Starting phenix.real_space_refine on Sat Aug 23 13:39:41 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7zlv_14790/08_2025/7zlv_14790.cif Found real_map, /net/cci-nas-00/data/ceres_data/7zlv_14790/08_2025/7zlv_14790.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.22 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7zlv_14790/08_2025/7zlv_14790.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7zlv_14790/08_2025/7zlv_14790.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7zlv_14790/08_2025/7zlv_14790.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7zlv_14790/08_2025/7zlv_14790.map" } resolution = 4.22 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= 0.002 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: 4 Type Number sf(0) Gaussians S 39 5.16 5 C 7794 2.51 5 N 2040 2.21 5 O 2361 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 12234 Number of models: 1 Model: "" Number of chains: 1 Chain: "i" Number of atoms: 4078 Number of conformers: 1 Conformer: "" Number of residues, atoms: 527, 4078 Classifications: {'peptide': 527} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 21, 'TRANS': 505} Chain breaks: 1 Restraints were copied for chains: h, j Time building chain proxies: 3.45, per 1000 atoms: 0.28 Number of scatterers: 12234 At special positions: 0 Unit cell: (78.358, 74.305, 274.253, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 39 16.00 O 2361 8.00 N 2040 7.00 C 7794 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: 1.15 Conformation dependent library (CDL) restraints added in 568.3 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 3138 Ramachandran restraints generated. 1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2910 Finding SS restraints... Secondary structure from input PDB file: 6 helices and 39 sheets defined 2.8% alpha, 34.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.49 Creating SS restraints... Processing helix chain 'i' and resid 83 through 90 Processing helix chain 'i' and resid 258 through 264 removed outlier: 3.863A pdb=" N VAL i 262 " --> pdb=" O SER i 258 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N ARG i 263 " --> pdb=" O ALA i 259 " (cutoff:3.500A) Processing helix chain 'h' and resid 83 through 90 Processing helix chain 'h' and resid 258 through 264 removed outlier: 3.863A pdb=" N VAL h 262 " --> pdb=" O SER h 258 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N ARG h 263 " --> pdb=" O ALA h 259 " (cutoff:3.500A) Processing helix chain 'j' and resid 83 through 90 Processing helix chain 'j' and resid 258 through 264 removed outlier: 3.863A pdb=" N VAL j 262 " --> pdb=" O SER j 258 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N ARG j 263 " --> pdb=" O ALA j 259 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'i' and resid 12 through 17 Processing sheet with id=AA2, first strand: chain 'i' and resid 47 through 53 removed outlier: 7.175A pdb=" N TYR i 78 " --> pdb=" O ILE i 35 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'i' and resid 47 through 53 removed outlier: 3.904A pdb=" N GLN i 99 " --> pdb=" O VAL i 73 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'i' and resid 109 through 115 removed outlier: 3.669A pdb=" N VAL i 128 " --> pdb=" O PHE i 167 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N PHE i 167 " --> pdb=" O VAL i 128 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'i' and resid 154 through 159 removed outlier: 7.272A pdb=" N ILE i 141 " --> pdb=" O TYR i 156 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N VAL i 158 " --> pdb=" O CYS i 139 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N CYS i 139 " --> pdb=" O VAL i 158 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N THR i 140 " --> pdb=" O SER i 180 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'i' and resid 154 through 159 removed outlier: 7.272A pdb=" N ILE i 141 " --> pdb=" O TYR i 156 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N VAL i 158 " --> pdb=" O CYS i 139 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N CYS i 139 " --> pdb=" O VAL i 158 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N THR i 140 " --> pdb=" O SER i 180 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N TYR i 175 " --> pdb=" O PHE i 203 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N PHE i 203 " --> pdb=" O TYR i 175 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'i' and resid 182 through 184 Processing sheet with id=AA8, first strand: chain 'i' and resid 216 through 223 removed outlier: 4.366A pdb=" N ASN i 217 " --> pdb=" O ASP i 239 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ASP i 239 " --> pdb=" O ASN i 217 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LYS i 221 " --> pdb=" O ARG i 235 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'i' and resid 270 through 274 removed outlier: 4.103A pdb=" N PHE i 251 " --> pdb=" O VAL i 274 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'i' and resid 270 through 274 removed outlier: 4.103A pdb=" N PHE i 251 " --> pdb=" O VAL i 274 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'i' and resid 333 through 335 Processing sheet with id=AB3, first strand: chain 'i' and resid 413 through 415 removed outlier: 4.025A pdb=" N GLY i 431 " --> pdb=" O LYS i 440 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N LYS i 440 " --> pdb=" O GLY i 431 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'i' and resid 676 through 679 removed outlier: 3.828A pdb=" N HIS i 686 " --> pdb=" O LYS i 677 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'h' and resid 12 through 17 Processing sheet with id=AB6, first strand: chain 'h' and resid 47 through 53 removed outlier: 7.175A pdb=" N TYR h 78 " --> pdb=" O ILE h 35 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'h' and resid 47 through 53 removed outlier: 3.904A pdb=" N GLN h 99 " --> pdb=" O VAL h 73 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'h' and resid 109 through 115 removed outlier: 3.670A pdb=" N VAL h 128 " --> pdb=" O PHE h 167 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N PHE h 167 " --> pdb=" O VAL h 128 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'h' and resid 154 through 159 removed outlier: 7.273A pdb=" N ILE h 141 " --> pdb=" O TYR h 156 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N VAL h 158 " --> pdb=" O CYS h 139 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N CYS h 139 " --> pdb=" O VAL h 158 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N THR h 140 " --> pdb=" O SER h 180 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'h' and resid 154 through 159 removed outlier: 7.273A pdb=" N ILE h 141 " --> pdb=" O TYR h 156 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N VAL h 158 " --> pdb=" O CYS h 139 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N CYS h 139 " --> pdb=" O VAL h 158 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N THR h 140 " --> pdb=" O SER h 180 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N TYR h 175 " --> pdb=" O PHE h 203 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N PHE h 203 " --> pdb=" O TYR h 175 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'h' and resid 182 through 184 Processing sheet with id=AC3, first strand: chain 'h' and resid 216 through 223 removed outlier: 4.366A pdb=" N ASN h 217 " --> pdb=" O ASP h 239 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ASP h 239 " --> pdb=" O ASN h 217 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LYS h 221 " --> pdb=" O ARG h 235 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'h' and resid 270 through 274 removed outlier: 4.103A pdb=" N PHE h 251 " --> pdb=" O VAL h 274 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'h' and resid 270 through 274 removed outlier: 4.103A pdb=" N PHE h 251 " --> pdb=" O VAL h 274 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'h' and resid 333 through 335 Processing sheet with id=AC7, first strand: chain 'h' and resid 413 through 415 removed outlier: 4.025A pdb=" N GLY h 431 " --> pdb=" O LYS h 440 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N LYS h 440 " --> pdb=" O GLY h 431 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'h' and resid 676 through 679 removed outlier: 3.829A pdb=" N HIS h 686 " --> pdb=" O LYS h 677 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'j' and resid 12 through 17 Processing sheet with id=AD1, first strand: chain 'j' and resid 47 through 53 removed outlier: 7.175A pdb=" N TYR j 78 " --> pdb=" O ILE j 35 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'j' and resid 47 through 53 removed outlier: 3.903A pdb=" N GLN j 99 " --> pdb=" O VAL j 73 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'j' and resid 109 through 115 removed outlier: 3.670A pdb=" N VAL j 128 " --> pdb=" O PHE j 167 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N PHE j 167 " --> pdb=" O VAL j 128 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'j' and resid 154 through 159 removed outlier: 7.273A pdb=" N ILE j 141 " --> pdb=" O TYR j 156 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N VAL j 158 " --> pdb=" O CYS j 139 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N CYS j 139 " --> pdb=" O VAL j 158 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N THR j 140 " --> pdb=" O SER j 180 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'j' and resid 154 through 159 removed outlier: 7.273A pdb=" N ILE j 141 " --> pdb=" O TYR j 156 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N VAL j 158 " --> pdb=" O CYS j 139 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N CYS j 139 " --> pdb=" O VAL j 158 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N THR j 140 " --> pdb=" O SER j 180 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N TYR j 175 " --> pdb=" O PHE j 203 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N PHE j 203 " --> pdb=" O TYR j 175 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'j' and resid 182 through 184 Processing sheet with id=AD7, first strand: chain 'j' and resid 216 through 223 removed outlier: 4.366A pdb=" N ASN j 217 " --> pdb=" O ASP j 239 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ASP j 239 " --> pdb=" O ASN j 217 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LYS j 221 " --> pdb=" O ARG j 235 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'j' and resid 270 through 274 removed outlier: 4.103A pdb=" N PHE j 251 " --> pdb=" O VAL j 274 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'j' and resid 270 through 274 removed outlier: 4.103A pdb=" N PHE j 251 " --> pdb=" O VAL j 274 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'j' and resid 333 through 335 Processing sheet with id=AE2, first strand: chain 'j' and resid 413 through 415 removed outlier: 4.025A pdb=" N GLY j 431 " --> pdb=" O LYS j 440 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N LYS j 440 " --> pdb=" O GLY j 431 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'j' and resid 676 through 679 removed outlier: 3.828A pdb=" N HIS j 686 " --> pdb=" O LYS j 677 " (cutoff:3.500A) 351 hydrogen bonds defined for protein. 945 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.02 Time building geometry restraints manager: 1.50 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3966 1.34 - 1.46: 2810 1.46 - 1.58: 5647 1.58 - 1.69: 0 1.69 - 1.81: 72 Bond restraints: 12495 Sorted by residual: bond pdb=" N MET j 1 " pdb=" CA MET j 1 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.88e+00 bond pdb=" N MET h 1 " pdb=" CA MET h 1 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.86e+00 bond pdb=" N MET i 1 " pdb=" CA MET i 1 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.82e+00 bond pdb=" N VAL i 639 " pdb=" CA VAL i 639 " ideal model delta sigma weight residual 1.459 1.472 -0.014 1.22e-02 6.72e+03 1.25e+00 bond pdb=" N VAL j 639 " pdb=" CA VAL j 639 " ideal model delta sigma weight residual 1.459 1.472 -0.013 1.22e-02 6.72e+03 1.22e+00 ... (remaining 12490 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.93: 15455 0.93 - 1.86: 1217 1.86 - 2.79: 237 2.79 - 3.72: 71 3.72 - 4.65: 21 Bond angle restraints: 17001 Sorted by residual: angle pdb=" N PRO h 439 " pdb=" CA PRO h 439 " pdb=" C PRO h 439 " ideal model delta sigma weight residual 111.03 114.57 -3.54 1.54e+00 4.22e-01 5.28e+00 angle pdb=" N PRO i 439 " pdb=" CA PRO i 439 " pdb=" C PRO i 439 " ideal model delta sigma weight residual 111.03 114.54 -3.51 1.54e+00 4.22e-01 5.20e+00 angle pdb=" N PRO j 439 " pdb=" CA PRO j 439 " pdb=" C PRO j 439 " ideal model delta sigma weight residual 111.03 114.53 -3.50 1.54e+00 4.22e-01 5.18e+00 angle pdb=" N ASN j 682 " pdb=" CA ASN j 682 " pdb=" C ASN j 682 " ideal model delta sigma weight residual 110.61 113.26 -2.65 1.25e+00 6.40e-01 4.48e+00 angle pdb=" N ALA i 641 " pdb=" CA ALA i 641 " pdb=" C ALA i 641 " ideal model delta sigma weight residual 107.73 111.11 -3.38 1.61e+00 3.86e-01 4.41e+00 ... (remaining 16996 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.55: 6690 17.55 - 35.10: 594 35.10 - 52.66: 87 52.66 - 70.21: 6 70.21 - 87.76: 12 Dihedral angle restraints: 7389 sinusoidal: 2829 harmonic: 4560 Sorted by residual: dihedral pdb=" CA THR h 321 " pdb=" C THR h 321 " pdb=" N PRO h 322 " pdb=" CA PRO h 322 " ideal model delta harmonic sigma weight residual 180.00 155.25 24.75 0 5.00e+00 4.00e-02 2.45e+01 dihedral pdb=" CA THR i 321 " pdb=" C THR i 321 " pdb=" N PRO i 322 " pdb=" CA PRO i 322 " ideal model delta harmonic sigma weight residual 180.00 155.29 24.71 0 5.00e+00 4.00e-02 2.44e+01 dihedral pdb=" CA THR j 321 " pdb=" C THR j 321 " pdb=" N PRO j 322 " pdb=" CA PRO j 322 " ideal model delta harmonic sigma weight residual 180.00 155.30 24.70 0 5.00e+00 4.00e-02 2.44e+01 ... (remaining 7386 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 1157 0.032 - 0.065: 444 0.065 - 0.097: 148 0.097 - 0.130: 148 0.130 - 0.162: 29 Chirality restraints: 1926 Sorted by residual: chirality pdb=" CA ILE j 414 " pdb=" N ILE j 414 " pdb=" C ILE j 414 " pdb=" CB ILE j 414 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.16 2.00e-01 2.50e+01 6.55e-01 chirality pdb=" CA ILE i 414 " pdb=" N ILE i 414 " pdb=" C ILE i 414 " pdb=" CB ILE i 414 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.48e-01 chirality pdb=" CA ILE h 414 " pdb=" N ILE h 414 " pdb=" C ILE h 414 " pdb=" CB ILE h 414 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.48e-01 ... (remaining 1923 not shown) Planarity restraints: 2184 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR h 321 " 0.050 5.00e-02 4.00e+02 7.54e-02 9.08e+00 pdb=" N PRO h 322 " -0.130 5.00e-02 4.00e+02 pdb=" CA PRO h 322 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO h 322 " 0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR i 321 " -0.050 5.00e-02 4.00e+02 7.53e-02 9.08e+00 pdb=" N PRO i 322 " 0.130 5.00e-02 4.00e+02 pdb=" CA PRO i 322 " -0.039 5.00e-02 4.00e+02 pdb=" CD PRO i 322 " -0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR j 321 " -0.050 5.00e-02 4.00e+02 7.52e-02 9.06e+00 pdb=" N PRO j 322 " 0.130 5.00e-02 4.00e+02 pdb=" CA PRO j 322 " -0.039 5.00e-02 4.00e+02 pdb=" CD PRO j 322 " -0.041 5.00e-02 4.00e+02 ... (remaining 2181 not shown) Histogram of nonbonded interaction distances: 1.81 - 2.43: 118 2.43 - 3.05: 8777 3.05 - 3.67: 18272 3.67 - 4.28: 26892 4.28 - 4.90: 44598 Nonbonded interactions: 98657 Sorted by model distance: nonbonded pdb=" O LEU h 651 " pdb=" NE ARG j 662 " model vdw 1.813 3.120 nonbonded pdb=" NE ARG i 662 " pdb=" O LEU j 651 " model vdw 1.877 3.120 nonbonded pdb=" O LEU i 651 " pdb=" NE ARG h 662 " model vdw 1.905 3.120 nonbonded pdb=" O VAL i 645 " pdb=" O ALA h 641 " model vdw 1.935 3.040 nonbonded pdb=" O VAL h 645 " pdb=" O ALA j 641 " model vdw 1.979 3.040 ... (remaining 98652 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: 0.03 Found NCS groups: ncs_group { reference = chain 'i' selection = chain 'h' selection = chain 'j' } 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=0.00 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: 6.020 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.280 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 12.860 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.020 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:1.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6751 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 12495 Z= 0.135 Angle : 0.596 4.650 17001 Z= 0.338 Chirality : 0.050 0.162 1926 Planarity : 0.006 0.110 2184 Dihedral : 13.596 87.761 4479 Min Nonbonded Distance : 1.813 Molprobity Statistics. All-atom Clashscore : 25.12 Ramachandran Plot: Outliers : 0.19 % Allowed : 10.52 % Favored : 89.29 % Rotamer: Outliers : 0.00 % Allowed : 0.30 % Favored : 99.70 % 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 aren not related in a simple way. whole: -3.64 (0.19), residues: 1569 helix: -1.46 (1.01), residues: 39 sheet: -1.44 (0.26), residues: 381 loop : -3.06 (0.16), residues: 1149 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG h 458 TYR 0.011 0.001 TYR j 71 PHE 0.008 0.001 PHE h 101 TRP 0.008 0.001 TRP j 300 HIS 0.004 0.001 HIS j 630 Details of bonding type rmsd covalent geometry : bond 0.00265 (12495) covalent geometry : angle 0.59571 (17001) hydrogen bonds : bond 0.26352 ( 276) hydrogen bonds : angle 12.55220 ( 945) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3138 Ramachandran restraints generated. 1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3138 Ramachandran restraints generated. 1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 141 time to evaluate : 0.520 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: i 633 MET cc_start: 0.1901 (mmt) cc_final: -0.0124 (mtt) REVERT: i 676 MET cc_start: -0.0860 (pmm) cc_final: -0.1637 (pmm) REVERT: h 433 ASP cc_start: 0.4555 (t0) cc_final: 0.4339 (t0) REVERT: h 633 MET cc_start: 0.1119 (mmt) cc_final: 0.0243 (mtt) REVERT: h 676 MET cc_start: -0.0972 (pmm) cc_final: -0.1362 (pmm) REVERT: j 108 ARG cc_start: 0.6533 (mmp-170) cc_final: 0.6220 (mmm160) REVERT: j 433 ASP cc_start: 0.4134 (t0) cc_final: 0.3834 (t0) outliers start: 0 outliers final: 0 residues processed: 141 average time/residue: 0.0992 time to fit residues: 21.5629 Evaluate side-chains 98 residues out of total 1323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 98 time to evaluate : 0.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 98 optimal weight: 0.7980 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 0.9990 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 6.9990 chunk 149 optimal weight: 5.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** i 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 217 ASN ** i 397 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 397 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.099284 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.081817 restraints weight = 48986.700| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.083334 restraints weight = 30459.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.084313 restraints weight = 20591.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.085119 restraints weight = 15085.375| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.085558 restraints weight = 11766.233| |-----------------------------------------------------------------------------| r_work (final): 0.3591 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3591 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3591 r_free = 0.3591 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3590 r_free = 0.3590 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.3590 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7016 moved from start: 0.1806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 12495 Z= 0.267 Angle : 0.788 8.569 17001 Z= 0.425 Chirality : 0.055 0.179 1926 Planarity : 0.007 0.113 2184 Dihedral : 7.357 40.962 1704 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 19.45 Ramachandran Plot: Outliers : 0.19 % Allowed : 12.11 % Favored : 87.70 % Rotamer: Outliers : 0.08 % Allowed : 11.19 % Favored : 88.74 % 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 aren not related in a simple way. whole: -3.75 (0.18), residues: 1569 helix: -0.75 (1.29), residues: 24 sheet: -1.39 (0.24), residues: 402 loop : -3.21 (0.15), residues: 1143 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG j 249 TYR 0.014 0.002 TYR i 138 PHE 0.027 0.003 PHE i 261 TRP 0.011 0.002 TRP j 429 HIS 0.012 0.003 HIS i 630 Details of bonding type rmsd covalent geometry : bond 0.00591 (12495) covalent geometry : angle 0.78842 (17001) hydrogen bonds : bond 0.04846 ( 276) hydrogen bonds : angle 8.30571 ( 945) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3138 Ramachandran restraints generated. 1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3138 Ramachandran restraints generated. 1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 1323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 117 time to evaluate : 0.484 Fit side-chains REVERT: i 433 ASP cc_start: 0.5785 (t0) cc_final: 0.5491 (t0) REVERT: h 433 ASP cc_start: 0.5793 (t0) cc_final: 0.5591 (t0) REVERT: h 627 MET cc_start: 0.0036 (ptm) cc_final: -0.0298 (ptm) REVERT: j 433 ASP cc_start: 0.5070 (t0) cc_final: 0.4807 (t0) outliers start: 1 outliers final: 0 residues processed: 118 average time/residue: 0.0918 time to fit residues: 17.0235 Evaluate side-chains 87 residues out of total 1323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 87 time to evaluate : 0.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 4 optimal weight: 1.9990 chunk 35 optimal weight: 3.9990 chunk 103 optimal weight: 3.9990 chunk 28 optimal weight: 0.9990 chunk 31 optimal weight: 0.0980 chunk 129 optimal weight: 1.9990 chunk 136 optimal weight: 0.0270 chunk 58 optimal weight: 2.9990 chunk 63 optimal weight: 1.9990 chunk 152 optimal weight: 0.1980 chunk 6 optimal weight: 0.7980 overall best weight: 0.4240 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** i 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 217 ASN ** i 397 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 397 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.104011 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.086045 restraints weight = 46719.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.087697 restraints weight = 28147.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.088845 restraints weight = 18444.038| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 66)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.089578 restraints weight = 13130.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.090014 restraints weight = 10185.408| |-----------------------------------------------------------------------------| r_work (final): 0.3672 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3671 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3671 r_free = 0.3671 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3671 r_free = 0.3671 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.3671 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6869 moved from start: 0.2271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 12495 Z= 0.135 Angle : 0.667 6.704 17001 Z= 0.359 Chirality : 0.052 0.214 1926 Planarity : 0.005 0.066 2184 Dihedral : 6.603 35.247 1704 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 13.16 Ramachandran Plot: Outliers : 0.19 % Allowed : 8.16 % Favored : 91.65 % Rotamer: Outliers : 0.08 % Allowed : 5.29 % Favored : 94.63 % 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 aren not related in a simple way. whole: -3.42 (0.18), residues: 1569 helix: -0.35 (1.22), residues: 24 sheet: -1.54 (0.21), residues: 474 loop : -2.86 (0.16), residues: 1071 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG i 178 TYR 0.010 0.001 TYR j 449 PHE 0.010 0.001 PHE h 401 TRP 0.017 0.001 TRP i 153 HIS 0.004 0.001 HIS i 630 Details of bonding type rmsd covalent geometry : bond 0.00291 (12495) covalent geometry : angle 0.66691 (17001) hydrogen bonds : bond 0.03700 ( 276) hydrogen bonds : angle 7.02114 ( 945) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3138 Ramachandran restraints generated. 1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3138 Ramachandran restraints generated. 1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 139 time to evaluate : 0.489 Fit side-chains REVERT: i 433 ASP cc_start: 0.5603 (t0) cc_final: 0.5322 (t0) REVERT: i 676 MET cc_start: -0.1225 (pmm) cc_final: -0.1610 (pmm) REVERT: h 232 TYR cc_start: 0.6969 (m-80) cc_final: 0.6671 (m-80) REVERT: h 433 ASP cc_start: 0.5216 (t0) cc_final: 0.4880 (t0) REVERT: j 154 VAL cc_start: 0.7371 (m) cc_final: 0.7169 (p) REVERT: j 433 ASP cc_start: 0.4788 (t0) cc_final: 0.4531 (t0) outliers start: 1 outliers final: 0 residues processed: 140 average time/residue: 0.1011 time to fit residues: 21.6530 Evaluate side-chains 88 residues out of total 1323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 88 time to evaluate : 0.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 147 optimal weight: 6.9990 chunk 111 optimal weight: 4.9990 chunk 29 optimal weight: 3.9990 chunk 75 optimal weight: 2.9990 chunk 9 optimal weight: 3.9990 chunk 53 optimal weight: 0.9990 chunk 150 optimal weight: 4.9990 chunk 127 optimal weight: 5.9990 chunk 148 optimal weight: 6.9990 chunk 112 optimal weight: 0.6980 chunk 146 optimal weight: 0.6980 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** i 352 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 397 ASN ** 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 = 0.3890 r_free = 0.3890 target = 0.100449 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.082446 restraints weight = 47464.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.084035 restraints weight = 28526.969| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.085110 restraints weight = 18941.672| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.085868 restraints weight = 13648.689| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.086317 restraints weight = 10513.686| |-----------------------------------------------------------------------------| r_work (final): 0.3601 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3601 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3601 r_free = 0.3601 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3601 r_free = 0.3601 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.3601 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6965 moved from start: 0.2511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 12495 Z= 0.238 Angle : 0.737 7.589 17001 Z= 0.397 Chirality : 0.053 0.223 1926 Planarity : 0.006 0.120 2184 Dihedral : 7.035 44.302 1704 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 18.95 Ramachandran Plot: Outliers : 0.19 % Allowed : 12.43 % Favored : 87.38 % Rotamer: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % 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 aren not related in a simple way. whole: -3.55 (0.18), residues: 1569 helix: -0.64 (1.27), residues: 24 sheet: -1.63 (0.23), residues: 438 loop : -2.93 (0.15), residues: 1107 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG i 249 TYR 0.015 0.002 TYR i 138 PHE 0.025 0.003 PHE j 261 TRP 0.021 0.002 TRP i 266 HIS 0.011 0.003 HIS i 630 Details of bonding type rmsd covalent geometry : bond 0.00533 (12495) covalent geometry : angle 0.73743 (17001) hydrogen bonds : bond 0.03604 ( 276) hydrogen bonds : angle 7.14903 ( 945) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3138 Ramachandran restraints generated. 1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3138 Ramachandran restraints generated. 1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 1323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 119 time to evaluate : 0.573 Fit side-chains REVERT: i 676 MET cc_start: -0.1324 (pmm) cc_final: -0.1688 (pmm) REVERT: h 257 ASP cc_start: 0.6094 (t0) cc_final: 0.5662 (t70) REVERT: h 433 ASP cc_start: 0.5075 (t0) cc_final: 0.4807 (t0) outliers start: 0 outliers final: 0 residues processed: 119 average time/residue: 0.1082 time to fit residues: 19.8094 Evaluate side-chains 84 residues out of total 1323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 84 time to evaluate : 0.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 129 optimal weight: 2.9990 chunk 100 optimal weight: 0.6980 chunk 42 optimal weight: 6.9990 chunk 50 optimal weight: 8.9990 chunk 86 optimal weight: 0.7980 chunk 111 optimal weight: 4.9990 chunk 137 optimal weight: 2.9990 chunk 65 optimal weight: 3.9990 chunk 27 optimal weight: 2.9990 chunk 118 optimal weight: 1.9990 chunk 7 optimal weight: 3.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** i 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 352 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 397 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 409 GLN ** j 397 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.099982 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.082278 restraints weight = 46955.149| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.083830 restraints weight = 28495.756| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.084915 restraints weight = 18958.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.085617 restraints weight = 13588.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.086042 restraints weight = 10472.744| |-----------------------------------------------------------------------------| r_work (final): 0.3595 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3595 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3595 r_free = 0.3595 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3595 r_free = 0.3595 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.3595 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6988 moved from start: 0.2821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 12495 Z= 0.235 Angle : 0.746 8.533 17001 Z= 0.398 Chirality : 0.054 0.189 1926 Planarity : 0.006 0.100 2184 Dihedral : 7.248 50.475 1704 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 20.89 Ramachandran Plot: Outliers : 0.19 % Allowed : 11.60 % Favored : 88.21 % Rotamer: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % 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 aren not related in a simple way. whole: -3.62 (0.19), residues: 1569 helix: -0.71 (1.25), residues: 24 sheet: -1.68 (0.22), residues: 507 loop : -3.02 (0.16), residues: 1038 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG j 249 TYR 0.018 0.002 TYR h 660 PHE 0.024 0.003 PHE j 261 TRP 0.040 0.002 TRP h 429 HIS 0.011 0.003 HIS h 630 Details of bonding type rmsd covalent geometry : bond 0.00528 (12495) covalent geometry : angle 0.74593 (17001) hydrogen bonds : bond 0.03531 ( 276) hydrogen bonds : angle 7.04607 ( 945) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3138 Ramachandran restraints generated. 1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3138 Ramachandran restraints generated. 1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 1323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 118 time to evaluate : 0.465 Fit side-chains revert: symmetry clash REVERT: i 433 ASP cc_start: 0.5813 (t0) cc_final: 0.5484 (t0) REVERT: i 676 MET cc_start: -0.1420 (pmm) cc_final: -0.1668 (pmm) REVERT: h 257 ASP cc_start: 0.6043 (t0) cc_final: 0.5813 (t0) outliers start: 0 outliers final: 0 residues processed: 118 average time/residue: 0.1052 time to fit residues: 19.0394 Evaluate side-chains 76 residues out of total 1323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 76 time to evaluate : 0.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 135 optimal weight: 2.9990 chunk 12 optimal weight: 0.9980 chunk 109 optimal weight: 2.9990 chunk 74 optimal weight: 0.7980 chunk 53 optimal weight: 0.9990 chunk 56 optimal weight: 0.8980 chunk 47 optimal weight: 8.9990 chunk 55 optimal weight: 0.8980 chunk 115 optimal weight: 0.7980 chunk 36 optimal weight: 1.9990 chunk 43 optimal weight: 8.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** i 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 352 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 397 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 630 HIS ** h 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 397 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.102320 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.084257 restraints weight = 46584.519| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.085856 restraints weight = 28186.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.086867 restraints weight = 18669.148| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.087709 restraints weight = 13579.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 56)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.088351 restraints weight = 10540.930| |-----------------------------------------------------------------------------| r_work (final): 0.3641 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3641 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3641 r_free = 0.3641 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3641 r_free = 0.3641 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.3641 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6918 moved from start: 0.3008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 12495 Z= 0.150 Angle : 0.673 7.003 17001 Z= 0.360 Chirality : 0.053 0.292 1926 Planarity : 0.005 0.075 2184 Dihedral : 6.883 47.948 1704 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 18.17 Ramachandran Plot: Outliers : 0.19 % Allowed : 10.26 % Favored : 89.55 % Rotamer: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % 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 aren not related in a simple way. whole: -3.43 (0.19), residues: 1569 helix: -0.15 (1.27), residues: 24 sheet: -1.48 (0.24), residues: 444 loop : -2.88 (0.16), residues: 1101 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG i 458 TYR 0.019 0.002 TYR j 449 PHE 0.015 0.002 PHE j 378 TRP 0.040 0.002 TRP h 429 HIS 0.008 0.002 HIS h 630 Details of bonding type rmsd covalent geometry : bond 0.00329 (12495) covalent geometry : angle 0.67343 (17001) hydrogen bonds : bond 0.03144 ( 276) hydrogen bonds : angle 6.44232 ( 945) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3138 Ramachandran restraints generated. 1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3138 Ramachandran restraints generated. 1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 1323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 124 time to evaluate : 0.339 Fit side-chains revert: symmetry clash REVERT: i 433 ASP cc_start: 0.5815 (t0) cc_final: 0.5536 (t0) REVERT: i 676 MET cc_start: -0.1645 (pmm) cc_final: -0.2154 (pmm) REVERT: h 108 ARG cc_start: 0.6510 (mmp-170) cc_final: 0.6135 (mmm160) REVERT: h 429 TRP cc_start: 0.3313 (t60) cc_final: 0.2180 (t60) REVERT: j 429 TRP cc_start: 0.2576 (t60) cc_final: 0.2263 (t60) outliers start: 0 outliers final: 0 residues processed: 124 average time/residue: 0.1039 time to fit residues: 19.5323 Evaluate side-chains 84 residues out of total 1323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 84 time to evaluate : 0.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 151 optimal weight: 0.4980 chunk 127 optimal weight: 2.9990 chunk 48 optimal weight: 7.9990 chunk 86 optimal weight: 0.0980 chunk 32 optimal weight: 5.9990 chunk 77 optimal weight: 4.9990 chunk 31 optimal weight: 6.9990 chunk 71 optimal weight: 4.9990 chunk 10 optimal weight: 0.5980 chunk 6 optimal weight: 1.9990 chunk 103 optimal weight: 5.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** i 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 397 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 630 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 397 ASN ** 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 = 0.3909 r_free = 0.3909 target = 0.101594 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.083332 restraints weight = 47341.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.084942 restraints weight = 28677.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.086044 restraints weight = 19237.998| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.086812 restraints weight = 13869.969| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.087317 restraints weight = 10777.966| |-----------------------------------------------------------------------------| r_work (final): 0.3620 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3620 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3620 r_free = 0.3620 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3620 r_free = 0.3620 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.3620 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6934 moved from start: 0.3192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 12495 Z= 0.175 Angle : 0.686 9.037 17001 Z= 0.365 Chirality : 0.053 0.205 1926 Planarity : 0.005 0.077 2184 Dihedral : 6.828 48.314 1704 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 19.04 Ramachandran Plot: Outliers : 0.19 % Allowed : 10.07 % Favored : 89.74 % Rotamer: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % 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 aren not related in a simple way. whole: -3.51 (0.19), residues: 1569 helix: -0.21 (1.29), residues: 24 sheet: -1.69 (0.23), residues: 474 loop : -2.88 (0.16), residues: 1071 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG j 458 TYR 0.015 0.002 TYR j 138 PHE 0.023 0.002 PHE i 378 TRP 0.045 0.002 TRP h 429 HIS 0.003 0.001 HIS h 630 Details of bonding type rmsd covalent geometry : bond 0.00391 (12495) covalent geometry : angle 0.68562 (17001) hydrogen bonds : bond 0.03150 ( 276) hydrogen bonds : angle 6.37989 ( 945) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3138 Ramachandran restraints generated. 1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3138 Ramachandran restraints generated. 1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 1323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 123 time to evaluate : 0.471 Fit side-chains revert: symmetry clash REVERT: i 108 ARG cc_start: 0.6208 (mmp-170) cc_final: 0.5947 (mmm160) REVERT: i 421 TRP cc_start: 0.6624 (t60) cc_final: 0.6174 (t60) REVERT: i 433 ASP cc_start: 0.5899 (t0) cc_final: 0.5586 (t0) REVERT: i 627 MET cc_start: 0.1642 (mtp) cc_final: 0.1210 (mtp) REVERT: i 676 MET cc_start: -0.1681 (pmm) cc_final: -0.2049 (pmm) REVERT: h 429 TRP cc_start: 0.3640 (t60) cc_final: 0.2411 (t60) REVERT: j 429 TRP cc_start: 0.3314 (t60) cc_final: 0.3085 (t60) outliers start: 0 outliers final: 0 residues processed: 123 average time/residue: 0.0984 time to fit residues: 18.6690 Evaluate side-chains 81 residues out of total 1323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 81 time to evaluate : 0.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 40 optimal weight: 2.9990 chunk 92 optimal weight: 0.5980 chunk 17 optimal weight: 5.9990 chunk 128 optimal weight: 0.0670 chunk 41 optimal weight: 0.6980 chunk 8 optimal weight: 3.9990 chunk 148 optimal weight: 2.9990 chunk 2 optimal weight: 0.7980 chunk 110 optimal weight: 0.0020 chunk 0 optimal weight: 2.9990 chunk 45 optimal weight: 0.5980 overall best weight: 0.3926 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** i 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 397 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 630 HIS j 4 ASN ** j 397 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 630 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.104480 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.086040 restraints weight = 46832.017| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.087707 restraints weight = 28185.663| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.088857 restraints weight = 18683.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 20)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.089561 restraints weight = 13420.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 58)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.090280 restraints weight = 10419.390| |-----------------------------------------------------------------------------| r_work (final): 0.3679 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3678 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3678 r_free = 0.3678 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3678 r_free = 0.3678 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.3678 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6831 moved from start: 0.3441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 12495 Z= 0.118 Angle : 0.627 5.962 17001 Z= 0.336 Chirality : 0.051 0.171 1926 Planarity : 0.005 0.069 2184 Dihedral : 6.391 43.446 1704 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 16.36 Ramachandran Plot: Outliers : 0.19 % Allowed : 8.86 % Favored : 90.95 % Rotamer: Outliers : 0.08 % Allowed : 0.45 % Favored : 99.47 % 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 aren not related in a simple way. whole: -3.29 (0.19), residues: 1569 helix: 0.58 (1.29), residues: 24 sheet: -1.49 (0.23), residues: 474 loop : -2.77 (0.16), residues: 1071 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG j 458 TYR 0.014 0.001 TYR j 449 PHE 0.010 0.001 PHE j 378 TRP 0.041 0.002 TRP h 429 HIS 0.002 0.001 HIS h 291 Details of bonding type rmsd covalent geometry : bond 0.00261 (12495) covalent geometry : angle 0.62681 (17001) hydrogen bonds : bond 0.02997 ( 276) hydrogen bonds : angle 5.86053 ( 945) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3138 Ramachandran restraints generated. 1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3138 Ramachandran restraints generated. 1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 1323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 130 time to evaluate : 0.483 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: i 421 TRP cc_start: 0.6537 (t60) cc_final: 0.6131 (t60) REVERT: i 433 ASP cc_start: 0.5638 (t0) cc_final: 0.5332 (t0) REVERT: h 103 MET cc_start: 0.4074 (ttp) cc_final: 0.3765 (tmm) REVERT: j 421 TRP cc_start: 0.6726 (t60) cc_final: 0.5731 (t60) outliers start: 1 outliers final: 0 residues processed: 131 average time/residue: 0.0934 time to fit residues: 18.5708 Evaluate side-chains 92 residues out of total 1323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 92 time to evaluate : 0.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 65 optimal weight: 1.9990 chunk 72 optimal weight: 2.9990 chunk 153 optimal weight: 10.0000 chunk 34 optimal weight: 3.9990 chunk 147 optimal weight: 3.9990 chunk 64 optimal weight: 0.3980 chunk 51 optimal weight: 1.9990 chunk 69 optimal weight: 3.9990 chunk 54 optimal weight: 3.9990 chunk 105 optimal weight: 5.9990 chunk 128 optimal weight: 0.0170 overall best weight: 1.4824 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** i 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 630 HIS ** 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 = 0.3917 r_free = 0.3917 target = 0.101971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.083429 restraints weight = 47429.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.085052 restraints weight = 28665.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 56)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.086164 restraints weight = 18962.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.086855 restraints weight = 13673.389| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.087400 restraints weight = 10668.277| |-----------------------------------------------------------------------------| r_work (final): 0.3624 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3621 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3621 r_free = 0.3621 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3621 r_free = 0.3621 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.3621 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6954 moved from start: 0.3476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 12495 Z= 0.189 Angle : 0.686 8.296 17001 Z= 0.364 Chirality : 0.052 0.184 1926 Planarity : 0.005 0.069 2184 Dihedral : 6.666 46.911 1704 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 19.49 Ramachandran Plot: Outliers : 0.19 % Allowed : 10.52 % Favored : 89.29 % Rotamer: Outliers : 0.00 % Allowed : 0.23 % Favored : 99.77 % 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 aren not related in a simple way. whole: -3.53 (0.19), residues: 1569 helix: -0.04 (1.29), residues: 24 sheet: -1.80 (0.22), residues: 525 loop : -2.87 (0.16), residues: 1020 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG j 458 TYR 0.017 0.002 TYR j 138 PHE 0.020 0.002 PHE h 261 TRP 0.070 0.003 TRP i 429 HIS 0.002 0.001 HIS h 291 Details of bonding type rmsd covalent geometry : bond 0.00425 (12495) covalent geometry : angle 0.68555 (17001) hydrogen bonds : bond 0.03178 ( 276) hydrogen bonds : angle 6.11353 ( 945) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3138 Ramachandran restraints generated. 1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3138 Ramachandran restraints generated. 1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 1323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 121 time to evaluate : 0.506 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: i 421 TRP cc_start: 0.6656 (t60) cc_final: 0.6003 (t60) REVERT: i 676 MET cc_start: -0.1834 (pmm) cc_final: -0.2101 (pmm) REVERT: h 233 ASP cc_start: 0.7178 (t0) cc_final: 0.6960 (t0) REVERT: h 429 TRP cc_start: 0.3486 (t60) cc_final: 0.2635 (t60) REVERT: j 108 ARG cc_start: 0.6569 (mmp-170) cc_final: 0.6311 (mmp-170) REVERT: j 421 TRP cc_start: 0.6748 (t60) cc_final: 0.6028 (t60) REVERT: j 633 MET cc_start: 0.1572 (mmt) cc_final: 0.0217 (mtp) outliers start: 0 outliers final: 0 residues processed: 121 average time/residue: 0.0916 time to fit residues: 17.0729 Evaluate side-chains 81 residues out of total 1323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 81 time to evaluate : 0.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 134 optimal weight: 0.5980 chunk 108 optimal weight: 0.7980 chunk 47 optimal weight: 10.0000 chunk 20 optimal weight: 0.9980 chunk 103 optimal weight: 9.9990 chunk 28 optimal weight: 0.9990 chunk 41 optimal weight: 0.7980 chunk 105 optimal weight: 3.9990 chunk 23 optimal weight: 0.9990 chunk 5 optimal weight: 4.9990 chunk 65 optimal weight: 4.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** i 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 397 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 146 ASN ** 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 = 0.3939 r_free = 0.3939 target = 0.103225 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.084697 restraints weight = 47600.289| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.086365 restraints weight = 28743.479| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.087388 restraints weight = 18979.461| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.088292 restraints weight = 13778.780| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.088763 restraints weight = 10542.422| |-----------------------------------------------------------------------------| r_work (final): 0.3650 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3650 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3650 r_free = 0.3650 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3650 r_free = 0.3650 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.3650 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6910 moved from start: 0.3588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 12495 Z= 0.137 Angle : 0.643 7.470 17001 Z= 0.342 Chirality : 0.051 0.174 1926 Planarity : 0.005 0.062 2184 Dihedral : 6.422 45.527 1704 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 18.30 Ramachandran Plot: Outliers : 0.19 % Allowed : 9.50 % Favored : 90.31 % Rotamer: Outliers : 0.00 % Allowed : 0.68 % Favored : 99.32 % 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 aren not related in a simple way. whole: -3.34 (0.19), residues: 1569 helix: 0.37 (1.29), residues: 24 sheet: -1.54 (0.23), residues: 483 loop : -2.79 (0.16), residues: 1062 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG j 662 TYR 0.016 0.002 TYR j 138 PHE 0.014 0.002 PHE i 401 TRP 0.058 0.002 TRP j 429 HIS 0.003 0.001 HIS j 291 Details of bonding type rmsd covalent geometry : bond 0.00305 (12495) covalent geometry : angle 0.64292 (17001) hydrogen bonds : bond 0.03008 ( 276) hydrogen bonds : angle 5.92058 ( 945) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3138 Ramachandran restraints generated. 1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3138 Ramachandran restraints generated. 1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 128 time to evaluate : 0.490 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: i 368 LEU cc_start: 0.7724 (mp) cc_final: 0.7118 (pp) REVERT: i 676 MET cc_start: -0.1879 (pmm) cc_final: -0.2160 (pmm) REVERT: h 429 TRP cc_start: 0.3414 (t60) cc_final: 0.1710 (t60) REVERT: h 627 MET cc_start: 0.1772 (mtp) cc_final: 0.1531 (mtp) REVERT: j 108 ARG cc_start: 0.6686 (mmp-170) cc_final: 0.6298 (mmm160) REVERT: j 421 TRP cc_start: 0.6667 (t60) cc_final: 0.6122 (t60) REVERT: j 429 TRP cc_start: 0.2846 (t60) cc_final: 0.2056 (t60) REVERT: j 633 MET cc_start: 0.1678 (mmt) cc_final: 0.0553 (mtp) outliers start: 0 outliers final: 0 residues processed: 128 average time/residue: 0.1070 time to fit residues: 20.5678 Evaluate side-chains 92 residues out of total 1323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 92 time to evaluate : 0.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 57 optimal weight: 1.9990 chunk 70 optimal weight: 0.0470 chunk 155 optimal weight: 7.9990 chunk 65 optimal weight: 2.9990 chunk 45 optimal weight: 3.9990 chunk 9 optimal weight: 3.9990 chunk 81 optimal weight: 0.9980 chunk 97 optimal weight: 2.9990 chunk 40 optimal weight: 3.9990 chunk 32 optimal weight: 0.0570 chunk 91 optimal weight: 3.9990 overall best weight: 1.2200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** i 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 630 HIS ** 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 = 0.3929 r_free = 0.3929 target = 0.102505 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.083939 restraints weight = 47686.455| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.085588 restraints weight = 28927.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.086714 restraints weight = 19217.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.087470 restraints weight = 13800.607| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.088002 restraints weight = 10644.267| |-----------------------------------------------------------------------------| r_work (final): 0.3636 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3636 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3636 r_free = 0.3636 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3636 r_free = 0.3636 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.3636 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6933 moved from start: 0.3679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 12495 Z= 0.165 Angle : 0.666 8.619 17001 Z= 0.353 Chirality : 0.051 0.177 1926 Planarity : 0.005 0.065 2184 Dihedral : 6.526 46.780 1704 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 19.00 Ramachandran Plot: Outliers : 0.19 % Allowed : 10.33 % Favored : 89.48 % Rotamer: Outliers : 0.00 % Allowed : 0.45 % Favored : 99.55 % 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 aren not related in a simple way. whole: -3.44 (0.19), residues: 1569 helix: 0.15 (1.30), residues: 24 sheet: -1.58 (0.22), residues: 552 loop : -2.93 (0.17), residues: 993 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG i 458 TYR 0.017 0.002 TYR i 138 PHE 0.018 0.002 PHE i 401 TRP 0.053 0.002 TRP j 429 HIS 0.003 0.001 HIS j 291 Details of bonding type rmsd covalent geometry : bond 0.00370 (12495) covalent geometry : angle 0.66600 (17001) hydrogen bonds : bond 0.03024 ( 276) hydrogen bonds : angle 6.09908 ( 945) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2141.02 seconds wall clock time: 37 minutes 56.06 seconds (2276.06 seconds total)