdb=" CBH Y01 R1000 " ideal model delta sigma weight residual 1.519 1.296 0.223 2.00e-02 2.50e+03 1.24e+02 bond pdb=" CAU Y01 R1000 " pdb=" CBI Y01 R1000 " ideal model delta sigma weight residual 1.530 1.733 -0.203 2.00e-02 2.50e+03 1.03e+02 bond pdb=" CAI Y01 R1000 " pdb=" CAZ Y01 R1000 " ideal model delta sigma weight residual 1.332 1.167 0.165 2.00e-02 2.50e+03 6.80e+01 ... (remaining 7304 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.83: 9703 1.83 - 3.65: 156 3.65 - 5.48: 28 5.48 - 7.30: 12 7.30 - 9.13: 4 Bond angle restraints: 9903 Sorted by residual: angle pdb=" CA PRO B 94 " pdb=" N PRO B 94 " pdb=" CD PRO B 94 " ideal model delta sigma weight residual 112.00 105.09 6.91 1.40e+00 5.10e-01 2.43e+01 angle pdb=" CAM Y01 R1000 " pdb=" CAY Y01 R1000 " pdb=" OAW Y01 R1000 " ideal model delta sigma weight residual 111.19 120.32 -9.13 3.00e+00 1.11e-01 9.26e+00 angle pdb=" CA MET N 83 " pdb=" CB MET N 83 " pdb=" CG MET N 83 " ideal model delta sigma weight residual 114.10 119.69 -5.59 2.00e+00 2.50e-01 7.82e+00 angle pdb=" CAS Y01 R1000 " pdb=" CAU Y01 R1000 " pdb=" CBI Y01 R1000 " ideal model delta sigma weight residual 111.64 103.30 8.34 3.00e+00 1.11e-01 7.72e+00 angle pdb=" N GLU A 27 " pdb=" CA GLU A 27 " pdb=" CB GLU A 27 " ideal model delta sigma weight residual 110.39 114.93 -4.54 1.66e+00 3.63e-01 7.48e+00 ... (remaining 9898 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.25: 4088 25.25 - 50.49: 205 50.49 - 75.74: 25 75.74 - 100.99: 7 100.99 - 126.24: 1 Dihedral angle restraints: 4326 sinusoidal: 1737 harmonic: 2589 Sorted by residual: dihedral pdb=" CA LEU A 291 " pdb=" C LEU A 291 " pdb=" N ASN A 292 " pdb=" CA ASN A 292 " ideal model delta harmonic sigma weight residual -180.00 -157.45 -22.55 0 5.00e+00 4.00e-02 2.03e+01 dihedral pdb=" CBC Y01 R1000 " pdb=" CAR Y01 R1000 " pdb=" CAT Y01 R1000 " pdb=" CBH Y01 R1000 " ideal model delta sinusoidal sigma weight residual -57.13 69.11 -126.24 1 3.00e+01 1.11e-03 1.70e+01 dihedral pdb=" CA PHE N 108 " pdb=" C PHE N 108 " pdb=" N ASP N 109 " pdb=" CA ASP N 109 " ideal model delta harmonic sigma weight residual -180.00 -159.73 -20.27 0 5.00e+00 4.00e-02 1.64e+01 ... (remaining 4323 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 904 0.054 - 0.108: 172 0.108 - 0.162: 27 0.162 - 0.216: 2 0.216 - 0.270: 3 Chirality restraints: 1108 Sorted by residual: chirality pdb=" CBF Y01 R1000 " pdb=" CAS Y01 R1000 " pdb=" CBD Y01 R1000 " pdb=" CBH Y01 R1000 " both_signs ideal model delta sigma weight residual False -2.45 -2.72 0.27 2.00e-01 2.50e+01 1.83e+00 chirality pdb=" CBG Y01 R1000 " pdb=" CAQ Y01 R1000 " pdb=" CBD Y01 R1000 " pdb=" CBI Y01 R1000 " both_signs ideal model delta sigma weight residual False -2.33 -2.58 0.25 2.00e-01 2.50e+01 1.56e+00 chirality pdb=" CBB Y01 R1000 " pdb=" CAC Y01 R1000 " pdb=" CAO Y01 R1000 " pdb=" CBE Y01 R1000 " both_signs ideal model delta sigma weight residual False 2.58 2.80 -0.23 2.00e-01 2.50e+01 1.31e+00 ... (remaining 1105 not shown) Planarity restraints: 1245 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE R 111 " 0.025 2.00e-02 2.50e+03 2.61e-02 1.19e+01 pdb=" CG PHE R 111 " -0.059 2.00e-02 2.50e+03 pdb=" CD1 PHE R 111 " 0.021 2.00e-02 2.50e+03 pdb=" CD2 PHE R 111 " 0.003 2.00e-02 2.50e+03 pdb=" CE1 PHE R 111 " -0.005 2.00e-02 2.50e+03 pdb=" CE2 PHE R 111 " 0.014 2.00e-02 2.50e+03 pdb=" CZ PHE R 111 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE B 93 " -0.044 5.00e-02 4.00e+02 6.38e-02 6.51e+00 pdb=" N PRO B 94 " 0.110 5.00e-02 4.00e+02 pdb=" CA PRO B 94 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO B 94 " -0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB ASN R 278 " -0.007 2.00e-02 2.50e+03 1.50e-02 2.24e+00 pdb=" CG ASN R 278 " 0.026 2.00e-02 2.50e+03 pdb=" OD1 ASN R 278 " -0.010 2.00e-02 2.50e+03 pdb=" ND2 ASN R 278 " -0.009 2.00e-02 2.50e+03 ... (remaining 1242 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 259 2.71 - 3.26: 7531 3.26 - 3.81: 12015 3.81 - 4.35: 14953 4.35 - 4.90: 25217 Nonbonded interactions: 59975 Sorted by model distance: nonbonded pdb=" O LEU R 273 " pdb=" OG SER R 276 " model vdw 2.165 3.040 nonbonded pdb=" OG SER A 275 " pdb=" O CYS N 107 " model vdw 2.204 3.040 nonbonded pdb=" O ILE B 58 " pdb=" OG SER B 316 " model vdw 2.225 3.040 nonbonded pdb=" OG SER B 147 " pdb=" OG SER B 160 " model vdw 2.226 3.040 nonbonded pdb=" O ARG A 356 " pdb=" NH2 ARG A 385 " model vdw 2.231 3.120 ... (remaining 59970 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.510 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.050 Construct map_model_manager: 0.000 Extract box with map and model: 0.260 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 18.970 Find NCS groups from input model: 0.080 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:11.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6565 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 : 0.008 0.257 7309 Z= 0.496 Angle : 0.647 9.130 9903 Z= 0.332 Chirality : 0.045 0.270 1108 Planarity : 0.004 0.064 1245 Dihedral : 14.738 126.235 2642 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 10.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 0.13 % Allowed : 0.26 % Favored : 99.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.56 (0.28), residues: 864 helix: 1.04 (0.29), residues: 317 sheet: -1.23 (0.34), residues: 208 loop : -1.06 (0.32), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP N 47 HIS 0.005 0.001 HIS R 269 PHE 0.059 0.002 PHE R 111 TYR 0.020 0.001 TYR R 106 ARG 0.005 0.000 ARG B 314 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1728 Ramachandran restraints generated. 864 Oldfield, 0 Emsley, 864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1728 Ramachandran restraints generated. 864 Oldfield, 0 Emsley, 864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 199 time to evaluate : 0.765 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 47 TYR cc_start: 0.7877 (t80) cc_final: 0.7317 (t80) REVERT: R 48 LEU cc_start: 0.8014 (mm) cc_final: 0.7793 (mp) REVERT: R 61 CYS cc_start: 0.7924 (m) cc_final: 0.7562 (m) REVERT: R 144 VAL cc_start: 0.8385 (t) cc_final: 0.8105 (m) REVERT: R 225 GLN cc_start: 0.7473 (OUTLIER) cc_final: 0.7238 (tt0) REVERT: R 238 LEU cc_start: 0.8318 (mm) cc_final: 0.8068 (mm) REVERT: A 34 LYS cc_start: 0.6770 (tttp) cc_final: 0.6367 (tttp) REVERT: A 37 TYR cc_start: 0.7312 (t80) cc_final: 0.6788 (t80) REVERT: A 283 ARG cc_start: 0.7309 (mtm110) cc_final: 0.6912 (mtm110) REVERT: A 370 GLU cc_start: 0.7291 (pp20) cc_final: 0.6822 (pp20) REVERT: B 46 ARG cc_start: 0.7156 (ptt-90) cc_final: 0.6798 (mpp80) REVERT: B 52 ARG cc_start: 0.7970 (ptp-110) cc_final: 0.7638 (ttm110) REVERT: B 114 CYS cc_start: 0.7683 (t) cc_final: 0.7137 (t) REVERT: B 209 LYS cc_start: 0.6752 (mttp) cc_final: 0.6447 (mttm) REVERT: B 217 MET cc_start: 0.5765 (ppp) cc_final: 0.5401 (pmm) REVERT: B 252 LEU cc_start: 0.7553 (tt) cc_final: 0.7339 (tt) REVERT: B 275 SER cc_start: 0.8193 (t) cc_final: 0.7781 (p) REVERT: B 286 LEU cc_start: 0.8128 (mp) cc_final: 0.7896 (mp) REVERT: B 301 LYS cc_start: 0.6475 (mptt) cc_final: 0.6061 (mptt) REVERT: B 318 LEU cc_start: 0.8012 (tt) cc_final: 0.7791 (tt) REVERT: B 335 PHE cc_start: 0.7592 (m-80) cc_final: 0.7359 (m-80) REVERT: B 337 LYS cc_start: 0.7698 (mttp) cc_final: 0.7219 (mttp) REVERT: N 72 ARG cc_start: 0.5978 (tmm-80) cc_final: 0.5462 (ttt-90) REVERT: N 103 PHE cc_start: 0.7094 (m-80) cc_final: 0.6580 (m-80) outliers start: 1 outliers final: 0 residues processed: 200 average time/residue: 0.9144 time to fit residues: 195.5937 Evaluate side-chains 146 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 145 time to evaluate : 0.854 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 225 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 73 optimal weight: 5.9990 chunk 65 optimal weight: 2.9990 chunk 36 optimal weight: 3.9990 chunk 22 optimal weight: 0.7980 chunk 44 optimal weight: 0.9990 chunk 35 optimal weight: 0.5980 chunk 68 optimal weight: 0.7980 chunk 26 optimal weight: 0.5980 chunk 41 optimal weight: 6.9990 chunk 50 optimal weight: 4.9990 chunk 79 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 131 GLN R 225 GLN R 227 GLN A 213 GLN A 220 HIS A 267 GLN A 371 ASN A 384 GLN B 125 ASN B 176 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4257 r_free = 0.4257 target = 0.195852 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.176508 restraints weight = 10606.515| |-----------------------------------------------------------------------------| r_work (start): 0.4074 rms_B_bonded: 2.24 r_work: 0.3998 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work (final): 0.3998 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7178 moved from start: 0.2013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 7309 Z= 0.212 Angle : 0.588 7.772 9903 Z= 0.309 Chirality : 0.043 0.187 1108 Planarity : 0.004 0.040 1245 Dihedral : 6.199 56.658 1048 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 10.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 3.49 % Allowed : 12.02 % Favored : 84.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.32 (0.28), residues: 864 helix: 1.26 (0.28), residues: 312 sheet: -1.01 (0.34), residues: 211 loop : -0.98 (0.32), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 169 HIS 0.007 0.001 HIS R 269 PHE 0.016 0.002 PHE R 241 TYR 0.020 0.002 TYR R 106 ARG 0.007 0.000 ARG R 210 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1728 Ramachandran restraints generated. 864 Oldfield, 0 Emsley, 864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1728 Ramachandran restraints generated. 864 Oldfield, 0 Emsley, 864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 163 time to evaluate : 0.796 Fit side-chains revert: symmetry clash REVERT: R 47 TYR cc_start: 0.8134 (t80) cc_final: 0.7372 (t80) REVERT: R 61 CYS cc_start: 0.8511 (m) cc_final: 0.8203 (m) REVERT: R 227 GLN cc_start: 0.8244 (OUTLIER) cc_final: 0.7896 (pp30) REVERT: A 34 LYS cc_start: 0.7563 (tttp) cc_final: 0.7093 (tttp) REVERT: A 37 TYR cc_start: 0.7545 (t80) cc_final: 0.7091 (t80) REVERT: A 213 GLN cc_start: 0.7397 (OUTLIER) cc_final: 0.7133 (pm20) REVERT: A 309 GLU cc_start: 0.5822 (pm20) cc_final: 0.5584 (pt0) REVERT: A 370 GLU cc_start: 0.7621 (pp20) cc_final: 0.7393 (pm20) REVERT: B 46 ARG cc_start: 0.7519 (ptt-90) cc_final: 0.7216 (mpp80) REVERT: B 52 ARG cc_start: 0.7992 (ptp-110) cc_final: 0.7747 (ttm110) REVERT: B 114 CYS cc_start: 0.7946 (t) cc_final: 0.7667 (t) REVERT: B 217 MET cc_start: 0.6023 (ppp) cc_final: 0.5733 (pmm) REVERT: B 262 MET cc_start: 0.7163 (tpt) cc_final: 0.6940 (tpp) REVERT: B 301 LYS cc_start: 0.7084 (mptt) cc_final: 0.6691 (mptt) REVERT: B 335 PHE cc_start: 0.8017 (m-80) cc_final: 0.7812 (m-80) outliers start: 27 outliers final: 12 residues processed: 176 average time/residue: 0.9159 time to fit residues: 172.7043 Evaluate side-chains 151 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 137 time to evaluate : 0.734 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 227 GLN Chi-restraints excluded: chain R residue 250 VAL Chi-restraints excluded: chain R residue 276 SER Chi-restraints excluded: chain R residue 280 VAL Chi-restraints excluded: chain R residue 284 VAL Chi-restraints excluded: chain A residue 54 SER Chi-restraints excluded: chain A residue 213 GLN Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 207 SER Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain N residue 111 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 36 optimal weight: 5.9990 chunk 44 optimal weight: 0.4980 chunk 11 optimal weight: 0.3980 chunk 69 optimal weight: 0.7980 chunk 42 optimal weight: 4.9990 chunk 6 optimal weight: 1.9990 chunk 79 optimal weight: 4.9990 chunk 5 optimal weight: 0.8980 chunk 2 optimal weight: 0.6980 chunk 0 optimal weight: 6.9990 chunk 47 optimal weight: 0.9980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 362 HIS B 176 GLN B 266 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4262 r_free = 0.4262 target = 0.196494 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.176931 restraints weight = 10716.684| |-----------------------------------------------------------------------------| r_work (start): 0.4081 rms_B_bonded: 2.27 r_work: 0.4004 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work (final): 0.4004 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7175 moved from start: 0.2417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7309 Z= 0.189 Angle : 0.555 6.846 9903 Z= 0.294 Chirality : 0.042 0.139 1108 Planarity : 0.004 0.040 1245 Dihedral : 5.993 57.569 1045 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 4.39 % Allowed : 14.47 % Favored : 81.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.31 (0.28), residues: 864 helix: 1.35 (0.28), residues: 312 sheet: -1.02 (0.34), residues: 210 loop : -1.04 (0.32), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 169 HIS 0.007 0.001 HIS R 269 PHE 0.015 0.001 PHE R 111 TYR 0.020 0.002 TYR A 318 ARG 0.013 0.001 ARG A 283 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1728 Ramachandran restraints generated. 864 Oldfield, 0 Emsley, 864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1728 Ramachandran restraints generated. 864 Oldfield, 0 Emsley, 864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 153 time to evaluate : 0.770 Fit side-chains revert: symmetry clash REVERT: R 47 TYR cc_start: 0.8180 (t80) cc_final: 0.7260 (t80) REVERT: R 61 CYS cc_start: 0.8528 (m) cc_final: 0.8206 (m) REVERT: R 144 VAL cc_start: 0.8473 (t) cc_final: 0.8239 (m) REVERT: R 227 GLN cc_start: 0.8391 (pp30) cc_final: 0.8085 (pp30) REVERT: R 238 LEU cc_start: 0.8521 (mm) cc_final: 0.8310 (mm) REVERT: R 285 LEU cc_start: 0.8627 (tm) cc_final: 0.8407 (tp) REVERT: A 27 GLU cc_start: 0.7679 (OUTLIER) cc_final: 0.6956 (mp0) REVERT: A 34 LYS cc_start: 0.7571 (tttp) cc_final: 0.7179 (tttp) REVERT: A 37 TYR cc_start: 0.7532 (t80) cc_final: 0.7132 (t80) REVERT: A 49 ASP cc_start: 0.7996 (m-30) cc_final: 0.7772 (m-30) REVERT: A 213 GLN cc_start: 0.7497 (OUTLIER) cc_final: 0.7198 (pm20) REVERT: A 362 HIS cc_start: 0.7703 (m-70) cc_final: 0.7479 (m90) REVERT: A 370 GLU cc_start: 0.7711 (pp20) cc_final: 0.7486 (pm20) REVERT: B 46 ARG cc_start: 0.7604 (ptt-90) cc_final: 0.7279 (mpp80) REVERT: B 52 ARG cc_start: 0.8013 (ptp-110) cc_final: 0.7747 (ttm110) REVERT: B 61 MET cc_start: 0.8123 (OUTLIER) cc_final: 0.7886 (ppp) REVERT: B 114 CYS cc_start: 0.7928 (t) cc_final: 0.7726 (t) REVERT: B 289 TYR cc_start: 0.8207 (m-80) cc_final: 0.7793 (m-80) REVERT: B 301 LYS cc_start: 0.7044 (mptt) cc_final: 0.6721 (mptt) REVERT: N 31 ASN cc_start: 0.6744 (m-40) cc_final: 0.6428 (m-40) REVERT: N 103 PHE cc_start: 0.7232 (m-80) cc_final: 0.6826 (m-80) outliers start: 34 outliers final: 15 residues processed: 166 average time/residue: 0.8534 time to fit residues: 152.4385 Evaluate side-chains 154 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 136 time to evaluate : 0.844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 250 VAL Chi-restraints excluded: chain R residue 276 SER Chi-restraints excluded: chain R residue 280 VAL Chi-restraints excluded: chain A residue 27 GLU Chi-restraints excluded: chain A residue 54 SER Chi-restraints excluded: chain A residue 213 GLN Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 207 SER Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain N residue 111 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 15 optimal weight: 7.9990 chunk 8 optimal weight: 2.9990 chunk 80 optimal weight: 4.9990 chunk 48 optimal weight: 0.9990 chunk 30 optimal weight: 2.9990 chunk 86 optimal weight: 3.9990 chunk 44 optimal weight: 3.9990 chunk 20 optimal weight: 2.9990 chunk 46 optimal weight: 6.9990 chunk 69 optimal weight: 7.9990 chunk 76 optimal weight: 0.0020 overall best weight: 1.9996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 83 GLN ** R 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 213 GLN B 176 GLN ** N 53 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 = 0.4172 r_free = 0.4172 target = 0.187572 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.167230 restraints weight = 10568.354| |-----------------------------------------------------------------------------| r_work (start): 0.3971 rms_B_bonded: 2.23 r_work: 0.3889 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work (final): 0.3889 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7349 moved from start: 0.3171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 7309 Z= 0.352 Angle : 0.684 7.225 9903 Z= 0.359 Chirality : 0.046 0.145 1108 Planarity : 0.005 0.052 1245 Dihedral : 6.431 53.240 1045 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 12.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 5.04 % Allowed : 17.18 % Favored : 77.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.64 (0.27), residues: 864 helix: 0.92 (0.28), residues: 310 sheet: -1.05 (0.34), residues: 201 loop : -1.18 (0.32), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 82 HIS 0.010 0.002 HIS R 269 PHE 0.023 0.002 PHE R 76 TYR 0.026 0.002 TYR R 106 ARG 0.010 0.001 ARG N 38 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1728 Ramachandran restraints generated. 864 Oldfield, 0 Emsley, 864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1728 Ramachandran restraints generated. 864 Oldfield, 0 Emsley, 864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 156 time to evaluate : 0.782 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 47 TYR cc_start: 0.8252 (t80) cc_final: 0.7577 (t80) REVERT: R 65 VAL cc_start: 0.8424 (OUTLIER) cc_final: 0.8141 (t) REVERT: R 234 VAL cc_start: 0.8161 (OUTLIER) cc_final: 0.7951 (p) REVERT: R 242 LEU cc_start: 0.8021 (tp) cc_final: 0.7730 (tm) REVERT: A 34 LYS cc_start: 0.7662 (tttp) cc_final: 0.7269 (tttp) REVERT: A 213 GLN cc_start: 0.7553 (OUTLIER) cc_final: 0.7333 (pm20) REVERT: A 239 ASN cc_start: 0.9076 (OUTLIER) cc_final: 0.8858 (p0) REVERT: A 362 HIS cc_start: 0.7837 (m-70) cc_final: 0.7613 (m90) REVERT: B 46 ARG cc_start: 0.7603 (ptt-90) cc_final: 0.7288 (mpp80) REVERT: B 52 ARG cc_start: 0.8005 (ptp-110) cc_final: 0.7682 (ttm110) REVERT: B 57 LYS cc_start: 0.8729 (OUTLIER) cc_final: 0.8168 (pttp) REVERT: B 117 LEU cc_start: 0.8353 (OUTLIER) cc_final: 0.7895 (mt) REVERT: B 217 MET cc_start: 0.5784 (ppp) cc_final: 0.5500 (pmm) REVERT: B 289 TYR cc_start: 0.8538 (m-80) cc_final: 0.8026 (m-80) REVERT: B 290 ASP cc_start: 0.7649 (m-30) cc_final: 0.7390 (m-30) REVERT: B 301 LYS cc_start: 0.7080 (mptt) cc_final: 0.6817 (mptt) REVERT: N 12 VAL cc_start: 0.5906 (p) cc_final: 0.5586 (m) REVERT: N 31 ASN cc_start: 0.6941 (m-40) cc_final: 0.6643 (m-40) outliers start: 39 outliers final: 17 residues processed: 173 average time/residue: 0.8025 time to fit residues: 150.0247 Evaluate side-chains 157 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 134 time to evaluate : 0.714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 65 VAL Chi-restraints excluded: chain R residue 71 ILE Chi-restraints excluded: chain R residue 234 VAL Chi-restraints excluded: chain R residue 250 VAL Chi-restraints excluded: chain R residue 276 SER Chi-restraints excluded: chain R residue 284 VAL Chi-restraints excluded: chain A residue 54 SER Chi-restraints excluded: chain A residue 213 GLN Chi-restraints excluded: chain A residue 239 ASN Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 57 LYS Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 149 CYS Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain N residue 111 THR Chi-restraints excluded: chain N residue 113 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 33 optimal weight: 0.6980 chunk 68 optimal weight: 0.8980 chunk 11 optimal weight: 0.7980 chunk 35 optimal weight: 0.8980 chunk 75 optimal weight: 0.7980 chunk 34 optimal weight: 0.9980 chunk 9 optimal weight: 0.7980 chunk 7 optimal weight: 0.7980 chunk 19 optimal weight: 0.9980 chunk 18 optimal weight: 0.7980 chunk 25 optimal weight: 0.5980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 176 GLN B 266 HIS N 53 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4224 r_free = 0.4224 target = 0.192615 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.172577 restraints weight = 10577.681| |-----------------------------------------------------------------------------| r_work (start): 0.4019 rms_B_bonded: 2.25 r_work: 0.3941 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work (final): 0.3941 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7251 moved from start: 0.3168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 7309 Z= 0.207 Angle : 0.598 9.261 9903 Z= 0.313 Chirality : 0.043 0.163 1108 Planarity : 0.004 0.047 1245 Dihedral : 6.070 56.770 1045 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 10.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 3.88 % Allowed : 20.93 % Favored : 75.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.53 (0.28), residues: 864 helix: 1.09 (0.28), residues: 311 sheet: -1.15 (0.34), residues: 208 loop : -1.06 (0.32), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 169 HIS 0.006 0.001 HIS R 269 PHE 0.017 0.001 PHE R 111 TYR 0.021 0.002 TYR R 106 ARG 0.010 0.001 ARG R 210 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1728 Ramachandran restraints generated. 864 Oldfield, 0 Emsley, 864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1728 Ramachandran restraints generated. 864 Oldfield, 0 Emsley, 864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 142 time to evaluate : 0.839 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 47 TYR cc_start: 0.8295 (t80) cc_final: 0.7537 (t80) REVERT: A 34 LYS cc_start: 0.7662 (tttp) cc_final: 0.7268 (tttp) REVERT: A 37 TYR cc_start: 0.7622 (t80) cc_final: 0.7216 (t80) REVERT: A 49 ASP cc_start: 0.7989 (m-30) cc_final: 0.7761 (m-30) REVERT: A 239 ASN cc_start: 0.8995 (OUTLIER) cc_final: 0.8673 (p0) REVERT: A 356 ARG cc_start: 0.6852 (mpp80) cc_final: 0.6369 (mpp-170) REVERT: A 362 HIS cc_start: 0.7760 (m-70) cc_final: 0.7517 (m90) REVERT: A 384 GLN cc_start: 0.7804 (mt0) cc_final: 0.7443 (tp40) REVERT: B 46 ARG cc_start: 0.7552 (ptt-90) cc_final: 0.7235 (mpp80) REVERT: B 52 ARG cc_start: 0.7990 (ptp-110) cc_final: 0.7714 (ttm110) REVERT: B 110 ASN cc_start: 0.6938 (p0) cc_final: 0.6532 (m-40) REVERT: B 289 TYR cc_start: 0.8328 (m-80) cc_final: 0.8020 (m-80) REVERT: B 301 LYS cc_start: 0.7110 (mptt) cc_final: 0.6877 (mptt) REVERT: B 317 CYS cc_start: 0.7929 (t) cc_final: 0.7710 (p) REVERT: N 12 VAL cc_start: 0.5800 (p) cc_final: 0.5403 (m) REVERT: N 31 ASN cc_start: 0.6891 (m-40) cc_final: 0.6575 (m-40) REVERT: N 38 ARG cc_start: 0.6466 (mtp180) cc_final: 0.6203 (ptp-110) outliers start: 30 outliers final: 19 residues processed: 159 average time/residue: 0.8014 time to fit residues: 137.9162 Evaluate side-chains 150 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 130 time to evaluate : 0.806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 65 VAL Chi-restraints excluded: chain R residue 71 ILE Chi-restraints excluded: chain R residue 276 SER Chi-restraints excluded: chain R residue 280 VAL Chi-restraints excluded: chain A residue 54 SER Chi-restraints excluded: chain A residue 239 ASN Chi-restraints excluded: chain B residue 45 MET Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 149 CYS Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 323 ASP Chi-restraints excluded: chain N residue 50 ASP Chi-restraints excluded: chain N residue 111 THR Chi-restraints excluded: chain N residue 113 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 19 optimal weight: 0.9980 chunk 67 optimal weight: 6.9990 chunk 80 optimal weight: 2.9990 chunk 70 optimal weight: 0.0980 chunk 59 optimal weight: 0.8980 chunk 44 optimal weight: 1.9990 chunk 48 optimal weight: 0.6980 chunk 53 optimal weight: 5.9990 chunk 3 optimal weight: 0.0870 chunk 65 optimal weight: 3.9990 chunk 77 optimal weight: 1.9990 overall best weight: 0.5558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 62 HIS B 176 GLN 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 = 0.194932 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.175068 restraints weight = 10628.442| |-----------------------------------------------------------------------------| r_work (start): 0.4042 rms_B_bonded: 2.33 r_work: 0.3962 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work (final): 0.3962 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7206 moved from start: 0.3302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 7309 Z= 0.182 Angle : 0.575 8.288 9903 Z= 0.300 Chirality : 0.042 0.139 1108 Planarity : 0.004 0.043 1245 Dihedral : 5.907 57.138 1045 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 10.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 4.13 % Allowed : 21.96 % Favored : 73.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.37 (0.28), residues: 864 helix: 1.23 (0.28), residues: 312 sheet: -1.09 (0.35), residues: 207 loop : -0.97 (0.33), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 169 HIS 0.006 0.001 HIS R 269 PHE 0.017 0.001 PHE N 68 TYR 0.020 0.001 TYR A 391 ARG 0.009 0.000 ARG R 251 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1728 Ramachandran restraints generated. 864 Oldfield, 0 Emsley, 864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1728 Ramachandran restraints generated. 864 Oldfield, 0 Emsley, 864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 142 time to evaluate : 0.785 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 47 TYR cc_start: 0.8301 (t80) cc_final: 0.7461 (t80) REVERT: R 144 VAL cc_start: 0.8524 (t) cc_final: 0.8309 (m) REVERT: A 34 LYS cc_start: 0.7700 (tttp) cc_final: 0.7269 (tttp) REVERT: A 37 TYR cc_start: 0.7611 (t80) cc_final: 0.7210 (t80) REVERT: A 239 ASN cc_start: 0.8937 (OUTLIER) cc_final: 0.8657 (p0) REVERT: A 356 ARG cc_start: 0.6916 (mpp80) cc_final: 0.6543 (mpp-170) REVERT: A 362 HIS cc_start: 0.7716 (m-70) cc_final: 0.7490 (m90) REVERT: B 46 ARG cc_start: 0.7590 (ptt-90) cc_final: 0.7261 (mpp80) REVERT: B 110 ASN cc_start: 0.6658 (p0) cc_final: 0.6349 (m-40) REVERT: B 111 TYR cc_start: 0.7183 (m-80) cc_final: 0.6900 (m-80) REVERT: B 246 ASP cc_start: 0.7925 (m-30) cc_final: 0.7628 (t0) REVERT: B 301 LYS cc_start: 0.7065 (mptt) cc_final: 0.6774 (mptt) REVERT: N 31 ASN cc_start: 0.6890 (m-40) cc_final: 0.6547 (m-40) REVERT: N 38 ARG cc_start: 0.6313 (mtp180) cc_final: 0.6061 (ptp-110) outliers start: 32 outliers final: 14 residues processed: 161 average time/residue: 0.8067 time to fit residues: 140.3874 Evaluate side-chains 143 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 128 time to evaluate : 0.826 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 250 VAL Chi-restraints excluded: chain R residue 276 SER Chi-restraints excluded: chain R residue 280 VAL Chi-restraints excluded: chain A residue 54 SER Chi-restraints excluded: chain A residue 239 ASN Chi-restraints excluded: chain A residue 335 THR Chi-restraints excluded: chain B residue 45 MET Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 149 CYS Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain N residue 111 THR Chi-restraints excluded: chain N residue 113 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 36 optimal weight: 0.0770 chunk 14 optimal weight: 2.9990 chunk 69 optimal weight: 0.6980 chunk 12 optimal weight: 4.9990 chunk 71 optimal weight: 6.9990 chunk 59 optimal weight: 0.0980 chunk 61 optimal weight: 0.0670 chunk 44 optimal weight: 3.9990 chunk 6 optimal weight: 2.9990 chunk 47 optimal weight: 0.7980 chunk 66 optimal weight: 0.9990 overall best weight: 0.3476 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 176 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4279 r_free = 0.4279 target = 0.198401 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.179054 restraints weight = 10643.964| |-----------------------------------------------------------------------------| r_work (start): 0.4101 rms_B_bonded: 2.27 r_work: 0.4024 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work (final): 0.4024 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7135 moved from start: 0.3443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7309 Z= 0.170 Angle : 0.594 9.358 9903 Z= 0.305 Chirality : 0.043 0.161 1108 Planarity : 0.004 0.050 1245 Dihedral : 5.702 56.997 1045 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 10.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 3.62 % Allowed : 23.90 % Favored : 72.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.34 (0.28), residues: 864 helix: 1.36 (0.28), residues: 312 sheet: -1.09 (0.35), residues: 204 loop : -1.07 (0.32), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 169 HIS 0.005 0.001 HIS R 269 PHE 0.014 0.001 PHE R 111 TYR 0.023 0.001 TYR R 155 ARG 0.009 0.001 ARG R 251 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1728 Ramachandran restraints generated. 864 Oldfield, 0 Emsley, 864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1728 Ramachandran restraints generated. 864 Oldfield, 0 Emsley, 864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 140 time to evaluate : 0.818 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 47 TYR cc_start: 0.8263 (t80) cc_final: 0.7374 (t80) REVERT: R 72 CYS cc_start: 0.8592 (m) cc_final: 0.8289 (p) REVERT: R 238 LEU cc_start: 0.8562 (OUTLIER) cc_final: 0.8317 (mm) REVERT: A 37 TYR cc_start: 0.7564 (t80) cc_final: 0.7187 (t80) REVERT: A 239 ASN cc_start: 0.8894 (OUTLIER) cc_final: 0.8608 (p0) REVERT: A 356 ARG cc_start: 0.6824 (mpp80) cc_final: 0.6354 (mpp-170) REVERT: A 362 HIS cc_start: 0.7669 (m-70) cc_final: 0.7469 (m90) REVERT: A 384 GLN cc_start: 0.7732 (mt0) cc_final: 0.7334 (tp40) REVERT: B 46 ARG cc_start: 0.7614 (ptt-90) cc_final: 0.7281 (mpp80) REVERT: B 110 ASN cc_start: 0.6508 (p0) cc_final: 0.6239 (m-40) REVERT: B 111 TYR cc_start: 0.7152 (m-80) cc_final: 0.6941 (m-80) REVERT: B 168 LEU cc_start: 0.7226 (OUTLIER) cc_final: 0.6940 (tp) REVERT: B 246 ASP cc_start: 0.7863 (m-30) cc_final: 0.7552 (t0) REVERT: B 301 LYS cc_start: 0.6960 (mptt) cc_final: 0.6648 (mptt) REVERT: N 31 ASN cc_start: 0.6841 (m-40) cc_final: 0.6467 (m-40) REVERT: N 38 ARG cc_start: 0.6247 (mtp180) cc_final: 0.5990 (ptp-110) REVERT: N 103 PHE cc_start: 0.7259 (m-80) cc_final: 0.6865 (m-80) outliers start: 28 outliers final: 16 residues processed: 154 average time/residue: 0.7452 time to fit residues: 124.8642 Evaluate side-chains 148 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 129 time to evaluate : 0.735 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 65 VAL Chi-restraints excluded: chain R residue 238 LEU Chi-restraints excluded: chain R residue 250 VAL Chi-restraints excluded: chain R residue 276 SER Chi-restraints excluded: chain R residue 280 VAL Chi-restraints excluded: chain A residue 239 ASN Chi-restraints excluded: chain A residue 335 THR Chi-restraints excluded: chain B residue 45 MET Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain N residue 111 THR Chi-restraints excluded: chain N residue 113 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 36 optimal weight: 0.5980 chunk 76 optimal weight: 1.9990 chunk 53 optimal weight: 5.9990 chunk 45 optimal weight: 4.9990 chunk 10 optimal weight: 0.6980 chunk 64 optimal weight: 0.6980 chunk 0 optimal weight: 7.9990 chunk 48 optimal weight: 1.9990 chunk 83 optimal weight: 0.5980 chunk 26 optimal weight: 0.8980 chunk 47 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 104 ASN ** A 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 176 GLN B 220 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4251 r_free = 0.4251 target = 0.195947 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.175965 restraints weight = 10790.201| |-----------------------------------------------------------------------------| r_work (start): 0.4062 rms_B_bonded: 2.35 r_work: 0.3982 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work (final): 0.3982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7162 moved from start: 0.3515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 7309 Z= 0.197 Angle : 0.592 7.717 9903 Z= 0.308 Chirality : 0.043 0.176 1108 Planarity : 0.004 0.042 1245 Dihedral : 5.718 55.469 1045 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 11.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 3.88 % Allowed : 24.16 % Favored : 71.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.29 (0.28), residues: 864 helix: 1.28 (0.28), residues: 312 sheet: -0.97 (0.35), residues: 209 loop : -0.98 (0.33), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 169 HIS 0.007 0.001 HIS R 269 PHE 0.022 0.001 PHE N 68 TYR 0.022 0.002 TYR R 155 ARG 0.009 0.000 ARG R 251 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1728 Ramachandran restraints generated. 864 Oldfield, 0 Emsley, 864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1728 Ramachandran restraints generated. 864 Oldfield, 0 Emsley, 864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 132 time to evaluate : 0.783 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 47 TYR cc_start: 0.8226 (t80) cc_final: 0.7286 (t80) REVERT: R 72 CYS cc_start: 0.8578 (m) cc_final: 0.8271 (p) REVERT: A 37 TYR cc_start: 0.7667 (t80) cc_final: 0.7239 (t80) REVERT: A 239 ASN cc_start: 0.8920 (OUTLIER) cc_final: 0.8644 (p0) REVERT: A 356 ARG cc_start: 0.6789 (mpp80) cc_final: 0.6323 (mpp-170) REVERT: A 362 HIS cc_start: 0.7712 (m-70) cc_final: 0.7502 (m90) REVERT: B 46 ARG cc_start: 0.7632 (ptt-90) cc_final: 0.7295 (mpp80) REVERT: B 110 ASN cc_start: 0.6601 (p0) cc_final: 0.6258 (m-40) REVERT: B 111 TYR cc_start: 0.7233 (m-80) cc_final: 0.7023 (m-80) REVERT: B 246 ASP cc_start: 0.7864 (m-30) cc_final: 0.7550 (t0) REVERT: B 301 LYS cc_start: 0.7019 (mptt) cc_final: 0.6702 (mptt) REVERT: B 318 LEU cc_start: 0.8588 (tt) cc_final: 0.8312 (tt) REVERT: N 31 ASN cc_start: 0.6921 (m-40) cc_final: 0.6565 (m-40) REVERT: N 38 ARG cc_start: 0.6242 (mtp180) cc_final: 0.5971 (ptp-110) outliers start: 30 outliers final: 20 residues processed: 149 average time/residue: 0.7385 time to fit residues: 120.0259 Evaluate side-chains 155 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 134 time to evaluate : 0.836 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 61 CYS Chi-restraints excluded: chain R residue 65 VAL Chi-restraints excluded: chain R residue 104 ASN Chi-restraints excluded: chain R residue 226 ILE Chi-restraints excluded: chain R residue 250 VAL Chi-restraints excluded: chain R residue 276 SER Chi-restraints excluded: chain R residue 280 VAL Chi-restraints excluded: chain A residue 54 SER Chi-restraints excluded: chain A residue 239 ASN Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 335 THR Chi-restraints excluded: chain B residue 45 MET Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain N residue 111 THR Chi-restraints excluded: chain N residue 113 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 41 optimal weight: 0.0010 chunk 58 optimal weight: 5.9990 chunk 5 optimal weight: 0.7980 chunk 23 optimal weight: 2.9990 chunk 75 optimal weight: 0.5980 chunk 4 optimal weight: 0.7980 chunk 31 optimal weight: 0.8980 chunk 52 optimal weight: 0.9980 chunk 17 optimal weight: 0.7980 chunk 19 optimal weight: 0.9980 chunk 70 optimal weight: 0.8980 overall best weight: 0.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 104 ASN ** A 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 176 GLN B 220 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4263 r_free = 0.4263 target = 0.197012 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.177107 restraints weight = 10791.945| |-----------------------------------------------------------------------------| r_work (start): 0.4075 rms_B_bonded: 2.35 r_work: 0.3996 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work (final): 0.3996 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7141 moved from start: 0.3548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 7309 Z= 0.191 Angle : 0.615 9.634 9903 Z= 0.314 Chirality : 0.043 0.177 1108 Planarity : 0.004 0.056 1245 Dihedral : 5.693 54.442 1045 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 11.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 3.23 % Allowed : 24.81 % Favored : 71.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.32 (0.28), residues: 864 helix: 1.24 (0.28), residues: 313 sheet: -0.96 (0.35), residues: 209 loop : -0.99 (0.33), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 169 HIS 0.007 0.001 HIS R 269 PHE 0.010 0.001 PHE A 212 TYR 0.032 0.002 TYR R 155 ARG 0.013 0.000 ARG R 210 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1728 Ramachandran restraints generated. 864 Oldfield, 0 Emsley, 864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1728 Ramachandran restraints generated. 864 Oldfield, 0 Emsley, 864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 136 time to evaluate : 0.745 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 47 TYR cc_start: 0.8209 (t80) cc_final: 0.7285 (t80) REVERT: R 72 CYS cc_start: 0.8625 (m) cc_final: 0.8269 (p) REVERT: R 218 THR cc_start: 0.7790 (m) cc_final: 0.7589 (t) REVERT: A 37 TYR cc_start: 0.7634 (t80) cc_final: 0.7262 (t80) REVERT: A 239 ASN cc_start: 0.8898 (OUTLIER) cc_final: 0.8623 (p0) REVERT: A 356 ARG cc_start: 0.6793 (mpp80) cc_final: 0.6309 (mpp-170) REVERT: A 362 HIS cc_start: 0.7695 (m-70) cc_final: 0.7488 (m90) REVERT: B 46 ARG cc_start: 0.7653 (ptt-90) cc_final: 0.7309 (mpp80) REVERT: B 110 ASN cc_start: 0.6571 (p0) cc_final: 0.6123 (m-40) REVERT: B 246 ASP cc_start: 0.7858 (m-30) cc_final: 0.7545 (t0) REVERT: B 301 LYS cc_start: 0.6968 (mptt) cc_final: 0.6672 (mptt) REVERT: B 318 LEU cc_start: 0.8584 (tt) cc_final: 0.8295 (tt) REVERT: N 31 ASN cc_start: 0.6868 (m-40) cc_final: 0.6511 (m-40) REVERT: N 38 ARG cc_start: 0.6200 (mtp180) cc_final: 0.5969 (ptp-110) REVERT: N 68 PHE cc_start: 0.6386 (m-80) cc_final: 0.6147 (m-10) outliers start: 25 outliers final: 21 residues processed: 149 average time/residue: 0.7307 time to fit residues: 118.5127 Evaluate side-chains 151 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 129 time to evaluate : 0.807 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 56 LEU Chi-restraints excluded: chain R residue 61 CYS Chi-restraints excluded: chain R residue 65 VAL Chi-restraints excluded: chain R residue 104 ASN Chi-restraints excluded: chain R residue 250 VAL Chi-restraints excluded: chain R residue 276 SER Chi-restraints excluded: chain R residue 280 VAL Chi-restraints excluded: chain A residue 54 SER Chi-restraints excluded: chain A residue 239 ASN Chi-restraints excluded: chain A residue 335 THR Chi-restraints excluded: chain B residue 45 MET Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 323 ASP Chi-restraints excluded: chain N residue 111 THR Chi-restraints excluded: chain N residue 113 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 75 optimal weight: 0.0980 chunk 51 optimal weight: 0.8980 chunk 33 optimal weight: 0.8980 chunk 78 optimal weight: 5.9990 chunk 43 optimal weight: 2.9990 chunk 55 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 chunk 22 optimal weight: 0.7980 chunk 20 optimal weight: 3.9990 chunk 10 optimal weight: 0.6980 chunk 50 optimal weight: 0.9980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 176 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4256 r_free = 0.4256 target = 0.196286 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.176490 restraints weight = 10975.670| |-----------------------------------------------------------------------------| r_work (start): 0.4067 rms_B_bonded: 2.31 r_work: 0.3988 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work (final): 0.3988 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7175 moved from start: 0.3588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 7309 Z= 0.198 Angle : 0.616 9.575 9903 Z= 0.315 Chirality : 0.043 0.183 1108 Planarity : 0.004 0.055 1245 Dihedral : 5.712 53.552 1045 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 10.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 3.23 % Allowed : 25.32 % Favored : 71.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (0.28), residues: 864 helix: 1.25 (0.28), residues: 313 sheet: -0.90 (0.35), residues: 209 loop : -0.98 (0.33), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 169 HIS 0.007 0.001 HIS R 269 PHE 0.011 0.001 PHE B 335 TYR 0.028 0.002 TYR R 106 ARG 0.012 0.000 ARG R 210 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1728 Ramachandran restraints generated. 864 Oldfield, 0 Emsley, 864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1728 Ramachandran restraints generated. 864 Oldfield, 0 Emsley, 864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 133 time to evaluate : 0.729 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 47 TYR cc_start: 0.8214 (t80) cc_final: 0.7290 (t80) REVERT: R 111 PHE cc_start: 0.7336 (m-80) cc_final: 0.7009 (m-80) REVERT: R 218 THR cc_start: 0.7758 (m) cc_final: 0.7543 (t) REVERT: A 34 LYS cc_start: 0.7678 (tttp) cc_final: 0.7322 (tttp) REVERT: A 37 TYR cc_start: 0.7657 (t80) cc_final: 0.7343 (t80) REVERT: A 356 ARG cc_start: 0.6851 (mpp80) cc_final: 0.6331 (mpp-170) REVERT: A 362 HIS cc_start: 0.7695 (m-70) cc_final: 0.7488 (m90) REVERT: B 46 ARG cc_start: 0.7639 (ptt-90) cc_final: 0.7313 (mpp80) REVERT: B 110 ASN cc_start: 0.6559 (p0) cc_final: 0.6178 (m-40) REVERT: B 246 ASP cc_start: 0.7906 (m-30) cc_final: 0.7594 (t0) REVERT: B 301 LYS cc_start: 0.7100 (mptt) cc_final: 0.6803 (mptt) REVERT: B 318 LEU cc_start: 0.8614 (OUTLIER) cc_final: 0.8342 (tt) REVERT: N 31 ASN cc_start: 0.6906 (m-40) cc_final: 0.6554 (m-40) REVERT: N 38 ARG cc_start: 0.6204 (mtp180) cc_final: 0.5997 (ptp-110) outliers start: 25 outliers final: 20 residues processed: 144 average time/residue: 0.7311 time to fit residues: 114.7650 Evaluate side-chains 153 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 132 time to evaluate : 0.800 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 61 CYS Chi-restraints excluded: chain R residue 65 VAL Chi-restraints excluded: chain R residue 220 LYS Chi-restraints excluded: chain R residue 250 VAL Chi-restraints excluded: chain R residue 276 SER Chi-restraints excluded: chain R residue 280 VAL Chi-restraints excluded: chain A residue 54 SER Chi-restraints excluded: chain A residue 335 THR Chi-restraints excluded: chain B residue 45 MET Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 323 ASP Chi-restraints excluded: chain N residue 111 THR Chi-restraints excluded: chain N residue 113 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 81 optimal weight: 0.4980 chunk 1 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 35 optimal weight: 0.7980 chunk 29 optimal weight: 0.9980 chunk 15 optimal weight: 0.5980 chunk 49 optimal weight: 5.9990 chunk 65 optimal weight: 2.9990 chunk 78 optimal weight: 6.9990 chunk 8 optimal weight: 1.9990 chunk 60 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 176 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4253 r_free = 0.4253 target = 0.195949 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.175929 restraints weight = 10752.072| |-----------------------------------------------------------------------------| r_work (start): 0.4061 rms_B_bonded: 2.35 r_work: 0.3981 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work (final): 0.3981 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7166 moved from start: 0.3662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 7309 Z= 0.201 Angle : 0.627 11.086 9903 Z= 0.318 Chirality : 0.043 0.184 1108 Planarity : 0.004 0.051 1245 Dihedral : 5.772 54.456 1045 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 10.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 3.10 % Allowed : 26.36 % Favored : 70.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (0.28), residues: 864 helix: 1.34 (0.28), residues: 312 sheet: -0.92 (0.35), residues: 211 loop : -1.05 (0.33), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 169 HIS 0.007 0.001 HIS R 269 PHE 0.017 0.001 PHE N 68 TYR 0.026 0.002 TYR R 155 ARG 0.012 0.000 ARG R 210 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4360.90 seconds wall clock time: 77 minutes 53.56 seconds (4673.56 seconds total)