Starting phenix.real_space_refine on Wed Sep 17 07:04:05 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9f6u_50240/09_2025/9f6u_50240.cif Found real_map, /net/cci-nas-00/data/ceres_data/9f6u_50240/09_2025/9f6u_50240.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9f6u_50240/09_2025/9f6u_50240.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9f6u_50240/09_2025/9f6u_50240.map" model { file = "/net/cci-nas-00/data/ceres_data/9f6u_50240/09_2025/9f6u_50240.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9f6u_50240/09_2025/9f6u_50240.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.002 sd= 0.161 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 P 5 5.49 5 S 34 5.16 5 C 4166 2.51 5 N 1090 2.21 5 O 1275 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 6570 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3230 Number of conformers: 1 Conformer: "" Number of residues, atoms: 422, 3230 Classifications: {'peptide': 422} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 406} Chain: "B" Number of atoms: 3280 Number of conformers: 1 Conformer: "" Number of residues, atoms: 423, 3280 Classifications: {'peptide': 423} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 406} Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'GDP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'GTP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.66, per 1000 atoms: 0.25 Number of scatterers: 6570 At special positions: 0 Unit cell: (98.8, 78, 104, 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) S 34 16.00 P 5 15.00 O 1275 8.00 N 1090 7.00 C 4166 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.58 Conformation dependent library (CDL) restraints added in 352.7 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 1682 Ramachandran restraints generated. 841 Oldfield, 0 Emsley, 841 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1546 Finding SS restraints... Secondary structure from input PDB file: 37 helices and 4 sheets defined 49.3% alpha, 14.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.16 Creating SS restraints... Processing helix chain 'A' and resid 11 through 30 Processing helix chain 'A' and resid 44 through 47 Processing helix chain 'A' and resid 66 through 69 Processing helix chain 'A' and resid 70 through 75 Processing helix chain 'A' and resid 82 through 84 No H-bonds generated for 'chain 'A' and resid 82 through 84' Processing helix chain 'A' and resid 96 through 102 Processing helix chain 'A' and resid 105 through 122 Processing helix chain 'A' and resid 141 through 155 Processing helix chain 'A' and resid 176 through 192 removed outlier: 3.505A pdb=" N ASN A 180 " --> pdb=" O VAL A 176 " (cutoff:3.500A) Processing helix chain 'A' and resid 200 through 210 Processing helix chain 'A' and resid 217 through 234 removed outlier: 4.237A pdb=" N LEU A 223 " --> pdb=" O GLU A 219 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N ILE A 224 " --> pdb=" O ASP A 220 " (cutoff:3.500A) Processing helix chain 'A' and resid 235 through 237 No H-bonds generated for 'chain 'A' and resid 235 through 237' Processing helix chain 'A' and resid 245 through 254 Processing helix chain 'A' and resid 281 through 290 Processing helix chain 'A' and resid 291 through 295 Processing helix chain 'A' and resid 300 through 304 Processing helix chain 'A' and resid 318 through 331 removed outlier: 3.942A pdb=" N GLU A 324 " --> pdb=" O SER A 320 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 339 Processing helix chain 'A' and resid 368 through 382 removed outlier: 3.899A pdb=" N PHE A 372 " --> pdb=" O ILE A 368 " (cutoff:3.500A) Processing helix chain 'A' and resid 398 through 420 Processing helix chain 'B' and resid 11 through 29 Processing helix chain 'B' and resid 70 through 78 Processing helix chain 'B' and resid 85 through 87 No H-bonds generated for 'chain 'B' and resid 85 through 87' Processing helix chain 'B' and resid 99 through 106 Processing helix chain 'B' and resid 110 through 124 removed outlier: 4.229A pdb=" N ASN B 114 " --> pdb=" O ASP B 110 " (cutoff:3.500A) Processing helix chain 'B' and resid 140 through 158 Processing helix chain 'B' and resid 179 through 195 Processing helix chain 'B' and resid 203 through 213 Processing helix chain 'B' and resid 220 through 236 removed outlier: 3.965A pdb=" N HIS B 226 " --> pdb=" O ASP B 222 " (cutoff:3.500A) Processing helix chain 'B' and resid 237 through 241 removed outlier: 3.603A pdb=" N PHE B 241 " --> pdb=" O SER B 238 " (cutoff:3.500A) Processing helix chain 'B' and resid 248 through 257 Processing helix chain 'B' and resid 284 through 292 removed outlier: 4.875A pdb=" N ASN B 290 " --> pdb=" O SER B 286 " (cutoff:3.500A) Processing helix chain 'B' and resid 293 through 298 removed outlier: 6.542A pdb=" N ASN B 296 " --> pdb=" O PHE B 293 " (cutoff:3.500A) Processing helix chain 'B' and resid 321 through 330 removed outlier: 3.865A pdb=" N LEU B 330 " --> pdb=" O THR B 326 " (cutoff:3.500A) Processing helix chain 'B' and resid 370 through 388 removed outlier: 4.123A pdb=" N ILE B 374 " --> pdb=" O GLY B 370 " (cutoff:3.500A) Processing helix chain 'B' and resid 392 through 397 Processing helix chain 'B' and resid 401 through 421 Processing sheet with id=AA1, first strand: chain 'A' and resid 86 through 88 removed outlier: 8.271A pdb=" N VAL A 87 " --> pdb=" O ALA A 60 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N VAL A 62 " --> pdb=" O VAL A 87 " (cutoff:3.500A) removed outlier: 5.683A pdb=" N GLU A 4 " --> pdb=" O ILE A 126 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N GLY A 128 " --> pdb=" O GLU A 4 " (cutoff:3.500A) removed outlier: 4.858A pdb=" N SER A 134 " --> pdb=" O VAL A 10 " (cutoff:3.500A) removed outlier: 7.886A pdb=" N PHE A 161 " --> pdb=" O GLY A 127 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N PHE A 129 " --> pdb=" O PHE A 161 " (cutoff:3.500A) removed outlier: 7.788A pdb=" N PHE A 163 " --> pdb=" O PHE A 129 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N LEU A 131 " --> pdb=" O PHE A 163 " (cutoff:3.500A) removed outlier: 7.597A pdb=" N ILE A 165 " --> pdb=" O LEU A 131 " (cutoff:3.500A) removed outlier: 7.213A pdb=" N HIS A 133 " --> pdb=" O ILE A 165 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N CYS A 194 " --> pdb=" O ILE A 160 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N SER A 195 " --> pdb=" O LEU A 262 " (cutoff:3.500A) removed outlier: 7.440A pdb=" N ALA A 264 " --> pdb=" O SER A 195 " (cutoff:3.500A) removed outlier: 7.762A pdb=" N VAL A 197 " --> pdb=" O ALA A 264 " (cutoff:3.500A) removed outlier: 10.693A pdb=" N THR A 266 " --> pdb=" O VAL A 197 " (cutoff:3.500A) removed outlier: 13.744A pdb=" N ASP A 199 " --> pdb=" O THR A 266 " (cutoff:3.500A) removed outlier: 7.664A pdb=" N PHE A 261 " --> pdb=" O ASN A 365 " (cutoff:3.500A) removed outlier: 4.960A pdb=" N ASN A 365 " --> pdb=" O PHE A 261 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 49 through 51 Processing sheet with id=AA3, first strand: chain 'B' and resid 89 through 91 removed outlier: 7.891A pdb=" N ILE B 90 " --> pdb=" O ALA B 62 " (cutoff:3.500A) removed outlier: 6.023A pdb=" N LEU B 64 " --> pdb=" O ILE B 90 " (cutoff:3.500A) removed outlier: 8.471A pdb=" N LEU B 63 " --> pdb=" O VAL B 5 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N MET B 7 " --> pdb=" O LEU B 63 " (cutoff:3.500A) removed outlier: 7.625A pdb=" N ILE B 65 " --> pdb=" O MET B 7 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N HIS B 9 " --> pdb=" O ILE B 65 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N GLU B 4 " --> pdb=" O GLN B 130 " (cutoff:3.500A) removed outlier: 5.829A pdb=" N PHE B 132 " --> pdb=" O GLU B 4 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N ILE B 6 " --> pdb=" O PHE B 132 " (cutoff:3.500A) removed outlier: 5.357A pdb=" N MET B 134 " --> pdb=" O ILE B 6 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N LEU B 8 " --> pdb=" O MET B 134 " (cutoff:3.500A) removed outlier: 5.679A pdb=" N HIS B 136 " --> pdb=" O LEU B 8 " (cutoff:3.500A) removed outlier: 7.502A pdb=" N VAL B 10 " --> pdb=" O HIS B 136 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N GLN B 130 " --> pdb=" O ILE B 162 " (cutoff:3.500A) removed outlier: 8.021A pdb=" N TRP B 164 " --> pdb=" O GLN B 130 " (cutoff:3.500A) removed outlier: 6.111A pdb=" N PHE B 132 " --> pdb=" O TRP B 164 " (cutoff:3.500A) removed outlier: 7.682A pdb=" N TYR B 166 " --> pdb=" O PHE B 132 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N MET B 134 " --> pdb=" O TYR B 166 " (cutoff:3.500A) removed outlier: 8.068A pdb=" N ILE B 168 " --> pdb=" O MET B 134 " (cutoff:3.500A) removed outlier: 7.316A pdb=" N HIS B 136 " --> pdb=" O ILE B 168 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N THR B 198 " --> pdb=" O LEU B 265 " (cutoff:3.500A) removed outlier: 7.462A pdb=" N ALA B 267 " --> pdb=" O THR B 198 " (cutoff:3.500A) removed outlier: 7.924A pdb=" N VAL B 200 " --> pdb=" O ALA B 267 " (cutoff:3.500A) removed outlier: 10.303A pdb=" N PHE B 269 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 12.617A pdb=" N ASP B 202 " --> pdb=" O PHE B 269 " (cutoff:3.500A) removed outlier: 7.576A pdb=" N PHE B 264 " --> pdb=" O HIS B 368 " (cutoff:3.500A) removed outlier: 5.065A pdb=" N HIS B 368 " --> pdb=" O PHE B 264 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N SER B 361 " --> pdb=" O PHE B 316 " (cutoff:3.500A) removed outlier: 4.893A pdb=" N PHE B 316 " --> pdb=" O SER B 361 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N SER B 363 " --> pdb=" O LEU B 314 " (cutoff:3.500A) removed outlier: 4.794A pdb=" N LEU B 314 " --> pdb=" O SER B 363 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N LEU B 365 " --> pdb=" O CYS B 312 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N CYS B 312 " --> pdb=" O LEU B 365 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N ASN B 367 " --> pdb=" O LEU B 310 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 50 through 52 322 hydrogen bonds defined for protein. 924 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: 0.91 Time building geometry restraints manager: 0.76 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 2006 1.33 - 1.46: 1582 1.46 - 1.58: 3047 1.58 - 1.71: 8 1.71 - 1.83: 57 Bond restraints: 6700 Sorted by residual: bond pdb=" CA HIS B 226 " pdb=" C HIS B 226 " ideal model delta sigma weight residual 1.524 1.449 0.075 1.24e-02 6.50e+03 3.70e+01 bond pdb=" CA PHE B 207 " pdb=" C PHE B 207 " ideal model delta sigma weight residual 1.524 1.466 0.058 1.24e-02 6.50e+03 2.20e+01 bond pdb=" CB ASN A 222 " pdb=" CG ASN A 222 " ideal model delta sigma weight residual 1.516 1.412 0.104 2.50e-02 1.60e+03 1.72e+01 bond pdb=" CA LEU B 206 " pdb=" C LEU B 206 " ideal model delta sigma weight residual 1.524 1.470 0.053 1.29e-02 6.01e+03 1.70e+01 bond pdb=" CG1 ILE B 38 " pdb=" CD1 ILE B 38 " ideal model delta sigma weight residual 1.513 1.353 0.160 3.90e-02 6.57e+02 1.69e+01 ... (remaining 6695 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.56: 8228 2.56 - 5.12: 754 5.12 - 7.68: 76 7.68 - 10.24: 14 10.24 - 12.80: 4 Bond angle restraints: 9076 Sorted by residual: angle pdb=" N ARG B 335 " pdb=" CA ARG B 335 " pdb=" C ARG B 335 " ideal model delta sigma weight residual 113.41 103.88 9.53 1.22e+00 6.72e-01 6.10e+01 angle pdb=" N GLN B 279 " pdb=" CA GLN B 279 " pdb=" C GLN B 279 " ideal model delta sigma weight residual 110.35 101.90 8.45 1.36e+00 5.41e-01 3.86e+01 angle pdb=" N SER A 395 " pdb=" CA SER A 395 " pdb=" C SER A 395 " ideal model delta sigma weight residual 110.61 103.29 7.32 1.25e+00 6.40e-01 3.43e+01 angle pdb=" C LEU B 245 " pdb=" CA LEU B 245 " pdb=" CB LEU B 245 " ideal model delta sigma weight residual 116.34 108.69 7.65 1.40e+00 5.10e-01 2.99e+01 angle pdb=" C HIS B 226 " pdb=" CA HIS B 226 " pdb=" CB HIS B 226 " ideal model delta sigma weight residual 110.95 103.00 7.95 1.55e+00 4.16e-01 2.63e+01 ... (remaining 9071 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.69: 3953 34.69 - 69.39: 38 69.39 - 104.08: 4 104.08 - 138.77: 1 138.77 - 173.47: 2 Dihedral angle restraints: 3998 sinusoidal: 1586 harmonic: 2412 Sorted by residual: dihedral pdb=" C4' GTP B 501 " pdb=" C5' GTP B 501 " pdb=" O5' GTP B 501 " pdb=" PA GTP B 501 " ideal model delta sinusoidal sigma weight residual 260.87 87.41 173.47 1 2.00e+01 2.50e-03 4.78e+01 dihedral pdb=" C8 GTP B 501 " pdb=" C1' GTP B 501 " pdb=" N9 GTP B 501 " pdb=" O4' GTP B 501 " ideal model delta sinusoidal sigma weight residual 104.59 -100.43 -154.97 1 2.00e+01 2.50e-03 4.57e+01 dihedral pdb=" O3B GTP B 501 " pdb=" O3A GTP B 501 " pdb=" PB GTP B 501 " pdb=" PA GTP B 501 " ideal model delta sinusoidal sigma weight residual -68.92 -179.70 110.78 1 2.00e+01 2.50e-03 3.25e+01 ... (remaining 3995 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 567 0.059 - 0.118: 318 0.118 - 0.177: 107 0.177 - 0.236: 22 0.236 - 0.294: 3 Chirality restraints: 1017 Sorted by residual: chirality pdb=" C2' GTP B 501 " pdb=" C1' GTP B 501 " pdb=" C3' GTP B 501 " pdb=" O2' GTP B 501 " both_signs ideal model delta sigma weight residual False -2.47 -2.77 0.29 2.00e-01 2.50e+01 2.17e+00 chirality pdb=" CA ASN A 187 " pdb=" N ASN A 187 " pdb=" C ASN A 187 " pdb=" CB ASN A 187 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.60e+00 chirality pdb=" CA MET A 113 " pdb=" N MET A 113 " pdb=" C MET A 113 " pdb=" CB MET A 113 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.45e+00 ... (remaining 1014 not shown) Planarity restraints: 1169 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE B 405 " -0.036 2.00e-02 2.50e+03 2.49e-02 1.09e+01 pdb=" CG PHE B 405 " 0.052 2.00e-02 2.50e+03 pdb=" CD1 PHE B 405 " 0.002 2.00e-02 2.50e+03 pdb=" CD2 PHE B 405 " 0.006 2.00e-02 2.50e+03 pdb=" CE1 PHE B 405 " -0.005 2.00e-02 2.50e+03 pdb=" CE2 PHE B 405 " -0.007 2.00e-02 2.50e+03 pdb=" CZ PHE B 405 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS B 29 " 0.033 2.00e-02 2.50e+03 2.62e-02 1.03e+01 pdb=" CG HIS B 29 " -0.050 2.00e-02 2.50e+03 pdb=" ND1 HIS B 29 " -0.004 2.00e-02 2.50e+03 pdb=" CD2 HIS B 29 " -0.008 2.00e-02 2.50e+03 pdb=" CE1 HIS B 29 " 0.008 2.00e-02 2.50e+03 pdb=" NE2 HIS B 29 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG B 335 " 0.016 2.00e-02 2.50e+03 3.20e-02 1.02e+01 pdb=" C ARG B 335 " -0.055 2.00e-02 2.50e+03 pdb=" O ARG B 335 " 0.021 2.00e-02 2.50e+03 pdb=" N ILE B 336 " 0.018 2.00e-02 2.50e+03 ... (remaining 1166 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 2049 2.80 - 3.33: 6540 3.33 - 3.85: 11164 3.85 - 4.38: 14022 4.38 - 4.90: 21673 Nonbonded interactions: 55448 Sorted by model distance: nonbonded pdb=" CD1 ILE A 73 " pdb=" CE2 PHE A 77 " model vdw 2.278 3.760 nonbonded pdb=" O GLU B 180 " pdb=" N ASN B 183 " model vdw 2.284 3.120 nonbonded pdb=" O GLU B 180 " pdb=" N TYR B 182 " model vdw 2.287 3.120 nonbonded pdb=" N ASP A 292 " pdb=" OD1 ASP A 292 " model vdw 2.322 3.120 nonbonded pdb=" O ASN A 15 " pdb=" CZ PHE A 77 " model vdw 2.387 3.340 ... (remaining 55443 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: 0.260 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.080 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.580 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 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:1.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5574 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 : 0.018 0.160 6700 Z= 1.017 Angle : 1.564 12.804 9076 Z= 0.986 Chirality : 0.077 0.294 1017 Planarity : 0.008 0.041 1169 Dihedral : 11.743 173.466 2452 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.11 (0.27), residues: 841 helix: -0.31 (0.25), residues: 340 sheet: 1.75 (0.45), residues: 120 loop : -0.32 (0.31), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 409 TYR 0.025 0.005 TYR A 191 PHE 0.052 0.006 PHE B 405 TRP 0.022 0.006 TRP A 338 HIS 0.013 0.003 HIS B 29 Details of bonding type rmsd covalent geometry : bond 0.01835 ( 6700) covalent geometry : angle 1.56426 ( 9076) hydrogen bonds : bond 0.18516 ( 322) hydrogen bonds : angle 7.46819 ( 924) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1682 Ramachandran restraints generated. 841 Oldfield, 0 Emsley, 841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1682 Ramachandran restraints generated. 841 Oldfield, 0 Emsley, 841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 276 time to evaluate : 0.249 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 113 MET cc_start: 0.8079 (mmm) cc_final: 0.7787 (mpp) REVERT: A 220 ASP cc_start: 0.6986 (m-30) cc_final: 0.6411 (t0) REVERT: A 305 ARG cc_start: 0.7759 (mmt-90) cc_final: 0.6293 (mtp85) REVERT: A 372 PHE cc_start: 0.6050 (m-80) cc_final: 0.5712 (m-10) REVERT: B 121 LYS cc_start: 0.8653 (mttt) cc_final: 0.8276 (mtmt) outliers start: 0 outliers final: 0 residues processed: 276 average time/residue: 0.0919 time to fit residues: 32.5286 Evaluate side-chains 145 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 145 time to evaluate : 0.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 49 optimal weight: 0.7980 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 3.9990 chunk 65 optimal weight: 0.8980 chunk 62 optimal weight: 0.9990 chunk 51 optimal weight: 0.7980 chunk 38 optimal weight: 5.9990 chunk 61 optimal weight: 1.9990 chunk 45 optimal weight: 0.7980 chunk 74 optimal weight: 0.3980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 9 GLN A 180 ASN ** A 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 332 GLN B 24 GLN B 230 GLN B 255 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4593 r_free = 0.4593 target = 0.216823 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4348 r_free = 0.4348 target = 0.185391 restraints weight = 7560.190| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.4400 r_free = 0.4400 target = 0.191653 restraints weight = 4221.696| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4433 r_free = 0.4433 target = 0.195924 restraints weight = 2781.486| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.4457 r_free = 0.4457 target = 0.198922 restraints weight = 2053.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4471 r_free = 0.4471 target = 0.200722 restraints weight = 1638.990| |-----------------------------------------------------------------------------| r_work (final): 0.4472 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5972 moved from start: 0.4117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 6700 Z= 0.187 Angle : 0.761 12.754 9076 Z= 0.402 Chirality : 0.049 0.210 1017 Planarity : 0.005 0.062 1169 Dihedral : 11.071 152.100 919 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 13.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 3.42 % Allowed : 10.26 % Favored : 86.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.04 (0.26), residues: 841 helix: 0.31 (0.24), residues: 353 sheet: 1.58 (0.45), residues: 118 loop : -0.83 (0.30), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 335 TYR 0.029 0.002 TYR A 179 PHE 0.022 0.003 PHE B 405 TRP 0.012 0.001 TRP B 394 HIS 0.003 0.001 HIS B 204 Details of bonding type rmsd covalent geometry : bond 0.00398 ( 6700) covalent geometry : angle 0.76139 ( 9076) hydrogen bonds : bond 0.06311 ( 322) hydrogen bonds : angle 5.37308 ( 924) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1682 Ramachandran restraints generated. 841 Oldfield, 0 Emsley, 841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1682 Ramachandran restraints generated. 841 Oldfield, 0 Emsley, 841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 154 time to evaluate : 0.185 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 220 ASP cc_start: 0.6715 (m-30) cc_final: 0.5998 (t0) REVERT: A 380 ASP cc_start: 0.7003 (t0) cc_final: 0.6788 (t0) REVERT: A 386 LYS cc_start: 0.7980 (OUTLIER) cc_final: 0.7194 (pttp) REVERT: B 3 ARG cc_start: 0.7628 (mtm-85) cc_final: 0.7196 (ptp90) REVERT: B 121 LYS cc_start: 0.8102 (mttt) cc_final: 0.7729 (mtmt) REVERT: B 249 MET cc_start: 0.5401 (mtm) cc_final: 0.5164 (mtm) outliers start: 24 outliers final: 15 residues processed: 169 average time/residue: 0.0739 time to fit residues: 16.7800 Evaluate side-chains 142 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 126 time to evaluate : 0.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 ILE Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 133 HIS Chi-restraints excluded: chain A residue 143 PHE Chi-restraints excluded: chain A residue 165 ILE Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 375 ILE Chi-restraints excluded: chain A residue 386 LYS Chi-restraints excluded: chain B residue 128 SER Chi-restraints excluded: chain B residue 163 LEU Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 285 THR Chi-restraints excluded: chain B residue 329 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 82 optimal weight: 6.9990 chunk 56 optimal weight: 5.9990 chunk 68 optimal weight: 1.9990 chunk 14 optimal weight: 0.8980 chunk 12 optimal weight: 3.9990 chunk 19 optimal weight: 8.9990 chunk 21 optimal weight: 9.9990 chunk 43 optimal weight: 3.9990 chunk 53 optimal weight: 0.8980 chunk 27 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 187 ASN B 77 ASN B 255 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4518 r_free = 0.4518 target = 0.210757 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4241 r_free = 0.4241 target = 0.177145 restraints weight = 7567.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.4292 r_free = 0.4292 target = 0.182970 restraints weight = 4480.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4327 r_free = 0.4327 target = 0.187207 restraints weight = 3078.219| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.4352 r_free = 0.4352 target = 0.190221 restraints weight = 2336.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4363 r_free = 0.4363 target = 0.191653 restraints weight = 1894.900| |-----------------------------------------------------------------------------| r_work (final): 0.4311 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6232 moved from start: 0.5007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 6700 Z= 0.202 Angle : 0.721 10.242 9076 Z= 0.377 Chirality : 0.048 0.183 1017 Planarity : 0.005 0.053 1169 Dihedral : 10.791 157.676 919 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 13.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 3.70 % Allowed : 13.11 % Favored : 83.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.33 (0.27), residues: 841 helix: 0.28 (0.25), residues: 361 sheet: 1.07 (0.46), residues: 120 loop : -1.15 (0.31), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 237 TYR 0.030 0.002 TYR B 348 PHE 0.027 0.003 PHE A 392 TRP 0.009 0.001 TRP A 338 HIS 0.004 0.001 HIS A 29 Details of bonding type rmsd covalent geometry : bond 0.00457 ( 6700) covalent geometry : angle 0.72092 ( 9076) hydrogen bonds : bond 0.05794 ( 322) hydrogen bonds : angle 5.23376 ( 924) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1682 Ramachandran restraints generated. 841 Oldfield, 0 Emsley, 841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1682 Ramachandran restraints generated. 841 Oldfield, 0 Emsley, 841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 137 time to evaluate : 0.219 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 180 ASN cc_start: 0.7182 (m-40) cc_final: 0.6905 (m110) REVERT: A 183 MET cc_start: 0.7753 (tpp) cc_final: 0.7531 (mmm) REVERT: A 204 PHE cc_start: 0.7723 (t80) cc_final: 0.7421 (t80) REVERT: A 386 LYS cc_start: 0.8129 (OUTLIER) cc_final: 0.7305 (pttp) REVERT: A 397 PHE cc_start: 0.5143 (m-80) cc_final: 0.4621 (m-80) REVERT: B 100 PHE cc_start: 0.5407 (t80) cc_final: 0.5183 (t80) REVERT: B 121 LYS cc_start: 0.8200 (mttt) cc_final: 0.7926 (mttp) REVERT: B 266 MET cc_start: 0.6137 (mtp) cc_final: 0.5890 (mtm) REVERT: B 379 LEU cc_start: 0.6880 (OUTLIER) cc_final: 0.6499 (mt) outliers start: 26 outliers final: 19 residues processed: 156 average time/residue: 0.0654 time to fit residues: 14.3832 Evaluate side-chains 144 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 123 time to evaluate : 0.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 ILE Chi-restraints excluded: chain A residue 52 ILE Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 133 HIS Chi-restraints excluded: chain A residue 143 PHE Chi-restraints excluded: chain A residue 164 SER Chi-restraints excluded: chain A residue 165 ILE Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 375 ILE Chi-restraints excluded: chain A residue 386 LYS Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain B residue 128 SER Chi-restraints excluded: chain B residue 163 LEU Chi-restraints excluded: chain B residue 165 SER Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 234 ASP Chi-restraints excluded: chain B residue 285 THR Chi-restraints excluded: chain B residue 368 HIS Chi-restraints excluded: chain B residue 379 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 5 optimal weight: 4.9990 chunk 19 optimal weight: 3.9990 chunk 46 optimal weight: 2.9990 chunk 43 optimal weight: 3.9990 chunk 24 optimal weight: 4.9990 chunk 3 optimal weight: 0.0470 chunk 26 optimal weight: 5.9990 chunk 34 optimal weight: 2.9990 chunk 18 optimal weight: 0.5980 chunk 13 optimal weight: 9.9990 chunk 45 optimal weight: 0.0970 overall best weight: 1.3480 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 136 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4508 r_free = 0.4508 target = 0.209580 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4240 r_free = 0.4240 target = 0.176484 restraints weight = 7531.330| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.4290 r_free = 0.4290 target = 0.182342 restraints weight = 4415.270| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.4324 r_free = 0.4324 target = 0.186520 restraints weight = 3011.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.4345 r_free = 0.4345 target = 0.189384 restraints weight = 2267.175| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4359 r_free = 0.4359 target = 0.191269 restraints weight = 1838.111| |-----------------------------------------------------------------------------| r_work (final): 0.4314 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6241 moved from start: 0.5545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 6700 Z= 0.172 Angle : 0.686 9.700 9076 Z= 0.355 Chirality : 0.046 0.200 1017 Planarity : 0.004 0.046 1169 Dihedral : 10.706 160.822 919 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 13.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 3.56 % Allowed : 14.96 % Favored : 81.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.45 (0.28), residues: 841 helix: 0.36 (0.26), residues: 360 sheet: 0.84 (0.47), residues: 120 loop : -1.35 (0.31), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 237 TYR 0.022 0.002 TYR A 179 PHE 0.020 0.002 PHE A 379 TRP 0.010 0.001 TRP A 22 HIS 0.003 0.001 HIS A 260 Details of bonding type rmsd covalent geometry : bond 0.00388 ( 6700) covalent geometry : angle 0.68560 ( 9076) hydrogen bonds : bond 0.05264 ( 322) hydrogen bonds : angle 5.09349 ( 924) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1682 Ramachandran restraints generated. 841 Oldfield, 0 Emsley, 841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1682 Ramachandran restraints generated. 841 Oldfield, 0 Emsley, 841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 132 time to evaluate : 0.156 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 180 ASN cc_start: 0.7161 (m-40) cc_final: 0.6874 (m110) REVERT: A 204 PHE cc_start: 0.7572 (t80) cc_final: 0.6793 (t80) REVERT: A 220 ASP cc_start: 0.6723 (m-30) cc_final: 0.5982 (t0) REVERT: A 391 TRP cc_start: 0.6595 (m100) cc_final: 0.6248 (m-10) REVERT: A 397 PHE cc_start: 0.5266 (m-80) cc_final: 0.4611 (m-80) REVERT: A 418 LYS cc_start: 0.8210 (tppt) cc_final: 0.7903 (tppt) REVERT: B 121 LYS cc_start: 0.8216 (mttt) cc_final: 0.7911 (mttp) REVERT: B 249 MET cc_start: 0.4901 (mtm) cc_final: 0.4299 (mtm) REVERT: B 266 MET cc_start: 0.6046 (mtp) cc_final: 0.5678 (mtm) outliers start: 25 outliers final: 20 residues processed: 151 average time/residue: 0.0671 time to fit residues: 14.0411 Evaluate side-chains 139 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 119 time to evaluate : 0.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 ILE Chi-restraints excluded: chain A residue 52 ILE Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 143 PHE Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 165 ILE Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 375 ILE Chi-restraints excluded: chain A residue 386 LYS Chi-restraints excluded: chain B residue 128 SER Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 163 LEU Chi-restraints excluded: chain B residue 165 SER Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 287 ASN Chi-restraints excluded: chain B residue 288 LEU Chi-restraints excluded: chain B residue 368 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 16 optimal weight: 0.9990 chunk 80 optimal weight: 0.9980 chunk 37 optimal weight: 0.9980 chunk 0 optimal weight: 8.9990 chunk 47 optimal weight: 0.0270 chunk 38 optimal weight: 5.9990 chunk 76 optimal weight: 8.9990 chunk 81 optimal weight: 0.8980 chunk 77 optimal weight: 9.9990 chunk 58 optimal weight: 0.0270 chunk 23 optimal weight: 1.9990 overall best weight: 0.5896 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 183 ASN B 263 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4541 r_free = 0.4541 target = 0.214438 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4277 r_free = 0.4277 target = 0.180893 restraints weight = 7631.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4326 r_free = 0.4326 target = 0.186856 restraints weight = 4458.524| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4359 r_free = 0.4359 target = 0.191105 restraints weight = 3029.471| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4378 r_free = 0.4378 target = 0.193824 restraints weight = 2275.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.4397 r_free = 0.4397 target = 0.196147 restraints weight = 1860.186| |-----------------------------------------------------------------------------| r_work (final): 0.4350 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6189 moved from start: 0.5882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 6700 Z= 0.135 Angle : 0.633 8.659 9076 Z= 0.323 Chirality : 0.044 0.213 1017 Planarity : 0.004 0.042 1169 Dihedral : 10.523 162.113 919 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 11.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 3.28 % Allowed : 15.53 % Favored : 81.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.29 (0.28), residues: 841 helix: 0.63 (0.26), residues: 361 sheet: 0.79 (0.48), residues: 120 loop : -1.38 (0.31), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 237 TYR 0.017 0.001 TYR A 179 PHE 0.022 0.002 PHE A 97 TRP 0.011 0.001 TRP A 22 HIS 0.003 0.001 HIS B 368 Details of bonding type rmsd covalent geometry : bond 0.00295 ( 6700) covalent geometry : angle 0.63301 ( 9076) hydrogen bonds : bond 0.04788 ( 322) hydrogen bonds : angle 4.92417 ( 924) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1682 Ramachandran restraints generated. 841 Oldfield, 0 Emsley, 841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1682 Ramachandran restraints generated. 841 Oldfield, 0 Emsley, 841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 128 time to evaluate : 0.254 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 180 ASN cc_start: 0.7116 (m-40) cc_final: 0.6875 (m-40) REVERT: A 204 PHE cc_start: 0.7537 (t80) cc_final: 0.6728 (t80) REVERT: A 220 ASP cc_start: 0.6513 (m-30) cc_final: 0.5882 (t0) REVERT: A 391 TRP cc_start: 0.6444 (m100) cc_final: 0.6200 (m-10) REVERT: A 418 LYS cc_start: 0.8189 (tppt) cc_final: 0.7960 (tppt) REVERT: B 121 LYS cc_start: 0.8146 (mttt) cc_final: 0.7824 (mttp) REVERT: B 249 MET cc_start: 0.4960 (mtm) cc_final: 0.4471 (mtm) REVERT: B 266 MET cc_start: 0.6450 (mtp) cc_final: 0.6129 (mtm) REVERT: B 272 MET cc_start: 0.4814 (ptt) cc_final: 0.4277 (mtm) REVERT: B 420 LYS cc_start: 0.8126 (tppt) cc_final: 0.7897 (tppt) outliers start: 23 outliers final: 18 residues processed: 145 average time/residue: 0.0740 time to fit residues: 14.9764 Evaluate side-chains 140 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 122 time to evaluate : 0.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 ILE Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 133 HIS Chi-restraints excluded: chain A residue 143 PHE Chi-restraints excluded: chain A residue 165 ILE Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 355 SER Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 375 ILE Chi-restraints excluded: chain A residue 386 LYS Chi-restraints excluded: chain B residue 128 SER Chi-restraints excluded: chain B residue 163 LEU Chi-restraints excluded: chain B residue 165 SER Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 287 ASN Chi-restraints excluded: chain B residue 368 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 30 optimal weight: 5.9990 chunk 37 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 55 optimal weight: 5.9990 chunk 49 optimal weight: 2.9990 chunk 34 optimal weight: 0.9980 chunk 76 optimal weight: 0.0050 chunk 52 optimal weight: 0.3980 chunk 53 optimal weight: 0.9980 chunk 58 optimal weight: 10.0000 chunk 48 optimal weight: 0.8980 overall best weight: 0.6594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 227 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 = 0.4546 r_free = 0.4546 target = 0.215085 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4280 r_free = 0.4280 target = 0.181197 restraints weight = 7679.602| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4330 r_free = 0.4330 target = 0.187179 restraints weight = 4526.809| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.4363 r_free = 0.4363 target = 0.191493 restraints weight = 3104.325| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.4382 r_free = 0.4382 target = 0.194147 restraints weight = 2339.837| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 47)----------------| | r_work = 0.4401 r_free = 0.4401 target = 0.196553 restraints weight = 1922.175| |-----------------------------------------------------------------------------| r_work (final): 0.4353 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6199 moved from start: 0.6100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6700 Z= 0.132 Angle : 0.632 7.544 9076 Z= 0.323 Chirality : 0.045 0.221 1017 Planarity : 0.004 0.042 1169 Dihedral : 10.377 161.975 919 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 10.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 3.85 % Allowed : 16.24 % Favored : 79.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.28 (0.28), residues: 841 helix: 0.68 (0.26), residues: 367 sheet: 0.64 (0.48), residues: 120 loop : -1.40 (0.31), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 237 TYR 0.020 0.001 TYR A 179 PHE 0.024 0.002 PHE A 379 TRP 0.020 0.001 TRP A 338 HIS 0.004 0.001 HIS B 368 Details of bonding type rmsd covalent geometry : bond 0.00285 ( 6700) covalent geometry : angle 0.63192 ( 9076) hydrogen bonds : bond 0.04644 ( 322) hydrogen bonds : angle 4.79377 ( 924) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1682 Ramachandran restraints generated. 841 Oldfield, 0 Emsley, 841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1682 Ramachandran restraints generated. 841 Oldfield, 0 Emsley, 841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 125 time to evaluate : 0.264 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 131 LEU cc_start: 0.8212 (OUTLIER) cc_final: 0.7935 (mp) REVERT: A 180 ASN cc_start: 0.7115 (m-40) cc_final: 0.6826 (m-40) REVERT: A 204 PHE cc_start: 0.7561 (t80) cc_final: 0.6806 (t80) REVERT: A 220 ASP cc_start: 0.6497 (m-30) cc_final: 0.5949 (t0) REVERT: A 391 TRP cc_start: 0.6468 (m100) cc_final: 0.6262 (m-10) REVERT: A 397 PHE cc_start: 0.4836 (m-80) cc_final: 0.4576 (m-80) REVERT: B 43 LYS cc_start: 0.6431 (tptt) cc_final: 0.6151 (tptt) REVERT: B 121 LYS cc_start: 0.8155 (mttt) cc_final: 0.7822 (mtmt) REVERT: B 268 SER cc_start: 0.6403 (t) cc_final: 0.5939 (p) outliers start: 27 outliers final: 23 residues processed: 143 average time/residue: 0.0776 time to fit residues: 15.3629 Evaluate side-chains 144 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 120 time to evaluate : 0.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 ILE Chi-restraints excluded: chain A residue 52 ILE Chi-restraints excluded: chain A residue 113 MET Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 143 PHE Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 165 ILE Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 224 ILE Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 355 SER Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 375 ILE Chi-restraints excluded: chain A residue 386 LYS Chi-restraints excluded: chain B residue 128 SER Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 163 LEU Chi-restraints excluded: chain B residue 165 SER Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 287 ASN Chi-restraints excluded: chain B residue 288 LEU Chi-restraints excluded: chain B residue 368 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 39 optimal weight: 0.0470 chunk 79 optimal weight: 0.9990 chunk 17 optimal weight: 0.0470 chunk 74 optimal weight: 7.9990 chunk 62 optimal weight: 0.3980 chunk 4 optimal weight: 0.0370 chunk 2 optimal weight: 3.9990 chunk 72 optimal weight: 5.9990 chunk 46 optimal weight: 0.5980 chunk 30 optimal weight: 6.9990 chunk 58 optimal weight: 0.5980 overall best weight: 0.2254 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 104 HIS B 130 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4601 r_free = 0.4601 target = 0.217038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4358 r_free = 0.4358 target = 0.185355 restraints weight = 7520.466| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.4404 r_free = 0.4404 target = 0.191283 restraints weight = 4180.116| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4435 r_free = 0.4435 target = 0.195381 restraints weight = 2786.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.4460 r_free = 0.4460 target = 0.198324 restraints weight = 2082.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4473 r_free = 0.4473 target = 0.200155 restraints weight = 1684.034| |-----------------------------------------------------------------------------| r_work (final): 0.4521 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6126 moved from start: 0.6321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6700 Z= 0.122 Angle : 0.634 7.808 9076 Z= 0.323 Chirality : 0.044 0.240 1017 Planarity : 0.004 0.059 1169 Dihedral : 10.285 163.129 919 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 10.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 3.28 % Allowed : 18.09 % Favored : 78.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.14 (0.28), residues: 841 helix: 0.95 (0.27), residues: 361 sheet: 0.55 (0.49), residues: 120 loop : -1.41 (0.31), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 314 TYR 0.022 0.002 TYR A 179 PHE 0.031 0.002 PHE B 100 TRP 0.022 0.001 TRP A 338 HIS 0.003 0.001 HIS A 260 Details of bonding type rmsd covalent geometry : bond 0.00257 ( 6700) covalent geometry : angle 0.63435 ( 9076) hydrogen bonds : bond 0.04357 ( 322) hydrogen bonds : angle 4.75994 ( 924) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1682 Ramachandran restraints generated. 841 Oldfield, 0 Emsley, 841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1682 Ramachandran restraints generated. 841 Oldfield, 0 Emsley, 841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 132 time to evaluate : 0.294 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 123 THR cc_start: 0.5834 (OUTLIER) cc_final: 0.5437 (m) REVERT: A 131 LEU cc_start: 0.8189 (OUTLIER) cc_final: 0.7840 (mp) REVERT: A 204 PHE cc_start: 0.7527 (t80) cc_final: 0.6808 (t80) REVERT: A 386 LYS cc_start: 0.7586 (OUTLIER) cc_final: 0.7016 (pttm) REVERT: A 421 GLU cc_start: 0.5954 (tp30) cc_final: 0.5738 (tp30) REVERT: B 121 LYS cc_start: 0.8081 (mttt) cc_final: 0.7685 (mtmt) REVERT: B 130 GLN cc_start: 0.6048 (OUTLIER) cc_final: 0.5793 (tt0) REVERT: B 246 ASN cc_start: 0.7303 (p0) cc_final: 0.6381 (p0) REVERT: B 268 SER cc_start: 0.6268 (t) cc_final: 0.5938 (p) REVERT: B 420 LYS cc_start: 0.8064 (tppt) cc_final: 0.7813 (tppt) outliers start: 23 outliers final: 15 residues processed: 147 average time/residue: 0.0779 time to fit residues: 15.7901 Evaluate side-chains 137 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 118 time to evaluate : 0.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 ILE Chi-restraints excluded: chain A residue 52 ILE Chi-restraints excluded: chain A residue 113 MET Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 143 PHE Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 165 ILE Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 375 ILE Chi-restraints excluded: chain A residue 386 LYS Chi-restraints excluded: chain B residue 128 SER Chi-restraints excluded: chain B residue 130 GLN Chi-restraints excluded: chain B residue 163 LEU Chi-restraints excluded: chain B residue 165 SER Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 368 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 21 optimal weight: 6.9990 chunk 2 optimal weight: 4.9990 chunk 20 optimal weight: 0.9990 chunk 18 optimal weight: 0.6980 chunk 26 optimal weight: 5.9990 chunk 67 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 19 optimal weight: 0.5980 chunk 32 optimal weight: 0.9990 chunk 46 optimal weight: 0.1980 chunk 15 optimal weight: 0.9990 overall best weight: 0.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 130 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 = 0.4575 r_free = 0.4575 target = 0.213800 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4329 r_free = 0.4329 target = 0.182054 restraints weight = 7602.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4378 r_free = 0.4378 target = 0.187960 restraints weight = 4207.004| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.4411 r_free = 0.4411 target = 0.192098 restraints weight = 2792.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.4430 r_free = 0.4430 target = 0.194627 restraints weight = 2085.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.4446 r_free = 0.4446 target = 0.196745 restraints weight = 1709.421| |-----------------------------------------------------------------------------| r_work (final): 0.4494 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6171 moved from start: 0.6517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6700 Z= 0.136 Angle : 0.664 9.528 9076 Z= 0.336 Chirality : 0.045 0.268 1017 Planarity : 0.004 0.043 1169 Dihedral : 10.206 162.869 919 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 11.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 3.42 % Allowed : 18.23 % Favored : 78.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.29 (0.28), residues: 841 helix: 0.87 (0.26), residues: 363 sheet: 0.45 (0.49), residues: 120 loop : -1.54 (0.31), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 237 TYR 0.027 0.002 TYR B 280 PHE 0.027 0.002 PHE A 379 TRP 0.021 0.001 TRP A 338 HIS 0.003 0.001 HIS B 368 Details of bonding type rmsd covalent geometry : bond 0.00298 ( 6700) covalent geometry : angle 0.66397 ( 9076) hydrogen bonds : bond 0.04510 ( 322) hydrogen bonds : angle 4.74539 ( 924) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1682 Ramachandran restraints generated. 841 Oldfield, 0 Emsley, 841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1682 Ramachandran restraints generated. 841 Oldfield, 0 Emsley, 841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 130 time to evaluate : 0.261 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 123 THR cc_start: 0.5989 (OUTLIER) cc_final: 0.5664 (m) REVERT: A 131 LEU cc_start: 0.8192 (OUTLIER) cc_final: 0.7838 (mp) REVERT: A 204 PHE cc_start: 0.7645 (t80) cc_final: 0.6856 (t80) REVERT: A 386 LYS cc_start: 0.7584 (OUTLIER) cc_final: 0.7046 (pttm) REVERT: B 121 LYS cc_start: 0.8079 (mttt) cc_final: 0.7769 (mtmt) REVERT: B 246 ASN cc_start: 0.7324 (p0) cc_final: 0.6449 (p0) REVERT: B 268 SER cc_start: 0.6423 (t) cc_final: 0.5926 (p) outliers start: 24 outliers final: 17 residues processed: 148 average time/residue: 0.0728 time to fit residues: 15.1103 Evaluate side-chains 141 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 121 time to evaluate : 0.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 ILE Chi-restraints excluded: chain A residue 52 ILE Chi-restraints excluded: chain A residue 113 MET Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 143 PHE Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 165 ILE Chi-restraints excluded: chain A residue 224 ILE Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 355 SER Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 386 LYS Chi-restraints excluded: chain B residue 163 LEU Chi-restraints excluded: chain B residue 165 SER Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain B residue 287 ASN Chi-restraints excluded: chain B residue 368 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 15 optimal weight: 0.9990 chunk 60 optimal weight: 3.9990 chunk 43 optimal weight: 4.9990 chunk 6 optimal weight: 0.3980 chunk 57 optimal weight: 1.9990 chunk 45 optimal weight: 10.0000 chunk 41 optimal weight: 0.8980 chunk 76 optimal weight: 1.9990 chunk 14 optimal weight: 0.6980 chunk 66 optimal weight: 0.5980 chunk 11 optimal weight: 2.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 ASN ** B 130 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 = 0.4580 r_free = 0.4580 target = 0.214423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4334 r_free = 0.4334 target = 0.183828 restraints weight = 7945.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.4380 r_free = 0.4380 target = 0.189219 restraints weight = 4669.050| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4411 r_free = 0.4411 target = 0.192976 restraints weight = 3220.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4428 r_free = 0.4428 target = 0.195296 restraints weight = 2471.893| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.4445 r_free = 0.4445 target = 0.197278 restraints weight = 2062.343| |-----------------------------------------------------------------------------| r_work (final): 0.4447 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6228 moved from start: 0.6693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6700 Z= 0.141 Angle : 0.684 10.866 9076 Z= 0.351 Chirality : 0.046 0.290 1017 Planarity : 0.004 0.044 1169 Dihedral : 10.174 162.691 919 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 12.10 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.62 % Favored : 97.27 % Rotamer: Outliers : 3.56 % Allowed : 18.09 % Favored : 78.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.38 (0.28), residues: 841 helix: 0.73 (0.26), residues: 368 sheet: 0.32 (0.48), residues: 124 loop : -1.52 (0.31), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 237 TYR 0.020 0.002 TYR A 179 PHE 0.030 0.002 PHE A 379 TRP 0.022 0.002 TRP A 338 HIS 0.003 0.001 HIS B 368 Details of bonding type rmsd covalent geometry : bond 0.00309 ( 6700) covalent geometry : angle 0.68448 ( 9076) hydrogen bonds : bond 0.04532 ( 322) hydrogen bonds : angle 4.75523 ( 924) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1682 Ramachandran restraints generated. 841 Oldfield, 0 Emsley, 841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1682 Ramachandran restraints generated. 841 Oldfield, 0 Emsley, 841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 125 time to evaluate : 0.251 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 97 PHE cc_start: 0.4914 (t80) cc_final: 0.4706 (t80) REVERT: A 131 LEU cc_start: 0.8164 (OUTLIER) cc_final: 0.7764 (mp) REVERT: A 220 ASP cc_start: 0.6341 (m-30) cc_final: 0.6025 (t0) REVERT: B 268 SER cc_start: 0.6480 (t) cc_final: 0.6068 (p) REVERT: B 420 LYS cc_start: 0.8079 (tppt) cc_final: 0.7857 (tppt) outliers start: 25 outliers final: 20 residues processed: 145 average time/residue: 0.0716 time to fit residues: 14.4721 Evaluate side-chains 141 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 120 time to evaluate : 0.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 ILE Chi-restraints excluded: chain A residue 52 ILE Chi-restraints excluded: chain A residue 113 MET Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 143 PHE Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 165 ILE Chi-restraints excluded: chain A residue 224 ILE Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 355 SER Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 386 LYS Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 163 LEU Chi-restraints excluded: chain B residue 165 SER Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain B residue 287 ASN Chi-restraints excluded: chain B residue 288 LEU Chi-restraints excluded: chain B residue 368 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 51 optimal weight: 5.9990 chunk 67 optimal weight: 3.9990 chunk 30 optimal weight: 0.9980 chunk 55 optimal weight: 1.9990 chunk 58 optimal weight: 0.9990 chunk 57 optimal weight: 0.9990 chunk 28 optimal weight: 0.9980 chunk 69 optimal weight: 3.9990 chunk 6 optimal weight: 4.9990 chunk 18 optimal weight: 0.7980 chunk 11 optimal weight: 3.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 ASN ** A 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 215 ASN A 227 GLN ** B 130 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 = 0.4558 r_free = 0.4558 target = 0.211964 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4305 r_free = 0.4305 target = 0.180482 restraints weight = 7840.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4353 r_free = 0.4353 target = 0.186140 restraints weight = 4452.684| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.4385 r_free = 0.4385 target = 0.190014 restraints weight = 3027.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4403 r_free = 0.4403 target = 0.192401 restraints weight = 2287.438| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.4421 r_free = 0.4421 target = 0.194461 restraints weight = 1895.108| |-----------------------------------------------------------------------------| r_work (final): 0.4424 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6190 moved from start: 0.6911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 6700 Z= 0.156 Angle : 0.725 12.592 9076 Z= 0.371 Chirality : 0.047 0.322 1017 Planarity : 0.005 0.105 1169 Dihedral : 10.184 162.065 919 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 12.63 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.85 % Favored : 97.03 % Rotamer: Outliers : 3.85 % Allowed : 18.66 % Favored : 77.49 % Cbeta Deviations : 0.13 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.41 (0.28), residues: 841 helix: 0.70 (0.26), residues: 367 sheet: 0.34 (0.48), residues: 124 loop : -1.55 (0.31), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 314 TYR 0.018 0.002 TYR B 104 PHE 0.030 0.002 PHE A 379 TRP 0.023 0.002 TRP A 338 HIS 0.003 0.001 HIS B 368 Details of bonding type rmsd covalent geometry : bond 0.00348 ( 6700) covalent geometry : angle 0.72520 ( 9076) hydrogen bonds : bond 0.04623 ( 322) hydrogen bonds : angle 4.83668 ( 924) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1682 Ramachandran restraints generated. 841 Oldfield, 0 Emsley, 841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1682 Ramachandran restraints generated. 841 Oldfield, 0 Emsley, 841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 127 time to evaluate : 0.255 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 131 LEU cc_start: 0.8196 (OUTLIER) cc_final: 0.7773 (mp) REVERT: A 180 ASN cc_start: 0.6829 (OUTLIER) cc_final: 0.6472 (m110) REVERT: A 183 MET cc_start: 0.7037 (mmm) cc_final: 0.6634 (mmm) REVERT: A 220 ASP cc_start: 0.6523 (m-30) cc_final: 0.6030 (t0) REVERT: A 259 LEU cc_start: 0.7511 (OUTLIER) cc_final: 0.7256 (tp) REVERT: B 246 ASN cc_start: 0.7422 (p0) cc_final: 0.6700 (p0) REVERT: B 268 SER cc_start: 0.6360 (t) cc_final: 0.5910 (p) outliers start: 27 outliers final: 21 residues processed: 146 average time/residue: 0.0720 time to fit residues: 14.6847 Evaluate side-chains 147 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 123 time to evaluate : 0.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 ILE Chi-restraints excluded: chain A residue 52 ILE Chi-restraints excluded: chain A residue 113 MET Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 133 HIS Chi-restraints excluded: chain A residue 143 PHE Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 165 ILE Chi-restraints excluded: chain A residue 180 ASN Chi-restraints excluded: chain A residue 187 ASN Chi-restraints excluded: chain A residue 224 ILE Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 355 SER Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 386 LYS Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 163 LEU Chi-restraints excluded: chain B residue 165 SER Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain B residue 287 ASN Chi-restraints excluded: chain B residue 288 LEU Chi-restraints excluded: chain B residue 368 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 80 optimal weight: 0.6980 chunk 64 optimal weight: 1.9990 chunk 39 optimal weight: 8.9990 chunk 27 optimal weight: 0.9990 chunk 34 optimal weight: 0.6980 chunk 68 optimal weight: 0.8980 chunk 63 optimal weight: 6.9990 chunk 38 optimal weight: 0.7980 chunk 3 optimal weight: 0.0010 chunk 47 optimal weight: 0.0670 chunk 15 optimal weight: 0.9980 overall best weight: 0.4524 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 215 ASN ** B 130 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 = 0.4581 r_free = 0.4581 target = 0.214128 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4343 r_free = 0.4343 target = 0.184228 restraints weight = 7704.049| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4389 r_free = 0.4389 target = 0.189735 restraints weight = 4423.522| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4421 r_free = 0.4421 target = 0.193519 restraints weight = 2975.057| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4439 r_free = 0.4439 target = 0.196002 restraints weight = 2240.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 49)----------------| | r_work = 0.4454 r_free = 0.4454 target = 0.197843 restraints weight = 1832.337| |-----------------------------------------------------------------------------| r_work (final): 0.4456 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6172 moved from start: 0.7066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6700 Z= 0.135 Angle : 0.684 12.476 9076 Z= 0.349 Chirality : 0.045 0.171 1017 Planarity : 0.005 0.078 1169 Dihedral : 10.153 162.587 919 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 12.71 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.62 % Favored : 97.27 % Rotamer: Outliers : 3.70 % Allowed : 18.80 % Favored : 77.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.42 (0.28), residues: 841 helix: 0.69 (0.26), residues: 368 sheet: 0.26 (0.47), residues: 125 loop : -1.54 (0.31), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 314 TYR 0.021 0.001 TYR B 104 PHE 0.031 0.002 PHE A 388 TRP 0.024 0.002 TRP A 338 HIS 0.003 0.001 HIS B 368 Details of bonding type rmsd covalent geometry : bond 0.00294 ( 6700) covalent geometry : angle 0.68360 ( 9076) hydrogen bonds : bond 0.04385 ( 322) hydrogen bonds : angle 4.79800 ( 924) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1394.53 seconds wall clock time: 24 minutes 45.05 seconds (1485.05 seconds total)