Starting phenix.real_space_refine on Tue Feb 3 18:57:23 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9x97_66661/02_2026/9x97_66661.cif Found real_map, /net/cci-nas-00/data/ceres_data/9x97_66661/02_2026/9x97_66661.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.89 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9x97_66661/02_2026/9x97_66661.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9x97_66661/02_2026/9x97_66661.map" model { file = "/net/cci-nas-00/data/ceres_data/9x97_66661/02_2026/9x97_66661.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9x97_66661/02_2026/9x97_66661.cif" } resolution = 2.89 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= 0.000 sd= 0.056 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 2 5.49 5 S 40 5.16 5 C 4156 2.51 5 N 1010 2.21 5 O 1122 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 23 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 6330 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3160 Number of conformers: 1 Conformer: "" Number of residues, atoms: 414, 3160 Classifications: {'peptide': 414} Link IDs: {'PTRANS': 15, 'TRANS': 398} Chain breaks: 1 Chain: "C" Number of atoms: 3160 Number of conformers: 1 Conformer: "" Number of residues, atoms: 414, 3160 Classifications: {'peptide': 414} Link IDs: {'PTRANS': 15, 'TRANS': 398} Chain breaks: 1 Chain: "A" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Unusual residues: {'PO4': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Unusual residues: {'PO4': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.13, per 1000 atoms: 0.18 Number of scatterers: 6330 At special positions: 0 Unit cell: (76.632, 94.76, 73.336, 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 40 16.00 P 2 15.00 O 1122 8.00 N 1010 7.00 C 4156 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: 0.46 Conformation dependent library (CDL) restraints added in 157.2 milliseconds 1640 Ramachandran restraints generated. 820 Oldfield, 0 Emsley, 820 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1492 Finding SS restraints... Secondary structure from input PDB file: 43 helices and 0 sheets defined 74.4% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.15 Creating SS restraints... Processing helix chain 'A' and resid 1 through 19 Processing helix chain 'A' and resid 20 through 29 removed outlier: 3.729A pdb=" N TYR A 24 " --> pdb=" O GLY A 20 " (cutoff:3.500A) Processing helix chain 'A' and resid 29 through 42 Proline residue: A 36 - end of helix removed outlier: 3.589A pdb=" N GLU A 40 " --> pdb=" O PRO A 36 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 64 removed outlier: 3.606A pdb=" N GLN A 56 " --> pdb=" O ILE A 52 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ILE A 62 " --> pdb=" O ALA A 58 " (cutoff:3.500A) Processing helix chain 'A' and resid 75 through 82 removed outlier: 3.561A pdb=" N SER A 81 " --> pdb=" O ARG A 77 " (cutoff:3.500A) Processing helix chain 'A' and resid 83 through 93 removed outlier: 3.561A pdb=" N ASN A 91 " --> pdb=" O VAL A 87 " (cutoff:3.500A) Processing helix chain 'A' and resid 99 through 115 removed outlier: 3.842A pdb=" N GLY A 115 " --> pdb=" O GLY A 111 " (cutoff:3.500A) Processing helix chain 'A' and resid 118 through 129 removed outlier: 3.872A pdb=" N VAL A 124 " --> pdb=" O PRO A 120 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N LYS A 127 " --> pdb=" O LYS A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 142 Processing helix chain 'A' and resid 143 through 156 Proline residue: A 153 - end of helix Processing helix chain 'A' and resid 164 through 185 removed outlier: 3.894A pdb=" N PHE A 181 " --> pdb=" O VAL A 177 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LEU A 182 " --> pdb=" O VAL A 178 " (cutoff:3.500A) Processing helix chain 'A' and resid 216 through 221 Processing helix chain 'A' and resid 225 through 247 removed outlier: 3.627A pdb=" N THR A 231 " --> pdb=" O TRP A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 260 through 291 removed outlier: 3.587A pdb=" N MET A 266 " --> pdb=" O GLY A 262 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ILE A 278 " --> pdb=" O LEU A 274 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N GLY A 281 " --> pdb=" O SER A 277 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LEU A 283 " --> pdb=" O ALA A 279 " (cutoff:3.500A) Processing helix chain 'A' and resid 301 through 321 removed outlier: 3.526A pdb=" N VAL A 313 " --> pdb=" O ALA A 309 " (cutoff:3.500A) Processing helix chain 'A' and resid 327 through 349 removed outlier: 3.536A pdb=" N ILE A 331 " --> pdb=" O PRO A 327 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N PHE A 338 " --> pdb=" O LEU A 334 " (cutoff:3.500A) Proline residue: A 345 - end of helix Processing helix chain 'A' and resid 350 through 357 removed outlier: 3.518A pdb=" N ASN A 354 " --> pdb=" O GLY A 350 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N GLU A 355 " --> pdb=" O VAL A 351 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 380 removed outlier: 3.941A pdb=" N ASN A 374 " --> pdb=" O GLY A 370 " (cutoff:3.500A) Processing helix chain 'A' and resid 381 through 391 Processing helix chain 'A' and resid 395 through 414 removed outlier: 3.629A pdb=" N VAL A 399 " --> pdb=" O THR A 395 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLU A 401 " --> pdb=" O PHE A 397 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N PHE A 412 " --> pdb=" O THR A 408 " (cutoff:3.500A) Processing helix chain 'C' and resid 2 through 19 removed outlier: 3.502A pdb=" N TYR C 9 " --> pdb=" O GLY C 5 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N PHE C 14 " --> pdb=" O ARG C 10 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ALA C 16 " --> pdb=" O VAL C 12 " (cutoff:3.500A) Processing helix chain 'C' and resid 21 through 27 Processing helix chain 'C' and resid 29 through 34 removed outlier: 3.597A pdb=" N VAL C 34 " --> pdb=" O THR C 30 " (cutoff:3.500A) Processing helix chain 'C' and resid 34 through 42 removed outlier: 3.771A pdb=" N GLU C 40 " --> pdb=" O PRO C 36 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLU C 41 " --> pdb=" O SER C 37 " (cutoff:3.500A) Processing helix chain 'C' and resid 45 through 62 removed outlier: 3.671A pdb=" N GLN C 56 " --> pdb=" O ILE C 52 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ILE C 62 " --> pdb=" O ALA C 58 " (cutoff:3.500A) Processing helix chain 'C' and resid 75 through 82 removed outlier: 3.572A pdb=" N SER C 81 " --> pdb=" O ARG C 77 " (cutoff:3.500A) Processing helix chain 'C' and resid 83 through 93 removed outlier: 3.601A pdb=" N ASN C 91 " --> pdb=" O VAL C 87 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ILE C 92 " --> pdb=" O GLY C 88 " (cutoff:3.500A) Processing helix chain 'C' and resid 99 through 113 Processing helix chain 'C' and resid 118 through 129 removed outlier: 3.903A pdb=" N VAL C 124 " --> pdb=" O PRO C 120 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ARG C 126 " --> pdb=" O GLY C 122 " (cutoff:3.500A) removed outlier: 4.986A pdb=" N LYS C 127 " --> pdb=" O LYS C 123 " (cutoff:3.500A) Processing helix chain 'C' and resid 137 through 142 removed outlier: 3.550A pdb=" N SER C 142 " --> pdb=" O TRP C 138 " (cutoff:3.500A) Processing helix chain 'C' and resid 143 through 156 removed outlier: 3.661A pdb=" N GLY C 150 " --> pdb=" O ASN C 146 " (cutoff:3.500A) Proline residue: C 153 - end of helix Processing helix chain 'C' and resid 157 through 161 removed outlier: 3.681A pdb=" N GLN C 161 " --> pdb=" O ILE C 158 " (cutoff:3.500A) Processing helix chain 'C' and resid 164 through 185 removed outlier: 3.750A pdb=" N LEU C 175 " --> pdb=" O LEU C 171 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N CYS C 176 " --> pdb=" O SER C 172 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N PHE C 181 " --> pdb=" O VAL C 177 " (cutoff:3.500A) Processing helix chain 'C' and resid 216 through 221 Processing helix chain 'C' and resid 230 through 246 Processing helix chain 'C' and resid 246 through 254 removed outlier: 4.032A pdb=" N PHE C 250 " --> pdb=" O TRP C 246 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LEU C 251 " --> pdb=" O GLY C 247 " (cutoff:3.500A) removed outlier: 5.159A pdb=" N ILE C 252 " --> pdb=" O GLN C 248 " (cutoff:3.500A) Processing helix chain 'C' and resid 260 through 291 removed outlier: 3.773A pdb=" N GLU C 270 " --> pdb=" O MET C 266 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N VAL C 275 " --> pdb=" O VAL C 271 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N GLY C 281 " --> pdb=" O SER C 277 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N LEU C 283 " --> pdb=" O ALA C 279 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ALA C 287 " --> pdb=" O LEU C 283 " (cutoff:3.500A) Processing helix chain 'C' and resid 301 through 321 removed outlier: 3.576A pdb=" N THR C 312 " --> pdb=" O MET C 308 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N VAL C 313 " --> pdb=" O ALA C 309 " (cutoff:3.500A) Processing helix chain 'C' and resid 327 through 347 removed outlier: 3.560A pdb=" N ILE C 331 " --> pdb=" O PRO C 327 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N PHE C 338 " --> pdb=" O LEU C 334 " (cutoff:3.500A) Proline residue: C 345 - end of helix Processing helix chain 'C' and resid 350 through 357 removed outlier: 3.510A pdb=" N ASN C 354 " --> pdb=" O GLY C 350 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N GLU C 355 " --> pdb=" O VAL C 351 " (cutoff:3.500A) Processing helix chain 'C' and resid 368 through 380 removed outlier: 3.962A pdb=" N ASN C 374 " --> pdb=" O GLY C 370 " (cutoff:3.500A) Processing helix chain 'C' and resid 381 through 391 removed outlier: 3.624A pdb=" N ILE C 387 " --> pdb=" O PRO C 383 " (cutoff:3.500A) Processing helix chain 'C' and resid 395 through 411 removed outlier: 3.623A pdb=" N VAL C 399 " --> pdb=" O THR C 395 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLU C 401 " --> pdb=" O PHE C 397 " (cutoff:3.500A) 367 hydrogen bonds defined for protein. 1098 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: 0.61 Time building geometry restraints manager: 0.58 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 956 1.32 - 1.44: 1930 1.44 - 1.56: 3550 1.56 - 1.69: 0 1.69 - 1.81: 66 Bond restraints: 6502 Sorted by residual: bond pdb=" CA SER A 223 " pdb=" C SER A 223 " ideal model delta sigma weight residual 1.525 1.482 0.043 1.13e-02 7.83e+03 1.42e+01 bond pdb=" CA TYR A 225 " pdb=" C TYR A 225 " ideal model delta sigma weight residual 1.522 1.475 0.047 1.32e-02 5.74e+03 1.25e+01 bond pdb=" C TYR A 225 " pdb=" N LEU A 226 " ideal model delta sigma weight residual 1.335 1.291 0.044 1.31e-02 5.83e+03 1.14e+01 bond pdb=" C GLY A 173 " pdb=" O GLY A 173 " ideal model delta sigma weight residual 1.234 1.197 0.037 1.19e-02 7.06e+03 9.83e+00 bond pdb=" O3 PO4 C 501 " pdb=" P PO4 C 501 " ideal model delta sigma weight residual 1.569 1.509 0.060 2.00e-02 2.50e+03 8.97e+00 ... (remaining 6497 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.67: 8252 1.67 - 3.33: 506 3.33 - 5.00: 70 5.00 - 6.66: 15 6.66 - 8.33: 3 Bond angle restraints: 8846 Sorted by residual: angle pdb=" CA VAL C 100 " pdb=" C VAL C 100 " pdb=" N PRO C 101 " ideal model delta sigma weight residual 120.83 123.88 -3.05 5.90e-01 2.87e+00 2.67e+01 angle pdb=" N TYR A 225 " pdb=" CA TYR A 225 " pdb=" C TYR A 225 " ideal model delta sigma weight residual 113.50 107.81 5.69 1.23e+00 6.61e-01 2.14e+01 angle pdb=" N VAL C 100 " pdb=" CA VAL C 100 " pdb=" CB VAL C 100 " ideal model delta sigma weight residual 110.52 113.24 -2.72 6.70e-01 2.23e+00 1.64e+01 angle pdb=" CA PHE A 33 " pdb=" CB PHE A 33 " pdb=" CG PHE A 33 " ideal model delta sigma weight residual 113.80 117.79 -3.99 1.00e+00 1.00e+00 1.59e+01 angle pdb=" N ILE A 368 " pdb=" CA ILE A 368 " pdb=" C ILE A 368 " ideal model delta sigma weight residual 111.45 107.75 3.70 9.30e-01 1.16e+00 1.58e+01 ... (remaining 8841 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.70: 2980 14.70 - 29.39: 464 29.39 - 44.09: 177 44.09 - 58.78: 60 58.78 - 73.48: 9 Dihedral angle restraints: 3690 sinusoidal: 1342 harmonic: 2348 Sorted by residual: dihedral pdb=" CA GLY A 247 " pdb=" C GLY A 247 " pdb=" N GLN A 248 " pdb=" CA GLN A 248 " ideal model delta harmonic sigma weight residual 180.00 160.56 19.44 0 5.00e+00 4.00e-02 1.51e+01 dihedral pdb=" CA ASN C 27 " pdb=" C ASN C 27 " pdb=" N ARG C 28 " pdb=" CA ARG C 28 " ideal model delta harmonic sigma weight residual 180.00 162.71 17.29 0 5.00e+00 4.00e-02 1.20e+01 dihedral pdb=" CA ASP A 193 " pdb=" CB ASP A 193 " pdb=" CG ASP A 193 " pdb=" OD1 ASP A 193 " ideal model delta sinusoidal sigma weight residual -30.00 -87.31 57.31 1 2.00e+01 2.50e-03 1.10e+01 ... (remaining 3687 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 826 0.052 - 0.105: 151 0.105 - 0.157: 13 0.157 - 0.209: 5 0.209 - 0.262: 3 Chirality restraints: 998 Sorted by residual: chirality pdb=" CB VAL A 351 " pdb=" CA VAL A 351 " pdb=" CG1 VAL A 351 " pdb=" CG2 VAL A 351 " both_signs ideal model delta sigma weight residual False -2.63 -2.37 -0.26 2.00e-01 2.50e+01 1.71e+00 chirality pdb=" CA TYR A 24 " pdb=" N TYR A 24 " pdb=" C TYR A 24 " pdb=" CB TYR A 24 " both_signs ideal model delta sigma weight residual False 2.51 2.75 -0.24 2.00e-01 2.50e+01 1.49e+00 chirality pdb=" CB VAL C 351 " pdb=" CA VAL C 351 " pdb=" CG1 VAL C 351 " pdb=" CG2 VAL C 351 " both_signs ideal model delta sigma weight residual False -2.63 -2.39 -0.24 2.00e-01 2.50e+01 1.42e+00 ... (remaining 995 not shown) Planarity restraints: 1084 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE A 249 " 0.012 2.00e-02 2.50e+03 2.37e-02 5.64e+00 pdb=" C PHE A 249 " -0.041 2.00e-02 2.50e+03 pdb=" O PHE A 249 " 0.015 2.00e-02 2.50e+03 pdb=" N PHE A 250 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY A 135 " 0.012 2.00e-02 2.50e+03 2.34e-02 5.50e+00 pdb=" C GLY A 135 " -0.041 2.00e-02 2.50e+03 pdb=" O GLY A 135 " 0.015 2.00e-02 2.50e+03 pdb=" N THR A 136 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TRP A 118 " -0.037 5.00e-02 4.00e+02 5.62e-02 5.06e+00 pdb=" N PRO A 119 " 0.097 5.00e-02 4.00e+02 pdb=" CA PRO A 119 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO A 119 " -0.031 5.00e-02 4.00e+02 ... (remaining 1081 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 481 2.74 - 3.28: 6375 3.28 - 3.82: 10822 3.82 - 4.36: 14158 4.36 - 4.90: 22954 Nonbonded interactions: 54790 Sorted by model distance: nonbonded pdb=" OH TYR C 6 " pdb=" O ARG C 197 " model vdw 2.198 3.040 nonbonded pdb=" ND2 ASN C 27 " pdb=" OG SER C 172 " model vdw 2.230 3.120 nonbonded pdb=" O LEU A 382 " pdb=" OG1 THR A 386 " model vdw 2.231 3.040 nonbonded pdb=" O LEU C 382 " pdb=" OG1 THR C 386 " model vdw 2.266 3.040 nonbonded pdb=" O TYR C 24 " pdb=" NE2 GLN C 114 " model vdw 2.287 3.120 ... (remaining 54785 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' } 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: 0.770 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.080 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 5.380 Find NCS groups from input model: 0.050 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:5.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 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 : 0.005 0.060 6502 Z= 0.286 Angle : 0.889 8.327 8846 Z= 0.593 Chirality : 0.043 0.262 998 Planarity : 0.007 0.068 1084 Dihedral : 17.993 73.479 2198 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 10.66 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.76 % Favored : 95.00 % Rotamer: Outliers : 6.31 % Allowed : 30.33 % Favored : 63.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: -4.37 (0.25), residues: 820 helix: -2.54 (0.17), residues: 692 sheet: None (None), residues: 0 loop : -3.40 (0.49), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 415 TYR 0.014 0.001 TYR A 24 PHE 0.021 0.002 PHE C 134 TRP 0.021 0.001 TRP C 107 HIS 0.003 0.001 HIS C 188 Details of bonding type rmsd covalent geometry : bond 0.00466 ( 6502) covalent geometry : angle 0.88913 ( 8846) hydrogen bonds : bond 0.26449 ( 367) hydrogen bonds : angle 10.09403 ( 1098) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1640 Ramachandran restraints generated. 820 Oldfield, 0 Emsley, 820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1640 Ramachandran restraints generated. 820 Oldfield, 0 Emsley, 820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 101 time to evaluate : 0.148 Fit side-chains REVERT: A 329 LEU cc_start: 0.8421 (tp) cc_final: 0.8181 (tp) REVERT: C 1 MET cc_start: 0.3676 (pmm) cc_final: 0.2674 (mtm) REVERT: C 365 SER cc_start: 0.8596 (t) cc_final: 0.8283 (m) outliers start: 42 outliers final: 32 residues processed: 140 average time/residue: 0.3107 time to fit residues: 46.2895 Evaluate side-chains 126 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 94 time to evaluate : 0.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 TYR Chi-restraints excluded: chain A residue 30 THR Chi-restraints excluded: chain A residue 55 SER Chi-restraints excluded: chain A residue 72 ASP Chi-restraints excluded: chain A residue 107 TRP Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 144 SER Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 216 THR Chi-restraints excluded: chain A residue 277 SER Chi-restraints excluded: chain A residue 294 SER Chi-restraints excluded: chain A residue 295 ASN Chi-restraints excluded: chain A residue 392 SER Chi-restraints excluded: chain A residue 407 SER Chi-restraints excluded: chain C residue 6 TYR Chi-restraints excluded: chain C residue 35 MET Chi-restraints excluded: chain C residue 55 SER Chi-restraints excluded: chain C residue 72 ASP Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 144 SER Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 172 SER Chi-restraints excluded: chain C residue 179 VAL Chi-restraints excluded: chain C residue 215 SER Chi-restraints excluded: chain C residue 267 SER Chi-restraints excluded: chain C residue 277 SER Chi-restraints excluded: chain C residue 294 SER Chi-restraints excluded: chain C residue 295 ASN Chi-restraints excluded: chain C residue 392 SER Chi-restraints excluded: chain C residue 407 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 49 optimal weight: 3.9990 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 0.7980 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 0.0030 chunk 62 optimal weight: 3.9990 chunk 51 optimal weight: 0.8980 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 0.9980 chunk 45 optimal weight: 0.0470 chunk 74 optimal weight: 0.0370 overall best weight: 0.3566 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 354 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.150397 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.108144 restraints weight = 7104.408| |-----------------------------------------------------------------------------| r_work (start): 0.3130 rms_B_bonded: 1.77 r_work: 0.3006 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2876 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.2876 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.1290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6502 Z= 0.129 Angle : 0.617 8.540 8846 Z= 0.318 Chirality : 0.039 0.326 998 Planarity : 0.006 0.051 1084 Dihedral : 8.042 59.387 923 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 4.50 % Allowed : 28.83 % Favored : 66.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: -3.04 (0.27), residues: 820 helix: -1.57 (0.18), residues: 690 sheet: None (None), residues: 0 loop : -3.36 (0.48), residues: 130 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 415 TYR 0.013 0.001 TYR A 24 PHE 0.008 0.001 PHE A 340 TRP 0.008 0.001 TRP C 107 HIS 0.003 0.001 HIS A 188 Details of bonding type rmsd covalent geometry : bond 0.00269 ( 6502) covalent geometry : angle 0.61721 ( 8846) hydrogen bonds : bond 0.04314 ( 367) hydrogen bonds : angle 5.16711 ( 1098) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1640 Ramachandran restraints generated. 820 Oldfield, 0 Emsley, 820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1640 Ramachandran restraints generated. 820 Oldfield, 0 Emsley, 820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 104 time to evaluate : 0.227 Fit side-chains REVERT: A 17 MET cc_start: 0.8401 (mtm) cc_final: 0.7937 (mtt) REVERT: A 40 GLU cc_start: 0.8363 (tt0) cc_final: 0.8069 (mt-10) REVERT: A 107 TRP cc_start: 0.9012 (OUTLIER) cc_final: 0.7285 (m-90) REVERT: A 143 THR cc_start: 0.7719 (OUTLIER) cc_final: 0.7425 (m) REVERT: A 270 GLU cc_start: 0.8152 (mm-30) cc_final: 0.7939 (tp30) REVERT: A 329 LEU cc_start: 0.8098 (tp) cc_final: 0.7874 (tp) REVERT: A 365 SER cc_start: 0.8711 (t) cc_final: 0.8333 (m) REVERT: A 415 ARG cc_start: 0.6998 (ttp-110) cc_final: 0.6552 (ttm110) REVERT: C 1 MET cc_start: 0.2969 (pmm) cc_final: 0.2730 (mtm) REVERT: C 107 TRP cc_start: 0.8954 (OUTLIER) cc_final: 0.7906 (m-90) REVERT: C 143 THR cc_start: 0.7631 (OUTLIER) cc_final: 0.7403 (m) REVERT: C 365 SER cc_start: 0.8590 (t) cc_final: 0.8252 (m) outliers start: 30 outliers final: 8 residues processed: 127 average time/residue: 0.2976 time to fit residues: 40.5507 Evaluate side-chains 109 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 97 time to evaluate : 0.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 ASP Chi-restraints excluded: chain A residue 107 TRP Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 164 SER Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 215 SER Chi-restraints excluded: chain A residue 407 SER Chi-restraints excluded: chain C residue 72 ASP Chi-restraints excluded: chain C residue 107 TRP Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 407 SER Chi-restraints excluded: chain C residue 424 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 29 optimal weight: 0.6980 chunk 16 optimal weight: 0.9990 chunk 50 optimal weight: 0.0570 chunk 58 optimal weight: 0.8980 chunk 8 optimal weight: 3.9990 chunk 31 optimal weight: 1.9990 chunk 15 optimal weight: 0.5980 chunk 19 optimal weight: 0.0040 chunk 55 optimal weight: 6.9990 chunk 62 optimal weight: 0.0870 chunk 53 optimal weight: 0.7980 overall best weight: 0.2888 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 354 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.153840 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.111226 restraints weight = 7012.871| |-----------------------------------------------------------------------------| r_work (start): 0.3148 rms_B_bonded: 1.75 r_work: 0.3018 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2887 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.2887 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.1747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 6502 Z= 0.109 Angle : 0.559 11.559 8846 Z= 0.285 Chirality : 0.038 0.341 998 Planarity : 0.005 0.050 1084 Dihedral : 6.248 58.375 892 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 2.25 % Allowed : 30.03 % Favored : 67.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: -2.09 (0.28), residues: 820 helix: -0.90 (0.19), residues: 686 sheet: None (None), residues: 0 loop : -3.09 (0.47), residues: 134 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 415 TYR 0.011 0.001 TYR C 24 PHE 0.009 0.001 PHE C 384 TRP 0.007 0.001 TRP C 107 HIS 0.001 0.000 HIS A 188 Details of bonding type rmsd covalent geometry : bond 0.00225 ( 6502) covalent geometry : angle 0.55862 ( 8846) hydrogen bonds : bond 0.03511 ( 367) hydrogen bonds : angle 4.63768 ( 1098) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1640 Ramachandran restraints generated. 820 Oldfield, 0 Emsley, 820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1640 Ramachandran restraints generated. 820 Oldfield, 0 Emsley, 820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 98 time to evaluate : 0.145 Fit side-chains REVERT: A 17 MET cc_start: 0.8347 (mtm) cc_final: 0.7872 (mtt) REVERT: A 107 TRP cc_start: 0.8966 (OUTLIER) cc_final: 0.7631 (m-90) REVERT: A 365 SER cc_start: 0.8711 (t) cc_final: 0.8318 (m) REVERT: A 412 PHE cc_start: 0.8464 (t80) cc_final: 0.8176 (t80) REVERT: A 415 ARG cc_start: 0.6927 (ttp-110) cc_final: 0.6445 (ttm110) REVERT: C 107 TRP cc_start: 0.8939 (OUTLIER) cc_final: 0.7501 (m-90) REVERT: C 365 SER cc_start: 0.8581 (t) cc_final: 0.8295 (m) outliers start: 15 outliers final: 3 residues processed: 109 average time/residue: 0.2226 time to fit residues: 26.5581 Evaluate side-chains 99 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 94 time to evaluate : 0.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 TRP Chi-restraints excluded: chain A residue 407 SER Chi-restraints excluded: chain C residue 107 TRP Chi-restraints excluded: chain C residue 216 THR Chi-restraints excluded: chain C residue 407 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 69 optimal weight: 9.9990 chunk 71 optimal weight: 3.9990 chunk 7 optimal weight: 0.2980 chunk 42 optimal weight: 1.9990 chunk 5 optimal weight: 4.9990 chunk 35 optimal weight: 0.6980 chunk 17 optimal weight: 5.9990 chunk 75 optimal weight: 4.9990 chunk 8 optimal weight: 0.8980 chunk 65 optimal weight: 0.0670 chunk 40 optimal weight: 0.0770 overall best weight: 0.4076 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 374 ASN C 354 ASN C 374 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.153131 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.110012 restraints weight = 7010.505| |-----------------------------------------------------------------------------| r_work (start): 0.3130 rms_B_bonded: 1.79 r_work: 0.3002 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2868 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.2868 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 moved from start: 0.2091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 6502 Z= 0.105 Angle : 0.529 12.206 8846 Z= 0.269 Chirality : 0.038 0.283 998 Planarity : 0.005 0.049 1084 Dihedral : 5.489 57.238 884 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 3.00 % Allowed : 28.38 % Favored : 68.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: -1.37 (0.29), residues: 820 helix: -0.42 (0.20), residues: 684 sheet: None (None), residues: 0 loop : -2.75 (0.47), residues: 136 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 300 TYR 0.011 0.001 TYR C 24 PHE 0.011 0.001 PHE C 340 TRP 0.008 0.001 TRP C 107 HIS 0.001 0.000 HIS C 366 Details of bonding type rmsd covalent geometry : bond 0.00227 ( 6502) covalent geometry : angle 0.52942 ( 8846) hydrogen bonds : bond 0.03177 ( 367) hydrogen bonds : angle 4.29074 ( 1098) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1640 Ramachandran restraints generated. 820 Oldfield, 0 Emsley, 820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1640 Ramachandran restraints generated. 820 Oldfield, 0 Emsley, 820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 98 time to evaluate : 0.177 Fit side-chains REVERT: A 17 MET cc_start: 0.8291 (mtm) cc_final: 0.7789 (mtt) REVERT: A 107 TRP cc_start: 0.8945 (OUTLIER) cc_final: 0.7534 (m-90) REVERT: A 300 ARG cc_start: 0.6367 (OUTLIER) cc_final: 0.5148 (mtp180) REVERT: A 365 SER cc_start: 0.8566 (t) cc_final: 0.8276 (m) REVERT: A 415 ARG cc_start: 0.6845 (ttp-110) cc_final: 0.6372 (ttm110) REVERT: C 107 TRP cc_start: 0.8922 (OUTLIER) cc_final: 0.7505 (m-90) REVERT: C 365 SER cc_start: 0.8507 (t) cc_final: 0.8215 (m) outliers start: 20 outliers final: 8 residues processed: 113 average time/residue: 0.2707 time to fit residues: 33.0329 Evaluate side-chains 104 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 93 time to evaluate : 0.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 TRP Chi-restraints excluded: chain A residue 164 SER Chi-restraints excluded: chain A residue 300 ARG Chi-restraints excluded: chain A residue 326 SER Chi-restraints excluded: chain A residue 407 SER Chi-restraints excluded: chain C residue 107 TRP Chi-restraints excluded: chain C residue 216 THR Chi-restraints excluded: chain C residue 326 SER Chi-restraints excluded: chain C residue 356 SER Chi-restraints excluded: chain C residue 407 SER Chi-restraints excluded: chain C residue 424 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 9 optimal weight: 0.8980 chunk 28 optimal weight: 5.9990 chunk 38 optimal weight: 2.9990 chunk 33 optimal weight: 0.0870 chunk 72 optimal weight: 0.9980 chunk 67 optimal weight: 0.7980 chunk 6 optimal weight: 0.6980 chunk 50 optimal weight: 0.7980 chunk 80 optimal weight: 0.7980 chunk 17 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 overall best weight: 0.6358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 374 ASN C 354 ASN C 374 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.154315 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.111551 restraints weight = 7090.715| |-----------------------------------------------------------------------------| r_work (start): 0.3123 rms_B_bonded: 1.79 r_work: 0.2993 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2859 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.2859 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 moved from start: 0.2156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 6502 Z= 0.111 Angle : 0.514 9.682 8846 Z= 0.262 Chirality : 0.039 0.286 998 Planarity : 0.005 0.049 1084 Dihedral : 5.271 57.104 884 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 2.55 % Allowed : 29.28 % Favored : 68.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: -0.99 (0.29), residues: 820 helix: -0.18 (0.20), residues: 684 sheet: None (None), residues: 0 loop : -2.51 (0.49), residues: 136 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 197 TYR 0.011 0.001 TYR C 24 PHE 0.011 0.001 PHE C 340 TRP 0.008 0.001 TRP C 107 HIS 0.001 0.000 HIS C 366 Details of bonding type rmsd covalent geometry : bond 0.00248 ( 6502) covalent geometry : angle 0.51378 ( 8846) hydrogen bonds : bond 0.03211 ( 367) hydrogen bonds : angle 4.19260 ( 1098) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1640 Ramachandran restraints generated. 820 Oldfield, 0 Emsley, 820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1640 Ramachandran restraints generated. 820 Oldfield, 0 Emsley, 820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 91 time to evaluate : 0.258 Fit side-chains REVERT: A 17 MET cc_start: 0.8270 (mtm) cc_final: 0.7794 (mtt) REVERT: A 107 TRP cc_start: 0.8944 (OUTLIER) cc_final: 0.7573 (m-90) REVERT: A 143 THR cc_start: 0.7593 (OUTLIER) cc_final: 0.7374 (m) REVERT: A 300 ARG cc_start: 0.6264 (OUTLIER) cc_final: 0.4989 (mtp180) REVERT: A 365 SER cc_start: 0.8530 (t) cc_final: 0.8218 (m) REVERT: A 415 ARG cc_start: 0.6831 (ttp-110) cc_final: 0.6413 (ttm110) REVERT: A 420 LYS cc_start: 0.7736 (OUTLIER) cc_final: 0.6659 (mptt) REVERT: C 365 SER cc_start: 0.8471 (t) cc_final: 0.8155 (m) REVERT: C 420 LYS cc_start: 0.7728 (OUTLIER) cc_final: 0.6668 (mptt) outliers start: 17 outliers final: 7 residues processed: 106 average time/residue: 0.3481 time to fit residues: 39.6091 Evaluate side-chains 100 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 88 time to evaluate : 0.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 TRP Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 300 ARG Chi-restraints excluded: chain A residue 326 SER Chi-restraints excluded: chain A residue 420 LYS Chi-restraints excluded: chain C residue 6 TYR Chi-restraints excluded: chain C residue 107 TRP Chi-restraints excluded: chain C residue 216 THR Chi-restraints excluded: chain C residue 326 SER Chi-restraints excluded: chain C residue 407 SER Chi-restraints excluded: chain C residue 420 LYS Chi-restraints excluded: chain C residue 424 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 26 optimal weight: 9.9990 chunk 31 optimal weight: 3.9990 chunk 56 optimal weight: 0.0970 chunk 14 optimal weight: 0.9980 chunk 71 optimal weight: 3.9990 chunk 76 optimal weight: 4.9990 chunk 79 optimal weight: 0.9990 chunk 24 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 45 optimal weight: 3.9990 chunk 17 optimal weight: 2.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 374 ASN C 354 ASN C 374 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.154729 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.112983 restraints weight = 7082.242| |-----------------------------------------------------------------------------| r_work (start): 0.3319 rms_B_bonded: 1.75 r_work: 0.3177 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3046 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3046 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8316 moved from start: 0.2078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 6502 Z= 0.160 Angle : 0.546 9.909 8846 Z= 0.278 Chirality : 0.040 0.221 998 Planarity : 0.005 0.049 1084 Dihedral : 5.224 58.055 883 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 3.00 % Allowed : 28.23 % Favored : 68.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: -0.87 (0.29), residues: 820 helix: -0.10 (0.20), residues: 680 sheet: None (None), residues: 0 loop : -2.35 (0.50), residues: 140 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG C 418 TYR 0.015 0.001 TYR C 24 PHE 0.013 0.002 PHE A 94 TRP 0.009 0.001 TRP C 107 HIS 0.002 0.001 HIS A 390 Details of bonding type rmsd covalent geometry : bond 0.00384 ( 6502) covalent geometry : angle 0.54618 ( 8846) hydrogen bonds : bond 0.03683 ( 367) hydrogen bonds : angle 4.28790 ( 1098) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1640 Ramachandran restraints generated. 820 Oldfield, 0 Emsley, 820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1640 Ramachandran restraints generated. 820 Oldfield, 0 Emsley, 820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 88 time to evaluate : 0.157 Fit side-chains REVERT: A 17 MET cc_start: 0.8357 (mtm) cc_final: 0.7920 (mtp) REVERT: A 107 TRP cc_start: 0.9011 (OUTLIER) cc_final: 0.7121 (m-90) REVERT: A 143 THR cc_start: 0.7810 (OUTLIER) cc_final: 0.7576 (m) REVERT: A 300 ARG cc_start: 0.6366 (OUTLIER) cc_final: 0.5061 (mtp180) REVERT: A 365 SER cc_start: 0.8664 (t) cc_final: 0.8329 (m) REVERT: A 415 ARG cc_start: 0.6922 (ttp-110) cc_final: 0.6629 (ttm110) REVERT: A 420 LYS cc_start: 0.7934 (OUTLIER) cc_final: 0.6861 (mptt) REVERT: C 365 SER cc_start: 0.8581 (t) cc_final: 0.8238 (m) outliers start: 20 outliers final: 6 residues processed: 104 average time/residue: 0.3200 time to fit residues: 35.7920 Evaluate side-chains 98 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 88 time to evaluate : 0.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 TRP Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 300 ARG Chi-restraints excluded: chain A residue 326 SER Chi-restraints excluded: chain A residue 420 LYS Chi-restraints excluded: chain C residue 6 TYR Chi-restraints excluded: chain C residue 107 TRP Chi-restraints excluded: chain C residue 216 THR Chi-restraints excluded: chain C residue 326 SER Chi-restraints excluded: chain C residue 424 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 65 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 chunk 9 optimal weight: 2.9990 chunk 48 optimal weight: 4.9990 chunk 45 optimal weight: 1.9990 chunk 47 optimal weight: 0.4980 chunk 50 optimal weight: 0.1980 chunk 27 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 75 optimal weight: 0.0970 chunk 24 optimal weight: 0.0030 overall best weight: 0.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 354 ASN A 374 ASN C 354 ASN C 374 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.157041 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.114160 restraints weight = 6949.834| |-----------------------------------------------------------------------------| r_work (start): 0.3112 rms_B_bonded: 1.83 r_work: 0.2979 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2844 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.2844 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.2343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 6502 Z= 0.099 Angle : 0.522 10.993 8846 Z= 0.264 Chirality : 0.039 0.329 998 Planarity : 0.005 0.050 1084 Dihedral : 4.910 56.306 882 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 2.55 % Allowed : 27.93 % Favored : 69.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: -0.51 (0.29), residues: 820 helix: 0.16 (0.20), residues: 684 sheet: None (None), residues: 0 loop : -2.43 (0.50), residues: 136 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 197 TYR 0.010 0.001 TYR C 24 PHE 0.012 0.001 PHE C 340 TRP 0.008 0.001 TRP C 107 HIS 0.001 0.000 HIS C 366 Details of bonding type rmsd covalent geometry : bond 0.00211 ( 6502) covalent geometry : angle 0.52233 ( 8846) hydrogen bonds : bond 0.02993 ( 367) hydrogen bonds : angle 4.08172 ( 1098) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1640 Ramachandran restraints generated. 820 Oldfield, 0 Emsley, 820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1640 Ramachandran restraints generated. 820 Oldfield, 0 Emsley, 820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 90 time to evaluate : 0.143 Fit side-chains REVERT: A 17 MET cc_start: 0.8207 (mtm) cc_final: 0.7765 (mtp) REVERT: A 107 TRP cc_start: 0.8936 (OUTLIER) cc_final: 0.7489 (m-90) REVERT: A 143 THR cc_start: 0.7609 (OUTLIER) cc_final: 0.7379 (m) REVERT: A 300 ARG cc_start: 0.6041 (OUTLIER) cc_final: 0.4716 (mtp180) REVERT: A 365 SER cc_start: 0.8573 (t) cc_final: 0.8179 (m) REVERT: A 415 ARG cc_start: 0.6671 (ttp-110) cc_final: 0.6314 (ttm110) REVERT: A 420 LYS cc_start: 0.7748 (OUTLIER) cc_final: 0.6677 (mptt) REVERT: C 107 TRP cc_start: 0.8950 (OUTLIER) cc_final: 0.7289 (m-90) REVERT: C 315 MET cc_start: 0.8323 (mtp) cc_final: 0.8085 (mtp) REVERT: C 365 SER cc_start: 0.8525 (t) cc_final: 0.8160 (m) REVERT: C 420 LYS cc_start: 0.7766 (OUTLIER) cc_final: 0.6680 (mptt) outliers start: 17 outliers final: 6 residues processed: 105 average time/residue: 0.3738 time to fit residues: 41.9073 Evaluate side-chains 99 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 87 time to evaluate : 0.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 TRP Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 300 ARG Chi-restraints excluded: chain A residue 326 SER Chi-restraints excluded: chain A residue 407 SER Chi-restraints excluded: chain A residue 420 LYS Chi-restraints excluded: chain C residue 6 TYR Chi-restraints excluded: chain C residue 107 TRP Chi-restraints excluded: chain C residue 326 SER Chi-restraints excluded: chain C residue 329 LEU Chi-restraints excluded: chain C residue 420 LYS Chi-restraints excluded: chain C residue 424 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 57 optimal weight: 5.9990 chunk 78 optimal weight: 0.4980 chunk 24 optimal weight: 0.2980 chunk 22 optimal weight: 2.9990 chunk 74 optimal weight: 2.9990 chunk 8 optimal weight: 4.9990 chunk 52 optimal weight: 0.4980 chunk 43 optimal weight: 0.9990 chunk 1 optimal weight: 5.9990 chunk 63 optimal weight: 0.8980 chunk 7 optimal weight: 0.8980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 354 ASN A 374 ASN C 354 ASN C 374 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.154008 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.110982 restraints weight = 6977.837| |-----------------------------------------------------------------------------| r_work (start): 0.3102 rms_B_bonded: 1.78 r_work: 0.2969 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2834 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.2834 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8133 moved from start: 0.2390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 6502 Z= 0.108 Angle : 0.526 10.602 8846 Z= 0.260 Chirality : 0.039 0.266 998 Planarity : 0.005 0.049 1084 Dihedral : 4.867 56.262 882 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 3.30 % Allowed : 27.18 % Favored : 69.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: -0.28 (0.29), residues: 820 helix: 0.33 (0.20), residues: 684 sheet: None (None), residues: 0 loop : -2.40 (0.49), residues: 136 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 126 TYR 0.010 0.001 TYR C 24 PHE 0.011 0.001 PHE C 340 TRP 0.008 0.001 TRP C 107 HIS 0.001 0.000 HIS C 366 Details of bonding type rmsd covalent geometry : bond 0.00244 ( 6502) covalent geometry : angle 0.52563 ( 8846) hydrogen bonds : bond 0.03071 ( 367) hydrogen bonds : angle 4.01463 ( 1098) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1640 Ramachandran restraints generated. 820 Oldfield, 0 Emsley, 820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1640 Ramachandran restraints generated. 820 Oldfield, 0 Emsley, 820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 89 time to evaluate : 0.140 Fit side-chains REVERT: A 17 MET cc_start: 0.8199 (mtm) cc_final: 0.7754 (mtp) REVERT: A 107 TRP cc_start: 0.8925 (OUTLIER) cc_final: 0.7419 (m-90) REVERT: A 143 THR cc_start: 0.7549 (OUTLIER) cc_final: 0.7319 (m) REVERT: A 300 ARG cc_start: 0.6022 (OUTLIER) cc_final: 0.4743 (mtp180) REVERT: A 415 ARG cc_start: 0.6569 (ttp-110) cc_final: 0.6205 (ttm110) REVERT: A 420 LYS cc_start: 0.7724 (OUTLIER) cc_final: 0.6658 (mptt) REVERT: C 420 LYS cc_start: 0.7734 (OUTLIER) cc_final: 0.6659 (mptt) outliers start: 22 outliers final: 10 residues processed: 108 average time/residue: 0.3847 time to fit residues: 44.2336 Evaluate side-chains 106 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 91 time to evaluate : 0.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 TRP Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 164 SER Chi-restraints excluded: chain A residue 215 SER Chi-restraints excluded: chain A residue 300 ARG Chi-restraints excluded: chain A residue 326 SER Chi-restraints excluded: chain A residue 407 SER Chi-restraints excluded: chain A residue 420 LYS Chi-restraints excluded: chain C residue 6 TYR Chi-restraints excluded: chain C residue 107 TRP Chi-restraints excluded: chain C residue 216 THR Chi-restraints excluded: chain C residue 326 SER Chi-restraints excluded: chain C residue 329 LEU Chi-restraints excluded: chain C residue 420 LYS Chi-restraints excluded: chain C residue 424 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 7 optimal weight: 5.9990 chunk 51 optimal weight: 0.4980 chunk 64 optimal weight: 0.6980 chunk 40 optimal weight: 4.9990 chunk 20 optimal weight: 4.9990 chunk 42 optimal weight: 4.9990 chunk 46 optimal weight: 0.6980 chunk 34 optimal weight: 0.0670 chunk 60 optimal weight: 10.0000 chunk 43 optimal weight: 1.9990 chunk 66 optimal weight: 0.9980 overall best weight: 0.5918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 374 ASN C 354 ASN C 374 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.156190 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.112941 restraints weight = 7023.374| |-----------------------------------------------------------------------------| r_work (start): 0.3114 rms_B_bonded: 1.83 r_work: 0.2980 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2846 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.2846 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.2468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 6502 Z= 0.108 Angle : 0.527 10.182 8846 Z= 0.262 Chirality : 0.039 0.240 998 Planarity : 0.005 0.049 1084 Dihedral : 4.851 56.127 882 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 2.55 % Allowed : 28.23 % Favored : 69.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: -0.12 (0.29), residues: 820 helix: 0.44 (0.20), residues: 684 sheet: None (None), residues: 0 loop : -2.39 (0.49), residues: 136 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 415 TYR 0.010 0.001 TYR C 24 PHE 0.011 0.001 PHE C 340 TRP 0.008 0.001 TRP C 107 HIS 0.001 0.000 HIS A 366 Details of bonding type rmsd covalent geometry : bond 0.00241 ( 6502) covalent geometry : angle 0.52652 ( 8846) hydrogen bonds : bond 0.03047 ( 367) hydrogen bonds : angle 3.98450 ( 1098) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1640 Ramachandran restraints generated. 820 Oldfield, 0 Emsley, 820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1640 Ramachandran restraints generated. 820 Oldfield, 0 Emsley, 820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 90 time to evaluate : 0.152 Fit side-chains REVERT: A 17 MET cc_start: 0.8263 (mtm) cc_final: 0.7810 (mtp) REVERT: A 107 TRP cc_start: 0.8974 (OUTLIER) cc_final: 0.7490 (m-90) REVERT: A 143 THR cc_start: 0.7639 (OUTLIER) cc_final: 0.7408 (m) REVERT: A 300 ARG cc_start: 0.6129 (OUTLIER) cc_final: 0.4833 (mtp180) REVERT: A 420 LYS cc_start: 0.7779 (OUTLIER) cc_final: 0.6716 (mptt) REVERT: C 10 ARG cc_start: 0.6811 (ttp80) cc_final: 0.6138 (ttp-170) REVERT: C 254 GLU cc_start: 0.8082 (mm-30) cc_final: 0.7789 (mt-10) outliers start: 17 outliers final: 9 residues processed: 105 average time/residue: 0.3631 time to fit residues: 40.7232 Evaluate side-chains 106 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 93 time to evaluate : 0.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 TRP Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 164 SER Chi-restraints excluded: chain A residue 215 SER Chi-restraints excluded: chain A residue 300 ARG Chi-restraints excluded: chain A residue 326 SER Chi-restraints excluded: chain A residue 407 SER Chi-restraints excluded: chain A residue 420 LYS Chi-restraints excluded: chain C residue 6 TYR Chi-restraints excluded: chain C residue 107 TRP Chi-restraints excluded: chain C residue 326 SER Chi-restraints excluded: chain C residue 329 LEU Chi-restraints excluded: chain C residue 424 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 53 optimal weight: 0.7980 chunk 38 optimal weight: 0.9990 chunk 59 optimal weight: 1.9990 chunk 14 optimal weight: 0.9990 chunk 41 optimal weight: 10.0000 chunk 24 optimal weight: 0.0970 chunk 67 optimal weight: 7.9990 chunk 42 optimal weight: 1.9990 chunk 15 optimal weight: 0.7980 chunk 7 optimal weight: 5.9990 chunk 49 optimal weight: 1.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 366 HIS A 374 ASN C 248 GLN C 354 ASN C 374 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.155159 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.112200 restraints weight = 6958.424| |-----------------------------------------------------------------------------| r_work (start): 0.3127 rms_B_bonded: 1.82 r_work: 0.2993 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2858 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.2858 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 moved from start: 0.2496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6502 Z= 0.115 Angle : 0.528 9.822 8846 Z= 0.264 Chirality : 0.039 0.236 998 Planarity : 0.005 0.049 1084 Dihedral : 4.865 56.231 882 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 2.25 % Allowed : 28.98 % Favored : 68.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: -0.03 (0.29), residues: 820 helix: 0.49 (0.20), residues: 682 sheet: None (None), residues: 0 loop : -2.21 (0.49), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 415 TYR 0.011 0.001 TYR C 24 PHE 0.011 0.001 PHE C 340 TRP 0.009 0.001 TRP C 107 HIS 0.001 0.001 HIS A 366 Details of bonding type rmsd covalent geometry : bond 0.00265 ( 6502) covalent geometry : angle 0.52809 ( 8846) hydrogen bonds : bond 0.03128 ( 367) hydrogen bonds : angle 3.99181 ( 1098) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1640 Ramachandran restraints generated. 820 Oldfield, 0 Emsley, 820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1640 Ramachandran restraints generated. 820 Oldfield, 0 Emsley, 820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 86 time to evaluate : 0.201 Fit side-chains REVERT: A 17 MET cc_start: 0.8286 (mtm) cc_final: 0.7898 (mtt) REVERT: A 107 TRP cc_start: 0.8984 (OUTLIER) cc_final: 0.7291 (m-90) REVERT: A 143 THR cc_start: 0.7681 (OUTLIER) cc_final: 0.7450 (m) REVERT: A 300 ARG cc_start: 0.6139 (OUTLIER) cc_final: 0.4811 (mtp180) REVERT: A 420 LYS cc_start: 0.7788 (OUTLIER) cc_final: 0.6730 (mptt) REVERT: C 10 ARG cc_start: 0.6786 (ttp80) cc_final: 0.6422 (ttm110) REVERT: C 254 GLU cc_start: 0.8009 (mm-30) cc_final: 0.7714 (mt-10) REVERT: C 420 LYS cc_start: 0.7715 (OUTLIER) cc_final: 0.6714 (mptt) outliers start: 15 outliers final: 9 residues processed: 100 average time/residue: 0.3735 time to fit residues: 39.9206 Evaluate side-chains 101 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 87 time to evaluate : 0.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 TRP Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 164 SER Chi-restraints excluded: chain A residue 215 SER Chi-restraints excluded: chain A residue 300 ARG Chi-restraints excluded: chain A residue 326 SER Chi-restraints excluded: chain A residue 407 SER Chi-restraints excluded: chain A residue 420 LYS Chi-restraints excluded: chain C residue 6 TYR Chi-restraints excluded: chain C residue 107 TRP Chi-restraints excluded: chain C residue 326 SER Chi-restraints excluded: chain C residue 329 LEU Chi-restraints excluded: chain C residue 420 LYS Chi-restraints excluded: chain C residue 424 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 50 optimal weight: 3.9990 chunk 13 optimal weight: 3.9990 chunk 2 optimal weight: 2.9990 chunk 80 optimal weight: 0.9980 chunk 18 optimal weight: 0.0070 chunk 0 optimal weight: 10.0000 chunk 23 optimal weight: 2.9990 chunk 19 optimal weight: 5.9990 chunk 60 optimal weight: 0.8980 chunk 66 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 overall best weight: 1.5802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 374 ASN C 248 GLN C 354 ASN C 374 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.151793 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.108630 restraints weight = 7023.066| |-----------------------------------------------------------------------------| r_work (start): 0.3028 rms_B_bonded: 1.81 r_work: 0.2892 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2759 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.2759 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 moved from start: 0.2393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 6502 Z= 0.168 Angle : 0.564 10.056 8846 Z= 0.283 Chirality : 0.042 0.232 998 Planarity : 0.005 0.049 1084 Dihedral : 5.041 57.483 882 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 2.40 % Allowed : 28.68 % Favored : 68.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: -0.24 (0.29), residues: 820 helix: 0.34 (0.20), residues: 680 sheet: None (None), residues: 0 loop : -2.20 (0.49), residues: 140 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 197 TYR 0.014 0.001 TYR C 24 PHE 0.014 0.002 PHE C 340 TRP 0.009 0.001 TRP C 107 HIS 0.002 0.001 HIS A 390 Details of bonding type rmsd covalent geometry : bond 0.00402 ( 6502) covalent geometry : angle 0.56430 ( 8846) hydrogen bonds : bond 0.03603 ( 367) hydrogen bonds : angle 4.15062 ( 1098) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1879.51 seconds wall clock time: 32 minutes 43.67 seconds (1963.67 seconds total)