Starting phenix.real_space_refine on Wed Feb 4 12:03:00 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9sly_55019/02_2026/9sly_55019.cif Found real_map, /net/cci-nas-00/data/ceres_data/9sly_55019/02_2026/9sly_55019.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.77 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9sly_55019/02_2026/9sly_55019.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9sly_55019/02_2026/9sly_55019.map" model { file = "/net/cci-nas-00/data/ceres_data/9sly_55019/02_2026/9sly_55019.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9sly_55019/02_2026/9sly_55019.cif" } resolution = 2.77 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.029 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 78 5.16 5 C 6528 2.51 5 N 1806 2.21 5 O 1938 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 66 residue(s): 0.01s 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: 10350 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 1725 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1725 Classifications: {'peptide': 221} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 204} Restraints were copied for chains: B, C, D, E, F Time building chain proxies: 1.64, per 1000 atoms: 0.16 Number of scatterers: 10350 At special positions: 0 Unit cell: (116.58, 111.22, 79.06, 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 78 16.00 O 1938 8.00 N 1806 7.00 C 6528 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: 0.89 Conformation dependent library (CDL) restraints added in 501.4 milliseconds 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2472 Finding SS restraints... Secondary structure from input PDB file: 72 helices and 6 sheets defined 70.6% alpha, 1.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.31 Creating SS restraints... Processing helix chain 'A' and resid 16 through 30 Processing helix chain 'A' and resid 35 through 44 Processing helix chain 'A' and resid 48 through 59 removed outlier: 4.288A pdb=" N VAL A 59 " --> pdb=" O MET A 55 " (cutoff:3.500A) Processing helix chain 'A' and resid 62 through 84 Processing helix chain 'A' and resid 100 through 105 removed outlier: 3.834A pdb=" N ALA A 105 " --> pdb=" O GLY A 101 " (cutoff:3.500A) Processing helix chain 'A' and resid 110 through 120 Processing helix chain 'A' and resid 125 through 146 removed outlier: 3.505A pdb=" N LYS A 140 " --> pdb=" O LEU A 136 " (cutoff:3.500A) Processing helix chain 'A' and resid 149 through 153 removed outlier: 3.587A pdb=" N ASP A 152 " --> pdb=" O SER A 149 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ILE A 153 " --> pdb=" O ILE A 150 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 149 through 153' Processing helix chain 'A' and resid 160 through 175 Processing helix chain 'A' and resid 179 through 193 removed outlier: 4.184A pdb=" N LEU A 190 " --> pdb=" O THR A 186 " (cutoff:3.500A) removed outlier: 5.577A pdb=" N VAL A 191 " --> pdb=" O GLU A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 206 Processing helix chain 'A' and resid 210 through 218 Processing helix chain 'B' and resid 16 through 30 Processing helix chain 'B' and resid 35 through 44 Processing helix chain 'B' and resid 48 through 59 removed outlier: 4.287A pdb=" N VAL B 59 " --> pdb=" O MET B 55 " (cutoff:3.500A) Processing helix chain 'B' and resid 62 through 84 Processing helix chain 'B' and resid 100 through 105 removed outlier: 3.835A pdb=" N ALA B 105 " --> pdb=" O GLY B 101 " (cutoff:3.500A) Processing helix chain 'B' and resid 110 through 120 Processing helix chain 'B' and resid 125 through 146 removed outlier: 3.504A pdb=" N LYS B 140 " --> pdb=" O LEU B 136 " (cutoff:3.500A) Processing helix chain 'B' and resid 149 through 153 removed outlier: 3.588A pdb=" N ASP B 152 " --> pdb=" O SER B 149 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ILE B 153 " --> pdb=" O ILE B 150 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 149 through 153' Processing helix chain 'B' and resid 160 through 175 Processing helix chain 'B' and resid 179 through 193 removed outlier: 4.183A pdb=" N LEU B 190 " --> pdb=" O THR B 186 " (cutoff:3.500A) removed outlier: 5.577A pdb=" N VAL B 191 " --> pdb=" O GLU B 187 " (cutoff:3.500A) Processing helix chain 'B' and resid 195 through 206 Processing helix chain 'B' and resid 210 through 218 Processing helix chain 'C' and resid 16 through 30 Processing helix chain 'C' and resid 35 through 44 Processing helix chain 'C' and resid 48 through 59 removed outlier: 4.288A pdb=" N VAL C 59 " --> pdb=" O MET C 55 " (cutoff:3.500A) Processing helix chain 'C' and resid 62 through 84 Processing helix chain 'C' and resid 100 through 105 removed outlier: 3.834A pdb=" N ALA C 105 " --> pdb=" O GLY C 101 " (cutoff:3.500A) Processing helix chain 'C' and resid 110 through 120 Processing helix chain 'C' and resid 125 through 146 removed outlier: 3.505A pdb=" N LYS C 140 " --> pdb=" O LEU C 136 " (cutoff:3.500A) Processing helix chain 'C' and resid 149 through 153 removed outlier: 3.588A pdb=" N ASP C 152 " --> pdb=" O SER C 149 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ILE C 153 " --> pdb=" O ILE C 150 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 149 through 153' Processing helix chain 'C' and resid 160 through 175 Processing helix chain 'C' and resid 179 through 193 removed outlier: 4.183A pdb=" N LEU C 190 " --> pdb=" O THR C 186 " (cutoff:3.500A) removed outlier: 5.576A pdb=" N VAL C 191 " --> pdb=" O GLU C 187 " (cutoff:3.500A) Processing helix chain 'C' and resid 195 through 206 Processing helix chain 'C' and resid 210 through 218 Processing helix chain 'D' and resid 16 through 30 Processing helix chain 'D' and resid 35 through 44 Processing helix chain 'D' and resid 48 through 59 removed outlier: 4.287A pdb=" N VAL D 59 " --> pdb=" O MET D 55 " (cutoff:3.500A) Processing helix chain 'D' and resid 62 through 84 Processing helix chain 'D' and resid 100 through 105 removed outlier: 3.834A pdb=" N ALA D 105 " --> pdb=" O GLY D 101 " (cutoff:3.500A) Processing helix chain 'D' and resid 110 through 120 Processing helix chain 'D' and resid 125 through 146 removed outlier: 3.504A pdb=" N LYS D 140 " --> pdb=" O LEU D 136 " (cutoff:3.500A) Processing helix chain 'D' and resid 149 through 153 removed outlier: 3.587A pdb=" N ASP D 152 " --> pdb=" O SER D 149 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ILE D 153 " --> pdb=" O ILE D 150 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 149 through 153' Processing helix chain 'D' and resid 160 through 175 Processing helix chain 'D' and resid 179 through 193 removed outlier: 4.183A pdb=" N LEU D 190 " --> pdb=" O THR D 186 " (cutoff:3.500A) removed outlier: 5.577A pdb=" N VAL D 191 " --> pdb=" O GLU D 187 " (cutoff:3.500A) Processing helix chain 'D' and resid 195 through 206 Processing helix chain 'D' and resid 210 through 218 Processing helix chain 'E' and resid 16 through 30 Processing helix chain 'E' and resid 35 through 44 Processing helix chain 'E' and resid 48 through 59 removed outlier: 4.287A pdb=" N VAL E 59 " --> pdb=" O MET E 55 " (cutoff:3.500A) Processing helix chain 'E' and resid 62 through 84 Processing helix chain 'E' and resid 100 through 105 removed outlier: 3.834A pdb=" N ALA E 105 " --> pdb=" O GLY E 101 " (cutoff:3.500A) Processing helix chain 'E' and resid 110 through 120 Processing helix chain 'E' and resid 125 through 146 removed outlier: 3.505A pdb=" N LYS E 140 " --> pdb=" O LEU E 136 " (cutoff:3.500A) Processing helix chain 'E' and resid 149 through 153 removed outlier: 3.587A pdb=" N ASP E 152 " --> pdb=" O SER E 149 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ILE E 153 " --> pdb=" O ILE E 150 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 149 through 153' Processing helix chain 'E' and resid 160 through 175 Processing helix chain 'E' and resid 179 through 193 removed outlier: 4.183A pdb=" N LEU E 190 " --> pdb=" O THR E 186 " (cutoff:3.500A) removed outlier: 5.577A pdb=" N VAL E 191 " --> pdb=" O GLU E 187 " (cutoff:3.500A) Processing helix chain 'E' and resid 195 through 206 Processing helix chain 'E' and resid 210 through 218 Processing helix chain 'F' and resid 16 through 30 Processing helix chain 'F' and resid 35 through 44 Processing helix chain 'F' and resid 48 through 59 removed outlier: 4.288A pdb=" N VAL F 59 " --> pdb=" O MET F 55 " (cutoff:3.500A) Processing helix chain 'F' and resid 62 through 84 Processing helix chain 'F' and resid 100 through 105 removed outlier: 3.835A pdb=" N ALA F 105 " --> pdb=" O GLY F 101 " (cutoff:3.500A) Processing helix chain 'F' and resid 110 through 120 Processing helix chain 'F' and resid 125 through 146 removed outlier: 3.506A pdb=" N LYS F 140 " --> pdb=" O LEU F 136 " (cutoff:3.500A) Processing helix chain 'F' and resid 149 through 153 removed outlier: 3.587A pdb=" N ASP F 152 " --> pdb=" O SER F 149 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ILE F 153 " --> pdb=" O ILE F 150 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 149 through 153' Processing helix chain 'F' and resid 160 through 175 Processing helix chain 'F' and resid 179 through 193 removed outlier: 4.183A pdb=" N LEU F 190 " --> pdb=" O THR F 186 " (cutoff:3.500A) removed outlier: 5.576A pdb=" N VAL F 191 " --> pdb=" O GLU F 187 " (cutoff:3.500A) Processing helix chain 'F' and resid 195 through 206 Processing helix chain 'F' and resid 210 through 218 Processing sheet with id=AA1, first strand: chain 'A' and resid 2 through 4 removed outlier: 4.284A pdb=" N VAL A 3 " --> pdb=" O VAL A 11 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N VAL A 11 " --> pdb=" O VAL A 3 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'B' and resid 2 through 4 removed outlier: 4.284A pdb=" N VAL B 3 " --> pdb=" O VAL B 11 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N VAL B 11 " --> pdb=" O VAL B 3 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'C' and resid 2 through 4 removed outlier: 4.284A pdb=" N VAL C 3 " --> pdb=" O VAL C 11 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N VAL C 11 " --> pdb=" O VAL C 3 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'D' and resid 2 through 4 removed outlier: 4.284A pdb=" N VAL D 3 " --> pdb=" O VAL D 11 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N VAL D 11 " --> pdb=" O VAL D 3 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'E' and resid 2 through 4 removed outlier: 4.283A pdb=" N VAL E 3 " --> pdb=" O VAL E 11 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N VAL E 11 " --> pdb=" O VAL E 3 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'F' and resid 2 through 4 removed outlier: 4.284A pdb=" N VAL F 3 " --> pdb=" O VAL F 11 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N VAL F 11 " --> pdb=" O VAL F 3 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 612 hydrogen bonds defined for protein. 1836 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.26 Time building geometry restraints manager: 1.20 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: 3474 1.34 - 1.46: 2024 1.46 - 1.58: 4942 1.58 - 1.70: 0 1.70 - 1.81: 144 Bond restraints: 10584 Sorted by residual: bond pdb=" CA ILE E 2 " pdb=" CB ILE E 2 " ideal model delta sigma weight residual 1.530 1.542 -0.012 1.05e-02 9.07e+03 1.25e+00 bond pdb=" CA ILE B 2 " pdb=" CB ILE B 2 " ideal model delta sigma weight residual 1.530 1.542 -0.012 1.05e-02 9.07e+03 1.23e+00 bond pdb=" CA ILE A 2 " pdb=" CB ILE A 2 " ideal model delta sigma weight residual 1.530 1.542 -0.011 1.05e-02 9.07e+03 1.18e+00 bond pdb=" CA ILE C 2 " pdb=" CB ILE C 2 " ideal model delta sigma weight residual 1.530 1.542 -0.011 1.05e-02 9.07e+03 1.13e+00 bond pdb=" CA ILE F 2 " pdb=" CB ILE F 2 " ideal model delta sigma weight residual 1.530 1.541 -0.011 1.05e-02 9.07e+03 1.11e+00 ... (remaining 10579 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.44: 14028 2.44 - 4.88: 270 4.88 - 7.32: 48 7.32 - 9.76: 30 9.76 - 12.20: 12 Bond angle restraints: 14388 Sorted by residual: angle pdb=" CA LYS E 170 " pdb=" CB LYS E 170 " pdb=" CG LYS E 170 " ideal model delta sigma weight residual 114.10 123.31 -9.21 2.00e+00 2.50e-01 2.12e+01 angle pdb=" CA LYS D 170 " pdb=" CB LYS D 170 " pdb=" CG LYS D 170 " ideal model delta sigma weight residual 114.10 123.28 -9.18 2.00e+00 2.50e-01 2.11e+01 angle pdb=" CA LYS B 170 " pdb=" CB LYS B 170 " pdb=" CG LYS B 170 " ideal model delta sigma weight residual 114.10 123.27 -9.17 2.00e+00 2.50e-01 2.10e+01 angle pdb=" CA LYS F 170 " pdb=" CB LYS F 170 " pdb=" CG LYS F 170 " ideal model delta sigma weight residual 114.10 123.26 -9.16 2.00e+00 2.50e-01 2.10e+01 angle pdb=" CA LYS A 170 " pdb=" CB LYS A 170 " pdb=" CG LYS A 170 " ideal model delta sigma weight residual 114.10 123.26 -9.16 2.00e+00 2.50e-01 2.10e+01 ... (remaining 14383 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.78: 5334 17.78 - 35.55: 780 35.55 - 53.33: 264 53.33 - 71.11: 60 71.11 - 88.88: 48 Dihedral angle restraints: 6486 sinusoidal: 2670 harmonic: 3816 Sorted by residual: dihedral pdb=" CA TYR E 169 " pdb=" C TYR E 169 " pdb=" N LYS E 170 " pdb=" CA LYS E 170 " ideal model delta harmonic sigma weight residual 180.00 160.03 19.97 0 5.00e+00 4.00e-02 1.59e+01 dihedral pdb=" CA TYR D 169 " pdb=" C TYR D 169 " pdb=" N LYS D 170 " pdb=" CA LYS D 170 " ideal model delta harmonic sigma weight residual 180.00 160.03 19.97 0 5.00e+00 4.00e-02 1.59e+01 dihedral pdb=" CA TYR A 169 " pdb=" C TYR A 169 " pdb=" N LYS A 170 " pdb=" CA LYS A 170 " ideal model delta harmonic sigma weight residual 180.00 160.06 19.94 0 5.00e+00 4.00e-02 1.59e+01 ... (remaining 6483 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 1004 0.033 - 0.065: 373 0.065 - 0.098: 171 0.098 - 0.130: 42 0.130 - 0.163: 18 Chirality restraints: 1608 Sorted by residual: chirality pdb=" CA LYS C 203 " pdb=" N LYS C 203 " pdb=" C LYS C 203 " pdb=" CB LYS C 203 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.61e-01 chirality pdb=" CA LYS D 203 " pdb=" N LYS D 203 " pdb=" C LYS D 203 " pdb=" CB LYS D 203 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.58e-01 chirality pdb=" CA LYS F 203 " pdb=" N LYS F 203 " pdb=" C LYS F 203 " pdb=" CB LYS F 203 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.55e-01 ... (remaining 1605 not shown) Planarity restraints: 1878 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR F 48 " -0.025 5.00e-02 4.00e+02 3.82e-02 2.33e+00 pdb=" N PRO F 49 " 0.066 5.00e-02 4.00e+02 pdb=" CA PRO F 49 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO F 49 " -0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR C 48 " 0.025 5.00e-02 4.00e+02 3.81e-02 2.32e+00 pdb=" N PRO C 49 " -0.066 5.00e-02 4.00e+02 pdb=" CA PRO C 49 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO C 49 " 0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR B 48 " 0.025 5.00e-02 4.00e+02 3.81e-02 2.32e+00 pdb=" N PRO B 49 " -0.066 5.00e-02 4.00e+02 pdb=" CA PRO B 49 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO B 49 " 0.021 5.00e-02 4.00e+02 ... (remaining 1875 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1095 2.74 - 3.28: 11569 3.28 - 3.82: 18098 3.82 - 4.36: 20054 4.36 - 4.90: 33395 Nonbonded interactions: 84211 Sorted by model distance: nonbonded pdb=" OD1 ASN D 53 " pdb=" OH TYR D 130 " model vdw 2.198 3.040 nonbonded pdb=" OD1 ASN E 53 " pdb=" OH TYR E 130 " model vdw 2.198 3.040 nonbonded pdb=" OD1 ASN C 53 " pdb=" OH TYR C 130 " model vdw 2.199 3.040 nonbonded pdb=" OD1 ASN A 53 " pdb=" OH TYR A 130 " model vdw 2.199 3.040 nonbonded pdb=" OD1 ASN F 53 " pdb=" OH TYR F 130 " model vdw 2.199 3.040 ... (remaining 84206 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: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.200 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 9.960 Find NCS groups from input model: 0.090 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:6.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7018 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 : 0.004 0.041 10584 Z= 0.182 Angle : 0.984 12.202 14388 Z= 0.504 Chirality : 0.044 0.163 1608 Planarity : 0.005 0.038 1878 Dihedral : 20.196 88.882 4014 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 20.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 1.68 % Allowed : 46.90 % Favored : 51.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: -0.13 (0.24), residues: 1314 helix: 0.45 (0.18), residues: 834 sheet: None (None), residues: 0 loop : -0.91 (0.32), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 154 TYR 0.013 0.002 TYR F 169 PHE 0.008 0.002 PHE A 32 TRP 0.020 0.002 TRP B 184 HIS 0.002 0.000 HIS C 62 Details of bonding type rmsd covalent geometry : bond 0.00403 (10584) covalent geometry : angle 0.98383 (14388) hydrogen bonds : bond 0.12153 ( 612) hydrogen bonds : angle 5.31527 ( 1836) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 1128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 314 time to evaluate : 0.404 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 VAL cc_start: 0.7456 (t) cc_final: 0.7027 (m) REVERT: A 51 ASP cc_start: 0.7835 (m-30) cc_final: 0.7536 (m-30) REVERT: A 79 GLU cc_start: 0.6538 (tp30) cc_final: 0.6122 (tm-30) REVERT: A 132 ARG cc_start: 0.7711 (ttp80) cc_final: 0.7360 (mtm110) REVERT: A 211 LEU cc_start: 0.5210 (OUTLIER) cc_final: 0.4509 (tp) REVERT: B 24 VAL cc_start: 0.8101 (t) cc_final: 0.7698 (m) REVERT: B 29 GLU cc_start: 0.7060 (mp0) cc_final: 0.6651 (mp0) REVERT: B 35 GLU cc_start: 0.7649 (pm20) cc_final: 0.7365 (pm20) REVERT: B 44 SER cc_start: 0.8072 (p) cc_final: 0.7830 (m) REVERT: B 115 ILE cc_start: 0.6580 (mm) cc_final: 0.6358 (mt) REVERT: B 128 GLU cc_start: 0.7722 (mp0) cc_final: 0.7275 (mp0) REVERT: B 136 LEU cc_start: 0.8409 (mt) cc_final: 0.8137 (mp) REVERT: B 139 ASN cc_start: 0.7822 (m-40) cc_final: 0.7487 (m-40) REVERT: B 142 VAL cc_start: 0.8087 (p) cc_final: 0.7799 (m) REVERT: B 211 LEU cc_start: 0.5618 (OUTLIER) cc_final: 0.5289 (tm) REVERT: B 215 MET cc_start: 0.6611 (ttm) cc_final: 0.6292 (mtp) REVERT: C 29 GLU cc_start: 0.6655 (mp0) cc_final: 0.6146 (mp0) REVERT: C 33 SER cc_start: 0.7905 (p) cc_final: 0.7669 (t) REVERT: C 35 GLU cc_start: 0.7849 (pm20) cc_final: 0.7639 (pm20) REVERT: C 36 VAL cc_start: 0.8240 (m) cc_final: 0.7975 (m) REVERT: C 76 GLU cc_start: 0.7446 (mm-30) cc_final: 0.7059 (mm-30) REVERT: C 140 LYS cc_start: 0.8082 (mtmt) cc_final: 0.7777 (mtmt) REVERT: C 211 LEU cc_start: 0.6080 (OUTLIER) cc_final: 0.5619 (tm) REVERT: C 214 MET cc_start: 0.7335 (mmt) cc_final: 0.7065 (mmt) REVERT: D 51 ASP cc_start: 0.7938 (m-30) cc_final: 0.7657 (m-30) REVERT: D 68 MET cc_start: 0.8225 (OUTLIER) cc_final: 0.7832 (mtt) REVERT: D 79 GLU cc_start: 0.6632 (tp30) cc_final: 0.6288 (tm-30) REVERT: D 136 LEU cc_start: 0.8503 (mt) cc_final: 0.8285 (mt) REVERT: D 211 LEU cc_start: 0.6194 (OUTLIER) cc_final: 0.5780 (tp) REVERT: D 212 GLU cc_start: 0.6544 (tm-30) cc_final: 0.6328 (tm-30) REVERT: D 215 MET cc_start: 0.6916 (ttm) cc_final: 0.6486 (mtm) REVERT: E 29 GLU cc_start: 0.6773 (mp0) cc_final: 0.6223 (mp0) REVERT: E 76 GLU cc_start: 0.7431 (mm-30) cc_final: 0.7126 (mm-30) REVERT: E 79 GLU cc_start: 0.6515 (tp30) cc_final: 0.6285 (tm-30) REVERT: E 148 THR cc_start: 0.7355 (m) cc_final: 0.7147 (m) REVERT: E 167 ARG cc_start: 0.7207 (ptm-80) cc_final: 0.6943 (ptm160) REVERT: E 211 LEU cc_start: 0.5966 (OUTLIER) cc_final: 0.5686 (tt) REVERT: E 213 GLU cc_start: 0.7298 (mm-30) cc_final: 0.7001 (mm-30) REVERT: F 29 GLU cc_start: 0.7295 (mp0) cc_final: 0.6634 (mp0) REVERT: F 55 MET cc_start: 0.8359 (mtp) cc_final: 0.8130 (ttm) REVERT: F 68 MET cc_start: 0.8170 (OUTLIER) cc_final: 0.7953 (mtt) REVERT: F 76 GLU cc_start: 0.7282 (mm-30) cc_final: 0.7065 (mm-30) REVERT: F 128 GLU cc_start: 0.7657 (mp0) cc_final: 0.7357 (mp0) REVERT: F 139 ASN cc_start: 0.8190 (m-40) cc_final: 0.7816 (m-40) REVERT: F 171 THR cc_start: 0.8174 (m) cc_final: 0.7780 (p) REVERT: F 180 GLU cc_start: 0.5984 (pm20) cc_final: 0.5743 (pm20) REVERT: F 211 LEU cc_start: 0.5715 (OUTLIER) cc_final: 0.5496 (tt) REVERT: F 212 GLU cc_start: 0.6536 (tm-30) cc_final: 0.6228 (tt0) REVERT: F 215 MET cc_start: 0.6887 (ttm) cc_final: 0.6668 (mtm) outliers start: 19 outliers final: 7 residues processed: 326 average time/residue: 0.6565 time to fit residues: 226.5743 Evaluate side-chains 302 residues out of total 1128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 287 time to evaluate : 0.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 HIS Chi-restraints excluded: chain A residue 211 LEU Chi-restraints excluded: chain B residue 120 HIS Chi-restraints excluded: chain B residue 211 LEU Chi-restraints excluded: chain C residue 120 HIS Chi-restraints excluded: chain C residue 211 LEU Chi-restraints excluded: chain D residue 41 SER Chi-restraints excluded: chain D residue 68 MET Chi-restraints excluded: chain D residue 120 HIS Chi-restraints excluded: chain D residue 211 LEU Chi-restraints excluded: chain E residue 120 HIS Chi-restraints excluded: chain E residue 211 LEU Chi-restraints excluded: chain F residue 68 MET Chi-restraints excluded: chain F residue 120 HIS Chi-restraints excluded: chain F residue 211 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 98 optimal weight: 5.9990 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 6.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 0.9980 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 5.9990 chunk 91 optimal weight: 0.7980 chunk 55 optimal weight: 2.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 63 GLN ** A 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 63 GLN ** B 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 63 GLN ** D 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 67 GLN ** E 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 63 GLN ** F 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4342 r_free = 0.4342 target = 0.182946 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.153777 restraints weight = 15066.160| |-----------------------------------------------------------------------------| r_work (start): 0.3995 rms_B_bonded: 2.43 r_work: 0.3851 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3851 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7201 moved from start: 0.2239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 10584 Z= 0.233 Angle : 0.708 6.961 14388 Z= 0.359 Chirality : 0.047 0.170 1608 Planarity : 0.005 0.048 1878 Dihedral : 5.707 45.748 1435 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 7.00 % Allowed : 36.44 % Favored : 56.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: 0.41 (0.24), residues: 1314 helix: 1.01 (0.18), residues: 840 sheet: None (None), residues: 0 loop : -1.02 (0.31), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 154 TYR 0.021 0.002 TYR D 169 PHE 0.009 0.001 PHE C 32 TRP 0.016 0.003 TRP A 184 HIS 0.003 0.001 HIS C 62 Details of bonding type rmsd covalent geometry : bond 0.00559 (10584) covalent geometry : angle 0.70790 (14388) hydrogen bonds : bond 0.04726 ( 612) hydrogen bonds : angle 4.40541 ( 1836) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 362 residues out of total 1128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 283 time to evaluate : 0.264 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 GLU cc_start: 0.7074 (OUTLIER) cc_final: 0.6584 (mp0) REVERT: A 51 ASP cc_start: 0.7564 (m-30) cc_final: 0.7350 (m-30) REVERT: A 74 ASN cc_start: 0.7433 (m-40) cc_final: 0.7095 (m110) REVERT: A 132 ARG cc_start: 0.7620 (ttp80) cc_final: 0.7286 (mtm110) REVERT: A 140 LYS cc_start: 0.8487 (mtmt) cc_final: 0.8264 (mtmm) REVERT: A 180 GLU cc_start: 0.6051 (pm20) cc_final: 0.5692 (pm20) REVERT: A 181 VAL cc_start: 0.8055 (m) cc_final: 0.7797 (t) REVERT: A 185 MET cc_start: 0.6390 (ptp) cc_final: 0.6050 (ptp) REVERT: A 210 THR cc_start: 0.5394 (OUTLIER) cc_final: 0.5094 (t) REVERT: B 29 GLU cc_start: 0.7298 (OUTLIER) cc_final: 0.6851 (mp0) REVERT: B 44 SER cc_start: 0.8243 (p) cc_final: 0.7936 (m) REVERT: B 97 ARG cc_start: 0.5493 (OUTLIER) cc_final: 0.4428 (ptt-90) REVERT: B 139 ASN cc_start: 0.8591 (m-40) cc_final: 0.8181 (m-40) REVERT: B 210 THR cc_start: 0.6298 (OUTLIER) cc_final: 0.6089 (t) REVERT: B 211 LEU cc_start: 0.6594 (OUTLIER) cc_final: 0.6391 (tt) REVERT: B 215 MET cc_start: 0.7289 (ttm) cc_final: 0.7058 (mtp) REVERT: C 29 GLU cc_start: 0.6810 (OUTLIER) cc_final: 0.6414 (mp0) REVERT: C 55 MET cc_start: 0.8482 (OUTLIER) cc_final: 0.7680 (mtp) REVERT: C 210 THR cc_start: 0.6319 (OUTLIER) cc_final: 0.5854 (t) REVERT: C 218 CYS cc_start: 0.7399 (t) cc_final: 0.6963 (m) REVERT: D 29 GLU cc_start: 0.7150 (OUTLIER) cc_final: 0.6681 (mp0) REVERT: D 51 ASP cc_start: 0.7717 (m-30) cc_final: 0.7485 (m-30) REVERT: D 210 THR cc_start: 0.5934 (OUTLIER) cc_final: 0.5621 (t) REVERT: D 215 MET cc_start: 0.7196 (ttm) cc_final: 0.6863 (mtp) REVERT: E 29 GLU cc_start: 0.7040 (OUTLIER) cc_final: 0.6610 (mp0) REVERT: E 55 MET cc_start: 0.8526 (OUTLIER) cc_final: 0.7892 (mtp) REVERT: E 71 GLU cc_start: 0.7834 (tt0) cc_final: 0.7473 (tt0) REVERT: E 76 GLU cc_start: 0.7702 (mm-30) cc_final: 0.7500 (OUTLIER) REVERT: E 132 ARG cc_start: 0.7544 (ttp80) cc_final: 0.7244 (mtm110) REVERT: E 167 ARG cc_start: 0.7515 (ptm-80) cc_final: 0.7243 (ptm160) REVERT: E 199 LYS cc_start: 0.7494 (OUTLIER) cc_final: 0.7188 (tptp) REVERT: E 210 THR cc_start: 0.6652 (OUTLIER) cc_final: 0.6352 (t) REVERT: E 218 CYS cc_start: 0.7430 (t) cc_final: 0.7066 (m) REVERT: F 29 GLU cc_start: 0.7506 (OUTLIER) cc_final: 0.6965 (mp0) REVERT: F 39 MET cc_start: 0.8281 (tpp) cc_final: 0.7988 (mmt) REVERT: F 67 GLN cc_start: 0.9029 (tp40) cc_final: 0.8409 (tp-100) REVERT: F 83 LEU cc_start: 0.6176 (OUTLIER) cc_final: 0.5605 (mm) REVERT: F 128 GLU cc_start: 0.7833 (mp0) cc_final: 0.7561 (mp0) REVERT: F 136 LEU cc_start: 0.8579 (mt) cc_final: 0.8311 (mp) REVERT: F 139 ASN cc_start: 0.8611 (m-40) cc_final: 0.8186 (m-40) REVERT: F 180 GLU cc_start: 0.6174 (pm20) cc_final: 0.5968 (pm20) REVERT: F 210 THR cc_start: 0.6705 (OUTLIER) cc_final: 0.6243 (t) REVERT: F 211 LEU cc_start: 0.6537 (OUTLIER) cc_final: 0.6257 (tt) REVERT: F 212 GLU cc_start: 0.6216 (tm-30) cc_final: 0.6001 (tt0) outliers start: 79 outliers final: 20 residues processed: 338 average time/residue: 0.6421 time to fit residues: 229.1687 Evaluate side-chains 310 residues out of total 1128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 272 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 GLU Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain B residue 29 GLU Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain B residue 97 ARG Chi-restraints excluded: chain B residue 110 THR Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 146 SER Chi-restraints excluded: chain B residue 210 THR Chi-restraints excluded: chain B residue 211 LEU Chi-restraints excluded: chain C residue 29 GLU Chi-restraints excluded: chain C residue 55 MET Chi-restraints excluded: chain C residue 58 THR Chi-restraints excluded: chain C residue 83 LEU Chi-restraints excluded: chain C residue 84 HIS Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain C residue 120 HIS Chi-restraints excluded: chain C residue 210 THR Chi-restraints excluded: chain D residue 29 GLU Chi-restraints excluded: chain D residue 58 THR Chi-restraints excluded: chain D residue 83 LEU Chi-restraints excluded: chain D residue 210 THR Chi-restraints excluded: chain E residue 29 GLU Chi-restraints excluded: chain E residue 55 MET Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 83 LEU Chi-restraints excluded: chain E residue 110 THR Chi-restraints excluded: chain E residue 199 LYS Chi-restraints excluded: chain E residue 210 THR Chi-restraints excluded: chain F residue 29 GLU Chi-restraints excluded: chain F residue 83 LEU Chi-restraints excluded: chain F residue 110 THR Chi-restraints excluded: chain F residue 167 ARG Chi-restraints excluded: chain F residue 210 THR Chi-restraints excluded: chain F residue 211 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 23 optimal weight: 0.9980 chunk 110 optimal weight: 4.9990 chunk 131 optimal weight: 0.4980 chunk 59 optimal weight: 6.9990 chunk 130 optimal weight: 0.0870 chunk 85 optimal weight: 3.9990 chunk 69 optimal weight: 0.4980 chunk 97 optimal weight: 7.9990 chunk 113 optimal weight: 0.4980 chunk 27 optimal weight: 0.6980 chunk 0 optimal weight: 5.9990 overall best weight: 0.4558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 155 GLN E 21 ASN ** E 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4381 r_free = 0.4381 target = 0.186042 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.157302 restraints weight = 15002.160| |-----------------------------------------------------------------------------| r_work (start): 0.4033 rms_B_bonded: 2.43 r_work: 0.3895 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3895 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7143 moved from start: 0.2564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10584 Z= 0.125 Angle : 0.590 6.924 14388 Z= 0.293 Chirality : 0.041 0.138 1608 Planarity : 0.005 0.043 1878 Dihedral : 4.180 37.103 1410 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 6.74 % Allowed : 35.46 % Favored : 57.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: 1.00 (0.24), residues: 1314 helix: 1.60 (0.18), residues: 840 sheet: None (None), residues: 0 loop : -1.05 (0.31), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG F 154 TYR 0.010 0.001 TYR F 169 PHE 0.009 0.001 PHE E 32 TRP 0.029 0.002 TRP A 184 HIS 0.002 0.001 HIS F 12 Details of bonding type rmsd covalent geometry : bond 0.00295 (10584) covalent geometry : angle 0.59046 (14388) hydrogen bonds : bond 0.03661 ( 612) hydrogen bonds : angle 4.17126 ( 1836) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 349 residues out of total 1128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 273 time to evaluate : 0.406 Fit side-chains revert: symmetry clash REVERT: A 29 GLU cc_start: 0.6915 (OUTLIER) cc_final: 0.6484 (mp0) REVERT: A 33 SER cc_start: 0.8066 (p) cc_final: 0.7769 (t) REVERT: A 35 GLU cc_start: 0.7798 (pm20) cc_final: 0.7119 (pm20) REVERT: A 74 ASN cc_start: 0.7278 (m-40) cc_final: 0.6963 (m110) REVERT: A 75 GLU cc_start: 0.7796 (mt-10) cc_final: 0.7548 (mt-10) REVERT: A 97 ARG cc_start: 0.5357 (OUTLIER) cc_final: 0.4986 (ptt-90) REVERT: A 180 GLU cc_start: 0.5939 (pm20) cc_final: 0.5713 (pm20) REVERT: A 213 GLU cc_start: 0.7089 (mm-30) cc_final: 0.6852 (mm-30) REVERT: B 29 GLU cc_start: 0.7089 (OUTLIER) cc_final: 0.6680 (mp0) REVERT: B 44 SER cc_start: 0.8163 (p) cc_final: 0.7880 (m) REVERT: B 51 ASP cc_start: 0.7702 (m-30) cc_final: 0.7502 (m-30) REVERT: B 73 ILE cc_start: 0.8086 (OUTLIER) cc_final: 0.7858 (mm) REVERT: B 139 ASN cc_start: 0.8381 (m-40) cc_final: 0.7973 (m-40) REVERT: B 173 ARG cc_start: 0.7763 (ttt-90) cc_final: 0.7515 (ttt180) REVERT: B 211 LEU cc_start: 0.6761 (OUTLIER) cc_final: 0.6535 (tt) REVERT: C 29 GLU cc_start: 0.6611 (OUTLIER) cc_final: 0.6230 (mp0) REVERT: C 58 THR cc_start: 0.8567 (OUTLIER) cc_final: 0.8259 (t) REVERT: C 97 ARG cc_start: 0.5620 (OUTLIER) cc_final: 0.5154 (tmm160) REVERT: C 167 ARG cc_start: 0.7382 (ptm160) cc_final: 0.7176 (ptm160) REVERT: C 210 THR cc_start: 0.6273 (OUTLIER) cc_final: 0.5902 (t) REVERT: C 218 CYS cc_start: 0.6867 (t) cc_final: 0.6636 (m) REVERT: D 29 GLU cc_start: 0.6918 (OUTLIER) cc_final: 0.6464 (mp0) REVERT: D 76 GLU cc_start: 0.7835 (OUTLIER) cc_final: 0.7594 (mm-30) REVERT: D 97 ARG cc_start: 0.5326 (OUTLIER) cc_final: 0.4905 (ptt-90) REVERT: D 162 ARG cc_start: 0.6859 (OUTLIER) cc_final: 0.6242 (ttm170) REVERT: D 173 ARG cc_start: 0.7665 (OUTLIER) cc_final: 0.6458 (ttt90) REVERT: E 29 GLU cc_start: 0.6812 (OUTLIER) cc_final: 0.6378 (mp0) REVERT: E 58 THR cc_start: 0.8639 (OUTLIER) cc_final: 0.8314 (t) REVERT: E 97 ARG cc_start: 0.5398 (OUTLIER) cc_final: 0.4862 (ttp80) REVERT: E 132 ARG cc_start: 0.7504 (ttp80) cc_final: 0.7226 (mtm110) REVERT: E 167 ARG cc_start: 0.7414 (ptm-80) cc_final: 0.7176 (ptm160) REVERT: E 210 THR cc_start: 0.6533 (OUTLIER) cc_final: 0.6058 (t) REVERT: E 213 GLU cc_start: 0.7175 (mm-30) cc_final: 0.6727 (mm-30) REVERT: E 218 CYS cc_start: 0.7043 (t) cc_final: 0.6793 (m) REVERT: F 29 GLU cc_start: 0.7353 (OUTLIER) cc_final: 0.6809 (mp0) REVERT: F 51 ASP cc_start: 0.7741 (m-30) cc_final: 0.7537 (m-30) REVERT: F 67 GLN cc_start: 0.8976 (tp40) cc_final: 0.8444 (tp40) REVERT: F 83 LEU cc_start: 0.6083 (OUTLIER) cc_final: 0.5537 (mm) REVERT: F 97 ARG cc_start: 0.5495 (OUTLIER) cc_final: 0.4839 (ptt-90) REVERT: F 128 GLU cc_start: 0.7674 (mp0) cc_final: 0.7392 (mp0) REVERT: F 139 ASN cc_start: 0.8414 (m-40) cc_final: 0.8002 (m-40) outliers start: 76 outliers final: 17 residues processed: 318 average time/residue: 0.6627 time to fit residues: 222.3283 Evaluate side-chains 307 residues out of total 1128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 269 time to evaluate : 0.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 GLU Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 97 ARG Chi-restraints excluded: chain B residue 29 GLU Chi-restraints excluded: chain B residue 30 LYS Chi-restraints excluded: chain B residue 58 THR Chi-restraints excluded: chain B residue 71 GLU Chi-restraints excluded: chain B residue 73 ILE Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain B residue 211 LEU Chi-restraints excluded: chain C residue 29 GLU Chi-restraints excluded: chain C residue 58 THR Chi-restraints excluded: chain C residue 83 LEU Chi-restraints excluded: chain C residue 97 ARG Chi-restraints excluded: chain C residue 210 THR Chi-restraints excluded: chain D residue 29 GLU Chi-restraints excluded: chain D residue 41 SER Chi-restraints excluded: chain D residue 76 GLU Chi-restraints excluded: chain D residue 83 LEU Chi-restraints excluded: chain D residue 97 ARG Chi-restraints excluded: chain D residue 120 HIS Chi-restraints excluded: chain D residue 162 ARG Chi-restraints excluded: chain D residue 173 ARG Chi-restraints excluded: chain D residue 192 GLN Chi-restraints excluded: chain D residue 210 THR Chi-restraints excluded: chain E residue 29 GLU Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 71 GLU Chi-restraints excluded: chain E residue 83 LEU Chi-restraints excluded: chain E residue 97 ARG Chi-restraints excluded: chain E residue 120 HIS Chi-restraints excluded: chain E residue 210 THR Chi-restraints excluded: chain F residue 29 GLU Chi-restraints excluded: chain F residue 30 LYS Chi-restraints excluded: chain F residue 83 LEU Chi-restraints excluded: chain F residue 97 ARG Chi-restraints excluded: chain F residue 120 HIS Chi-restraints excluded: chain F residue 192 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 73 optimal weight: 3.9990 chunk 105 optimal weight: 3.9990 chunk 97 optimal weight: 2.9990 chunk 43 optimal weight: 2.9990 chunk 31 optimal weight: 8.9990 chunk 22 optimal weight: 3.9990 chunk 3 optimal weight: 0.9990 chunk 13 optimal weight: 1.9990 chunk 129 optimal weight: 4.9990 chunk 53 optimal weight: 3.9990 chunk 77 optimal weight: 4.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 12 HIS ** E 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 12 HIS ** F 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4307 r_free = 0.4307 target = 0.179482 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.149148 restraints weight = 14891.821| |-----------------------------------------------------------------------------| r_work (start): 0.3941 rms_B_bonded: 2.49 r_work: 0.3796 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3796 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7280 moved from start: 0.3524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.074 10584 Z= 0.345 Angle : 0.723 7.592 14388 Z= 0.371 Chirality : 0.049 0.263 1608 Planarity : 0.006 0.057 1878 Dihedral : 4.569 28.850 1406 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 11.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.16 % Favored : 93.84 % Rotamer: Outliers : 8.69 % Allowed : 32.89 % Favored : 58.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: 0.43 (0.24), residues: 1314 helix: 1.00 (0.17), residues: 840 sheet: None (None), residues: 0 loop : -0.95 (0.32), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 143 TYR 0.028 0.003 TYR A 169 PHE 0.009 0.002 PHE E 168 TRP 0.022 0.003 TRP A 184 HIS 0.005 0.001 HIS A 84 Details of bonding type rmsd covalent geometry : bond 0.00817 (10584) covalent geometry : angle 0.72282 (14388) hydrogen bonds : bond 0.05394 ( 612) hydrogen bonds : angle 4.55833 ( 1836) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 381 residues out of total 1128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 283 time to evaluate : 0.339 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 GLU cc_start: 0.7027 (OUTLIER) cc_final: 0.6692 (mp0) REVERT: A 74 ASN cc_start: 0.7485 (m-40) cc_final: 0.7218 (m-40) REVERT: A 173 ARG cc_start: 0.7781 (OUTLIER) cc_final: 0.6689 (ttp-170) REVERT: A 203 LYS cc_start: 0.7382 (OUTLIER) cc_final: 0.7023 (mmtm) REVERT: A 213 GLU cc_start: 0.7287 (mm-30) cc_final: 0.6958 (mm-30) REVERT: B 29 GLU cc_start: 0.7227 (OUTLIER) cc_final: 0.6873 (mp0) REVERT: B 39 MET cc_start: 0.8277 (tpp) cc_final: 0.7972 (tpt) REVERT: B 44 SER cc_start: 0.8292 (p) cc_final: 0.7978 (m) REVERT: B 67 GLN cc_start: 0.8816 (tp40) cc_final: 0.8482 (tp40) REVERT: B 96 MET cc_start: 0.3723 (pp-130) cc_final: 0.3522 (pp-130) REVERT: B 97 ARG cc_start: 0.5584 (OUTLIER) cc_final: 0.4868 (ptt-90) REVERT: B 128 GLU cc_start: 0.7839 (mm-30) cc_final: 0.7541 (mm-30) REVERT: B 211 LEU cc_start: 0.6955 (OUTLIER) cc_final: 0.6660 (tt) REVERT: C 29 GLU cc_start: 0.6971 (OUTLIER) cc_final: 0.6607 (mp0) REVERT: C 55 MET cc_start: 0.8645 (OUTLIER) cc_final: 0.7902 (mtp) REVERT: C 162 ARG cc_start: 0.7158 (OUTLIER) cc_final: 0.6301 (ttm170) REVERT: C 210 THR cc_start: 0.6377 (OUTLIER) cc_final: 0.6087 (t) REVERT: C 218 CYS cc_start: 0.7742 (t) cc_final: 0.7238 (m) REVERT: D 29 GLU cc_start: 0.7067 (OUTLIER) cc_final: 0.6724 (mp0) REVERT: D 97 ARG cc_start: 0.5413 (OUTLIER) cc_final: 0.4927 (ptt-90) REVERT: D 162 ARG cc_start: 0.7051 (OUTLIER) cc_final: 0.6477 (ttm-80) REVERT: D 173 ARG cc_start: 0.7864 (OUTLIER) cc_final: 0.7268 (ttt180) REVERT: D 175 GLU cc_start: 0.6731 (tp30) cc_final: 0.6479 (tp30) REVERT: D 199 LYS cc_start: 0.8009 (tptp) cc_final: 0.7230 (tptt) REVERT: D 203 LYS cc_start: 0.7366 (OUTLIER) cc_final: 0.7009 (mppt) REVERT: D 210 THR cc_start: 0.6113 (OUTLIER) cc_final: 0.5831 (t) REVERT: D 214 MET cc_start: 0.7832 (OUTLIER) cc_final: 0.7233 (mtp) REVERT: E 29 GLU cc_start: 0.7170 (OUTLIER) cc_final: 0.6765 (mp0) REVERT: E 55 MET cc_start: 0.8599 (OUTLIER) cc_final: 0.7995 (mtp) REVERT: E 97 ARG cc_start: 0.5514 (OUTLIER) cc_final: 0.4813 (ptt-90) REVERT: E 132 ARG cc_start: 0.7598 (ttp80) cc_final: 0.7271 (mtm110) REVERT: E 136 LEU cc_start: 0.8716 (OUTLIER) cc_final: 0.8447 (tt) REVERT: E 167 ARG cc_start: 0.7477 (ptm-80) cc_final: 0.7233 (ptm160) REVERT: E 210 THR cc_start: 0.5988 (OUTLIER) cc_final: 0.5637 (t) REVERT: E 213 GLU cc_start: 0.7336 (mm-30) cc_final: 0.6871 (mm-30) REVERT: E 214 MET cc_start: 0.8557 (mtt) cc_final: 0.8333 (mtp) REVERT: E 218 CYS cc_start: 0.7756 (t) cc_final: 0.7403 (m) REVERT: F 29 GLU cc_start: 0.7436 (OUTLIER) cc_final: 0.7002 (mp0) REVERT: F 35 GLU cc_start: 0.7821 (pm20) cc_final: 0.7596 (pm20) REVERT: F 66 MET cc_start: 0.8282 (OUTLIER) cc_final: 0.8047 (mmm) REVERT: F 67 GLN cc_start: 0.8999 (tp40) cc_final: 0.8384 (tp40) REVERT: F 140 LYS cc_start: 0.8272 (mtmt) cc_final: 0.8051 (mtmt) REVERT: F 213 GLU cc_start: 0.7387 (mm-30) cc_final: 0.7014 (mm-30) outliers start: 98 outliers final: 41 residues processed: 336 average time/residue: 0.6932 time to fit residues: 245.5089 Evaluate side-chains 340 residues out of total 1128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 275 time to evaluate : 0.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 GLU Chi-restraints excluded: chain A residue 41 SER Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 97 ARG Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 173 ARG Chi-restraints excluded: chain A residue 185 MET Chi-restraints excluded: chain A residue 192 GLN Chi-restraints excluded: chain A residue 203 LYS Chi-restraints excluded: chain B residue 29 GLU Chi-restraints excluded: chain B residue 30 LYS Chi-restraints excluded: chain B residue 58 THR Chi-restraints excluded: chain B residue 71 GLU Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain B residue 97 ARG Chi-restraints excluded: chain B residue 110 THR Chi-restraints excluded: chain B residue 120 HIS Chi-restraints excluded: chain B residue 167 ARG Chi-restraints excluded: chain B residue 211 LEU Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 29 GLU Chi-restraints excluded: chain C residue 55 MET Chi-restraints excluded: chain C residue 58 THR Chi-restraints excluded: chain C residue 71 GLU Chi-restraints excluded: chain C residue 83 LEU Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain C residue 119 THR Chi-restraints excluded: chain C residue 120 HIS Chi-restraints excluded: chain C residue 162 ARG Chi-restraints excluded: chain C residue 170 LYS Chi-restraints excluded: chain C residue 172 LEU Chi-restraints excluded: chain C residue 192 GLN Chi-restraints excluded: chain C residue 210 THR Chi-restraints excluded: chain D residue 29 GLU Chi-restraints excluded: chain D residue 41 SER Chi-restraints excluded: chain D residue 83 LEU Chi-restraints excluded: chain D residue 97 ARG Chi-restraints excluded: chain D residue 120 HIS Chi-restraints excluded: chain D residue 162 ARG Chi-restraints excluded: chain D residue 173 ARG Chi-restraints excluded: chain D residue 192 GLN Chi-restraints excluded: chain D residue 203 LYS Chi-restraints excluded: chain D residue 210 THR Chi-restraints excluded: chain D residue 214 MET Chi-restraints excluded: chain E residue 29 GLU Chi-restraints excluded: chain E residue 30 LYS Chi-restraints excluded: chain E residue 55 MET Chi-restraints excluded: chain E residue 71 GLU Chi-restraints excluded: chain E residue 83 LEU Chi-restraints excluded: chain E residue 97 ARG Chi-restraints excluded: chain E residue 110 THR Chi-restraints excluded: chain E residue 120 HIS Chi-restraints excluded: chain E residue 136 LEU Chi-restraints excluded: chain E residue 172 LEU Chi-restraints excluded: chain E residue 192 GLN Chi-restraints excluded: chain E residue 210 THR Chi-restraints excluded: chain F residue 29 GLU Chi-restraints excluded: chain F residue 30 LYS Chi-restraints excluded: chain F residue 41 SER Chi-restraints excluded: chain F residue 66 MET Chi-restraints excluded: chain F residue 71 GLU Chi-restraints excluded: chain F residue 83 LEU Chi-restraints excluded: chain F residue 110 THR Chi-restraints excluded: chain F residue 120 HIS Chi-restraints excluded: chain F residue 192 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 31 optimal weight: 0.0770 chunk 44 optimal weight: 5.9990 chunk 7 optimal weight: 0.7980 chunk 30 optimal weight: 0.9990 chunk 50 optimal weight: 1.9990 chunk 40 optimal weight: 0.9980 chunk 95 optimal weight: 2.9990 chunk 33 optimal weight: 0.6980 chunk 98 optimal weight: 1.9990 chunk 73 optimal weight: 3.9990 chunk 78 optimal weight: 0.1980 overall best weight: 0.5538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 57 ASN ** A 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 4 GLN ** C 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 21 ASN ** C 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 183 ASN ** F 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4356 r_free = 0.4356 target = 0.184550 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.155329 restraints weight = 14960.880| |-----------------------------------------------------------------------------| r_work (start): 0.4000 rms_B_bonded: 2.47 r_work: 0.3859 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3859 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7191 moved from start: 0.3550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 10584 Z= 0.135 Angle : 0.606 7.648 14388 Z= 0.303 Chirality : 0.042 0.148 1608 Planarity : 0.005 0.050 1878 Dihedral : 4.226 30.442 1406 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 11.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.01 % Favored : 93.99 % Rotamer: Outliers : 6.56 % Allowed : 35.20 % Favored : 58.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: 0.93 (0.24), residues: 1314 helix: 1.54 (0.18), residues: 834 sheet: None (None), residues: 0 loop : -1.05 (0.31), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG F 143 TYR 0.013 0.002 TYR F 169 PHE 0.011 0.001 PHE D 32 TRP 0.033 0.002 TRP A 184 HIS 0.003 0.001 HIS D 12 Details of bonding type rmsd covalent geometry : bond 0.00326 (10584) covalent geometry : angle 0.60571 (14388) hydrogen bonds : bond 0.03892 ( 612) hydrogen bonds : angle 4.35028 ( 1836) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 350 residues out of total 1128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 276 time to evaluate : 0.368 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 GLU cc_start: 0.6897 (OUTLIER) cc_final: 0.6522 (mp0) REVERT: A 33 SER cc_start: 0.8138 (p) cc_final: 0.7779 (t) REVERT: A 35 GLU cc_start: 0.7766 (pm20) cc_final: 0.7111 (pm20) REVERT: A 213 GLU cc_start: 0.7272 (mm-30) cc_final: 0.6922 (mm-30) REVERT: B 29 GLU cc_start: 0.7218 (OUTLIER) cc_final: 0.6806 (mp0) REVERT: B 39 MET cc_start: 0.8116 (tpp) cc_final: 0.7808 (tpt) REVERT: B 44 SER cc_start: 0.8195 (p) cc_final: 0.7888 (m) REVERT: B 67 GLN cc_start: 0.8844 (tp40) cc_final: 0.8575 (tp40) REVERT: B 96 MET cc_start: 0.3559 (pp-130) cc_final: 0.3263 (pp-130) REVERT: B 128 GLU cc_start: 0.7679 (mm-30) cc_final: 0.7396 (mm-30) REVERT: B 173 ARG cc_start: 0.7732 (ttt-90) cc_final: 0.7497 (ttt180) REVERT: B 211 LEU cc_start: 0.6986 (OUTLIER) cc_final: 0.6533 (tt) REVERT: C 29 GLU cc_start: 0.6801 (OUTLIER) cc_final: 0.6419 (mp0) REVERT: C 113 GLU cc_start: 0.6224 (mt-10) cc_final: 0.5932 (mt-10) REVERT: C 210 THR cc_start: 0.6235 (OUTLIER) cc_final: 0.5948 (t) REVERT: C 211 LEU cc_start: 0.6631 (OUTLIER) cc_final: 0.6259 (tt) REVERT: C 218 CYS cc_start: 0.7164 (t) cc_final: 0.6842 (m) REVERT: D 29 GLU cc_start: 0.6957 (OUTLIER) cc_final: 0.6569 (mp0) REVERT: D 115 ILE cc_start: 0.6788 (OUTLIER) cc_final: 0.6417 (tp) REVERT: D 162 ARG cc_start: 0.7087 (OUTLIER) cc_final: 0.6233 (ttm-80) REVERT: D 180 GLU cc_start: 0.6336 (OUTLIER) cc_final: 0.5962 (pm20) REVERT: D 199 LYS cc_start: 0.7958 (tptp) cc_final: 0.7470 (mmtt) REVERT: D 203 LYS cc_start: 0.7148 (OUTLIER) cc_final: 0.6741 (mppt) REVERT: D 214 MET cc_start: 0.7791 (OUTLIER) cc_final: 0.7219 (mtp) REVERT: D 218 CYS cc_start: 0.7374 (t) cc_final: 0.7030 (m) REVERT: E 10 MET cc_start: 0.4558 (mpp) cc_final: 0.4308 (tpp) REVERT: E 29 GLU cc_start: 0.6990 (OUTLIER) cc_final: 0.6590 (mp0) REVERT: E 55 MET cc_start: 0.8543 (OUTLIER) cc_final: 0.7896 (mtp) REVERT: E 132 ARG cc_start: 0.7553 (ttp80) cc_final: 0.7250 (mtm110) REVERT: E 167 ARG cc_start: 0.7433 (ptm-80) cc_final: 0.7172 (ptm160) REVERT: E 213 GLU cc_start: 0.7293 (mm-30) cc_final: 0.6764 (mm-30) REVERT: E 218 CYS cc_start: 0.7319 (t) cc_final: 0.7017 (m) REVERT: F 29 GLU cc_start: 0.7365 (OUTLIER) cc_final: 0.6909 (mp0) REVERT: F 67 GLN cc_start: 0.8937 (tp40) cc_final: 0.8390 (tp40) REVERT: F 79 GLU cc_start: 0.5889 (tm-30) cc_final: 0.5652 (tm-30) REVERT: F 180 GLU cc_start: 0.6167 (OUTLIER) cc_final: 0.5749 (pm20) REVERT: F 215 MET cc_start: 0.7244 (OUTLIER) cc_final: 0.6958 (mtp) outliers start: 74 outliers final: 26 residues processed: 314 average time/residue: 0.6608 time to fit residues: 218.8999 Evaluate side-chains 314 residues out of total 1128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 271 time to evaluate : 0.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 GLU Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 97 ARG Chi-restraints excluded: chain A residue 120 HIS Chi-restraints excluded: chain A residue 192 GLN Chi-restraints excluded: chain B residue 29 GLU Chi-restraints excluded: chain B residue 30 LYS Chi-restraints excluded: chain B residue 58 THR Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain B residue 120 HIS Chi-restraints excluded: chain B residue 210 THR Chi-restraints excluded: chain B residue 211 LEU Chi-restraints excluded: chain C residue 29 GLU Chi-restraints excluded: chain C residue 58 THR Chi-restraints excluded: chain C residue 71 GLU Chi-restraints excluded: chain C residue 83 LEU Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain C residue 120 HIS Chi-restraints excluded: chain C residue 170 LYS Chi-restraints excluded: chain C residue 210 THR Chi-restraints excluded: chain C residue 211 LEU Chi-restraints excluded: chain D residue 29 GLU Chi-restraints excluded: chain D residue 30 LYS Chi-restraints excluded: chain D residue 41 SER Chi-restraints excluded: chain D residue 83 LEU Chi-restraints excluded: chain D residue 115 ILE Chi-restraints excluded: chain D residue 120 HIS Chi-restraints excluded: chain D residue 162 ARG Chi-restraints excluded: chain D residue 180 GLU Chi-restraints excluded: chain D residue 203 LYS Chi-restraints excluded: chain D residue 214 MET Chi-restraints excluded: chain E residue 29 GLU Chi-restraints excluded: chain E residue 30 LYS Chi-restraints excluded: chain E residue 55 MET Chi-restraints excluded: chain E residue 71 GLU Chi-restraints excluded: chain E residue 83 LEU Chi-restraints excluded: chain F residue 29 GLU Chi-restraints excluded: chain F residue 30 LYS Chi-restraints excluded: chain F residue 83 LEU Chi-restraints excluded: chain F residue 120 HIS Chi-restraints excluded: chain F residue 180 GLU Chi-restraints excluded: chain F residue 192 GLN Chi-restraints excluded: chain F residue 215 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 28 optimal weight: 0.6980 chunk 114 optimal weight: 0.9990 chunk 116 optimal weight: 0.9990 chunk 93 optimal weight: 0.9990 chunk 9 optimal weight: 7.9990 chunk 11 optimal weight: 2.9990 chunk 117 optimal weight: 1.9990 chunk 102 optimal weight: 0.4980 chunk 86 optimal weight: 5.9990 chunk 101 optimal weight: 0.6980 chunk 15 optimal weight: 3.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 57 ASN A 84 HIS ** A 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 12 HIS ** B 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4350 r_free = 0.4350 target = 0.183618 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.153654 restraints weight = 15032.433| |-----------------------------------------------------------------------------| r_work (start): 0.3999 rms_B_bonded: 2.50 r_work: 0.3860 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3860 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7201 moved from start: 0.3688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 10584 Z= 0.149 Angle : 0.615 8.663 14388 Z= 0.307 Chirality : 0.042 0.150 1608 Planarity : 0.005 0.050 1878 Dihedral : 4.165 31.178 1406 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 10.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.24 % Favored : 93.76 % Rotamer: Outliers : 6.74 % Allowed : 34.75 % Favored : 58.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: 0.94 (0.24), residues: 1314 helix: 1.47 (0.18), residues: 840 sheet: None (None), residues: 0 loop : -0.90 (0.31), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 154 TYR 0.015 0.002 TYR B 169 PHE 0.009 0.001 PHE F 32 TRP 0.034 0.002 TRP A 184 HIS 0.002 0.001 HIS C 120 Details of bonding type rmsd covalent geometry : bond 0.00365 (10584) covalent geometry : angle 0.61502 (14388) hydrogen bonds : bond 0.03984 ( 612) hydrogen bonds : angle 4.36540 ( 1836) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 361 residues out of total 1128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 285 time to evaluate : 0.308 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 10 MET cc_start: 0.4696 (tpp) cc_final: 0.4448 (tpp) REVERT: A 29 GLU cc_start: 0.6944 (OUTLIER) cc_final: 0.6557 (mp0) REVERT: A 75 GLU cc_start: 0.7917 (mt-10) cc_final: 0.7624 (mt-10) REVERT: A 83 LEU cc_start: 0.6401 (OUTLIER) cc_final: 0.5910 (mm) REVERT: A 210 THR cc_start: 0.5559 (OUTLIER) cc_final: 0.5174 (p) REVERT: A 213 GLU cc_start: 0.7347 (mm-30) cc_final: 0.7002 (mm-30) REVERT: A 214 MET cc_start: 0.7632 (OUTLIER) cc_final: 0.7185 (mtp) REVERT: A 219 GLN cc_start: 0.6568 (tp-100) cc_final: 0.6340 (tp40) REVERT: B 29 GLU cc_start: 0.7255 (OUTLIER) cc_final: 0.6846 (mp0) REVERT: B 39 MET cc_start: 0.8099 (tpp) cc_final: 0.7537 (tpt) REVERT: B 67 GLN cc_start: 0.8818 (tp40) cc_final: 0.8464 (tp40) REVERT: B 128 GLU cc_start: 0.7688 (mm-30) cc_final: 0.7381 (mm-30) REVERT: B 173 ARG cc_start: 0.7761 (ttt-90) cc_final: 0.7524 (ttt180) REVERT: B 211 LEU cc_start: 0.6961 (OUTLIER) cc_final: 0.6694 (tt) REVERT: B 214 MET cc_start: 0.8114 (OUTLIER) cc_final: 0.7883 (mtm) REVERT: C 29 GLU cc_start: 0.6831 (OUTLIER) cc_final: 0.6450 (mp0) REVERT: C 55 MET cc_start: 0.8549 (OUTLIER) cc_final: 0.7736 (mtp) REVERT: C 113 GLU cc_start: 0.6235 (mt-10) cc_final: 0.5959 (mt-10) REVERT: C 210 THR cc_start: 0.6324 (OUTLIER) cc_final: 0.6064 (t) REVERT: C 211 LEU cc_start: 0.6543 (OUTLIER) cc_final: 0.6167 (tt) REVERT: C 213 GLU cc_start: 0.7354 (mm-30) cc_final: 0.7090 (mm-30) REVERT: C 218 CYS cc_start: 0.7296 (t) cc_final: 0.6915 (m) REVERT: D 83 LEU cc_start: 0.6327 (OUTLIER) cc_final: 0.5855 (mm) REVERT: D 115 ILE cc_start: 0.6764 (OUTLIER) cc_final: 0.6405 (tp) REVERT: D 162 ARG cc_start: 0.7132 (OUTLIER) cc_final: 0.6302 (ttm-80) REVERT: D 173 ARG cc_start: 0.7781 (OUTLIER) cc_final: 0.6603 (ttp-170) REVERT: D 180 GLU cc_start: 0.6317 (OUTLIER) cc_final: 0.5949 (pm20) REVERT: D 199 LYS cc_start: 0.7949 (tptp) cc_final: 0.7459 (mmtt) REVERT: D 203 LYS cc_start: 0.7111 (OUTLIER) cc_final: 0.6696 (mppt) REVERT: D 214 MET cc_start: 0.7782 (OUTLIER) cc_final: 0.7233 (mtp) REVERT: D 218 CYS cc_start: 0.7460 (t) cc_final: 0.7027 (m) REVERT: E 10 MET cc_start: 0.4575 (mpp) cc_final: 0.4312 (tpp) REVERT: E 29 GLU cc_start: 0.7012 (OUTLIER) cc_final: 0.6559 (mp0) REVERT: E 35 GLU cc_start: 0.7889 (pm20) cc_final: 0.7663 (pm20) REVERT: E 55 MET cc_start: 0.8559 (OUTLIER) cc_final: 0.7959 (mtp) REVERT: E 132 ARG cc_start: 0.7569 (ttp80) cc_final: 0.7279 (mtm110) REVERT: E 136 LEU cc_start: 0.8714 (OUTLIER) cc_final: 0.8436 (tt) REVERT: E 167 ARG cc_start: 0.7447 (ptm-80) cc_final: 0.7180 (ptm160) REVERT: E 210 THR cc_start: 0.6680 (OUTLIER) cc_final: 0.6192 (t) REVERT: E 213 GLU cc_start: 0.7130 (mm-30) cc_final: 0.6659 (mm-30) REVERT: E 218 CYS cc_start: 0.7339 (t) cc_final: 0.7036 (m) REVERT: F 29 GLU cc_start: 0.7434 (OUTLIER) cc_final: 0.6947 (mp0) REVERT: F 67 GLN cc_start: 0.8971 (tp40) cc_final: 0.8426 (tp40) REVERT: F 79 GLU cc_start: 0.5854 (tm-30) cc_final: 0.5603 (tm-30) REVERT: F 128 GLU cc_start: 0.7667 (mp0) cc_final: 0.7374 (mp0) REVERT: F 215 MET cc_start: 0.7184 (OUTLIER) cc_final: 0.6879 (mtp) outliers start: 76 outliers final: 28 residues processed: 325 average time/residue: 0.6557 time to fit residues: 225.1707 Evaluate side-chains 334 residues out of total 1128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 282 time to evaluate : 0.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 GLU Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain A residue 120 HIS Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 192 GLN Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 214 MET Chi-restraints excluded: chain B residue 29 GLU Chi-restraints excluded: chain B residue 30 LYS Chi-restraints excluded: chain B residue 58 THR Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain B residue 110 THR Chi-restraints excluded: chain B residue 120 HIS Chi-restraints excluded: chain B residue 192 GLN Chi-restraints excluded: chain B residue 211 LEU Chi-restraints excluded: chain B residue 214 MET Chi-restraints excluded: chain C residue 29 GLU Chi-restraints excluded: chain C residue 55 MET Chi-restraints excluded: chain C residue 58 THR Chi-restraints excluded: chain C residue 71 GLU Chi-restraints excluded: chain C residue 83 LEU Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain C residue 120 HIS Chi-restraints excluded: chain C residue 210 THR Chi-restraints excluded: chain C residue 211 LEU Chi-restraints excluded: chain D residue 30 LYS Chi-restraints excluded: chain D residue 41 SER Chi-restraints excluded: chain D residue 83 LEU Chi-restraints excluded: chain D residue 115 ILE Chi-restraints excluded: chain D residue 120 HIS Chi-restraints excluded: chain D residue 162 ARG Chi-restraints excluded: chain D residue 172 LEU Chi-restraints excluded: chain D residue 173 ARG Chi-restraints excluded: chain D residue 175 GLU Chi-restraints excluded: chain D residue 180 GLU Chi-restraints excluded: chain D residue 200 THR Chi-restraints excluded: chain D residue 203 LYS Chi-restraints excluded: chain D residue 214 MET Chi-restraints excluded: chain E residue 29 GLU Chi-restraints excluded: chain E residue 55 MET Chi-restraints excluded: chain E residue 71 GLU Chi-restraints excluded: chain E residue 83 LEU Chi-restraints excluded: chain E residue 136 LEU Chi-restraints excluded: chain E residue 192 GLN Chi-restraints excluded: chain E residue 210 THR Chi-restraints excluded: chain F residue 29 GLU Chi-restraints excluded: chain F residue 30 LYS Chi-restraints excluded: chain F residue 71 GLU Chi-restraints excluded: chain F residue 83 LEU Chi-restraints excluded: chain F residue 192 GLN Chi-restraints excluded: chain F residue 215 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 82 optimal weight: 1.9990 chunk 115 optimal weight: 0.8980 chunk 38 optimal weight: 0.9990 chunk 83 optimal weight: 0.6980 chunk 88 optimal weight: 0.3980 chunk 8 optimal weight: 3.9990 chunk 68 optimal weight: 1.9990 chunk 75 optimal weight: 0.0020 chunk 93 optimal weight: 0.9990 chunk 77 optimal weight: 3.9990 chunk 57 optimal weight: 0.5980 overall best weight: 0.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 57 ASN ** A 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 183 ASN ** D 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4362 r_free = 0.4362 target = 0.184519 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.154450 restraints weight = 14892.077| |-----------------------------------------------------------------------------| r_work (start): 0.4012 rms_B_bonded: 2.52 r_work: 0.3873 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3873 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7180 moved from start: 0.3790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10584 Z= 0.134 Angle : 0.612 9.206 14388 Z= 0.306 Chirality : 0.042 0.182 1608 Planarity : 0.005 0.049 1878 Dihedral : 4.126 30.720 1406 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 10.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.39 % Favored : 93.61 % Rotamer: Outliers : 5.85 % Allowed : 35.20 % Favored : 58.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: 1.02 (0.24), residues: 1314 helix: 1.59 (0.18), residues: 834 sheet: None (None), residues: 0 loop : -0.97 (0.31), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 167 TYR 0.012 0.001 TYR B 169 PHE 0.010 0.001 PHE B 32 TRP 0.045 0.002 TRP A 184 HIS 0.003 0.001 HIS F 12 Details of bonding type rmsd covalent geometry : bond 0.00328 (10584) covalent geometry : angle 0.61212 (14388) hydrogen bonds : bond 0.03724 ( 612) hydrogen bonds : angle 4.38124 ( 1836) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 1128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 275 time to evaluate : 0.427 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 MET cc_start: 0.4743 (tpp) cc_final: 0.4481 (tpp) REVERT: A 29 GLU cc_start: 0.6902 (OUTLIER) cc_final: 0.6527 (mp0) REVERT: A 35 GLU cc_start: 0.7687 (pm20) cc_final: 0.7023 (pm20) REVERT: A 75 GLU cc_start: 0.7921 (mt-10) cc_final: 0.7643 (mt-10) REVERT: A 76 GLU cc_start: 0.7848 (mm-30) cc_final: 0.7497 (mp0) REVERT: A 83 LEU cc_start: 0.6355 (OUTLIER) cc_final: 0.5893 (mm) REVERT: A 185 MET cc_start: 0.7053 (ptp) cc_final: 0.6809 (ptm) REVERT: A 210 THR cc_start: 0.5562 (OUTLIER) cc_final: 0.5148 (p) REVERT: A 213 GLU cc_start: 0.7371 (mm-30) cc_final: 0.7011 (mm-30) REVERT: B 29 GLU cc_start: 0.7224 (OUTLIER) cc_final: 0.6814 (mp0) REVERT: B 39 MET cc_start: 0.8049 (tpp) cc_final: 0.7608 (tpt) REVERT: B 44 SER cc_start: 0.8269 (p) cc_final: 0.7867 (m) REVERT: B 67 GLN cc_start: 0.8840 (tp40) cc_final: 0.8505 (tp40) REVERT: B 128 GLU cc_start: 0.7605 (mm-30) cc_final: 0.7303 (mm-30) REVERT: B 173 ARG cc_start: 0.7738 (ttt-90) cc_final: 0.7499 (ttt180) REVERT: B 203 LYS cc_start: 0.7397 (OUTLIER) cc_final: 0.7090 (mmtm) REVERT: B 211 LEU cc_start: 0.6979 (OUTLIER) cc_final: 0.6697 (tt) REVERT: C 29 GLU cc_start: 0.6792 (OUTLIER) cc_final: 0.6436 (mp0) REVERT: C 58 THR cc_start: 0.8745 (OUTLIER) cc_final: 0.8506 (t) REVERT: C 113 GLU cc_start: 0.6201 (mt-10) cc_final: 0.5923 (mt-10) REVERT: C 211 LEU cc_start: 0.6592 (OUTLIER) cc_final: 0.6234 (tt) REVERT: C 218 CYS cc_start: 0.7117 (t) cc_final: 0.6812 (m) REVERT: D 144 MET cc_start: 0.7570 (ptt) cc_final: 0.7258 (ptp) REVERT: D 162 ARG cc_start: 0.7093 (OUTLIER) cc_final: 0.6249 (ttm-80) REVERT: D 173 ARG cc_start: 0.7696 (OUTLIER) cc_final: 0.6486 (ttp-170) REVERT: D 180 GLU cc_start: 0.6109 (OUTLIER) cc_final: 0.5755 (pm20) REVERT: D 203 LYS cc_start: 0.7055 (OUTLIER) cc_final: 0.6751 (mmtm) REVERT: D 214 MET cc_start: 0.7771 (OUTLIER) cc_final: 0.7250 (mtp) REVERT: D 218 CYS cc_start: 0.7352 (t) cc_final: 0.6940 (m) REVERT: E 10 MET cc_start: 0.4668 (mpp) cc_final: 0.4398 (tpp) REVERT: E 29 GLU cc_start: 0.6972 (OUTLIER) cc_final: 0.6533 (mp0) REVERT: E 35 GLU cc_start: 0.7890 (pm20) cc_final: 0.7602 (pm20) REVERT: E 55 MET cc_start: 0.8529 (OUTLIER) cc_final: 0.7904 (mtp) REVERT: E 132 ARG cc_start: 0.7497 (ttp80) cc_final: 0.7212 (mtm110) REVERT: E 167 ARG cc_start: 0.7480 (ptm-80) cc_final: 0.7222 (ptm160) REVERT: E 210 THR cc_start: 0.6676 (OUTLIER) cc_final: 0.6210 (t) REVERT: E 213 GLU cc_start: 0.7305 (mm-30) cc_final: 0.6772 (mm-30) REVERT: E 218 CYS cc_start: 0.7248 (t) cc_final: 0.6951 (m) REVERT: F 29 GLU cc_start: 0.7416 (OUTLIER) cc_final: 0.6922 (mp0) REVERT: F 67 GLN cc_start: 0.8958 (tp40) cc_final: 0.8412 (tp40) REVERT: F 215 MET cc_start: 0.7149 (OUTLIER) cc_final: 0.6857 (mtp) outliers start: 66 outliers final: 26 residues processed: 311 average time/residue: 0.6705 time to fit residues: 220.4382 Evaluate side-chains 312 residues out of total 1128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 267 time to evaluate : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 GLU Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain B residue 29 GLU Chi-restraints excluded: chain B residue 30 LYS Chi-restraints excluded: chain B residue 41 SER Chi-restraints excluded: chain B residue 58 THR Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain B residue 120 HIS Chi-restraints excluded: chain B residue 192 GLN Chi-restraints excluded: chain B residue 203 LYS Chi-restraints excluded: chain B residue 211 LEU Chi-restraints excluded: chain C residue 29 GLU Chi-restraints excluded: chain C residue 58 THR Chi-restraints excluded: chain C residue 71 GLU Chi-restraints excluded: chain C residue 83 LEU Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain C residue 120 HIS Chi-restraints excluded: chain C residue 170 LYS Chi-restraints excluded: chain C residue 192 GLN Chi-restraints excluded: chain C residue 211 LEU Chi-restraints excluded: chain D residue 41 SER Chi-restraints excluded: chain D residue 83 LEU Chi-restraints excluded: chain D residue 162 ARG Chi-restraints excluded: chain D residue 172 LEU Chi-restraints excluded: chain D residue 173 ARG Chi-restraints excluded: chain D residue 175 GLU Chi-restraints excluded: chain D residue 180 GLU Chi-restraints excluded: chain D residue 203 LYS Chi-restraints excluded: chain D residue 214 MET Chi-restraints excluded: chain E residue 29 GLU Chi-restraints excluded: chain E residue 30 LYS Chi-restraints excluded: chain E residue 55 MET Chi-restraints excluded: chain E residue 71 GLU Chi-restraints excluded: chain E residue 83 LEU Chi-restraints excluded: chain E residue 119 THR Chi-restraints excluded: chain E residue 192 GLN Chi-restraints excluded: chain E residue 210 THR Chi-restraints excluded: chain F residue 29 GLU Chi-restraints excluded: chain F residue 30 LYS Chi-restraints excluded: chain F residue 83 LEU Chi-restraints excluded: chain F residue 110 THR Chi-restraints excluded: chain F residue 120 HIS Chi-restraints excluded: chain F residue 192 GLN Chi-restraints excluded: chain F residue 215 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 19 optimal weight: 0.8980 chunk 107 optimal weight: 3.9990 chunk 53 optimal weight: 8.9990 chunk 22 optimal weight: 3.9990 chunk 6 optimal weight: 0.3980 chunk 47 optimal weight: 0.7980 chunk 45 optimal weight: 6.9990 chunk 119 optimal weight: 20.0000 chunk 37 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 129 optimal weight: 4.9990 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 12 HIS A 57 ASN ** A 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 183 ASN ** D 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4339 r_free = 0.4339 target = 0.183403 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.153783 restraints weight = 14938.393| |-----------------------------------------------------------------------------| r_work (start): 0.3974 rms_B_bonded: 2.48 r_work: 0.3833 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3833 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7228 moved from start: 0.4021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 10584 Z= 0.214 Angle : 0.673 10.941 14388 Z= 0.339 Chirality : 0.046 0.204 1608 Planarity : 0.005 0.051 1878 Dihedral : 4.349 31.293 1406 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 11.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.54 % Favored : 93.46 % Rotamer: Outliers : 6.21 % Allowed : 35.64 % Favored : 58.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: 0.73 (0.24), residues: 1314 helix: 1.30 (0.18), residues: 834 sheet: None (None), residues: 0 loop : -0.96 (0.31), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 167 TYR 0.020 0.002 TYR B 169 PHE 0.008 0.001 PHE D 32 TRP 0.034 0.003 TRP C 184 HIS 0.003 0.001 HIS D 12 Details of bonding type rmsd covalent geometry : bond 0.00521 (10584) covalent geometry : angle 0.67257 (14388) hydrogen bonds : bond 0.04447 ( 612) hydrogen bonds : angle 4.54545 ( 1836) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 355 residues out of total 1128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 285 time to evaluate : 0.423 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 MET cc_start: 0.4760 (tpp) cc_final: 0.4479 (tpp) REVERT: A 29 GLU cc_start: 0.6942 (OUTLIER) cc_final: 0.6582 (mp0) REVERT: A 30 LYS cc_start: 0.8680 (OUTLIER) cc_final: 0.8361 (mmmm) REVERT: A 35 GLU cc_start: 0.7679 (pm20) cc_final: 0.6891 (pm20) REVERT: A 76 GLU cc_start: 0.7804 (mm-30) cc_final: 0.7459 (mp0) REVERT: A 83 LEU cc_start: 0.6426 (OUTLIER) cc_final: 0.5918 (mm) REVERT: A 203 LYS cc_start: 0.7551 (OUTLIER) cc_final: 0.7287 (mppt) REVERT: A 213 GLU cc_start: 0.7238 (mm-30) cc_final: 0.6898 (mm-30) REVERT: A 219 GLN cc_start: 0.6390 (tp-100) cc_final: 0.6170 (tp40) REVERT: B 29 GLU cc_start: 0.7273 (OUTLIER) cc_final: 0.6882 (mp0) REVERT: B 39 MET cc_start: 0.8146 (tpp) cc_final: 0.7732 (tpt) REVERT: B 44 SER cc_start: 0.8314 (p) cc_final: 0.7911 (m) REVERT: B 128 GLU cc_start: 0.7745 (mm-30) cc_final: 0.7458 (mm-30) REVERT: B 173 ARG cc_start: 0.7820 (ttt-90) cc_final: 0.7576 (ttt180) REVERT: B 203 LYS cc_start: 0.7535 (OUTLIER) cc_final: 0.7136 (mppt) REVERT: C 29 GLU cc_start: 0.6832 (OUTLIER) cc_final: 0.6452 (mp0) REVERT: C 55 MET cc_start: 0.8477 (OUTLIER) cc_final: 0.7646 (mtp) REVERT: C 113 GLU cc_start: 0.6214 (mt-10) cc_final: 0.5934 (mt-10) REVERT: C 210 THR cc_start: 0.6405 (OUTLIER) cc_final: 0.6138 (t) REVERT: C 211 LEU cc_start: 0.6508 (OUTLIER) cc_final: 0.6148 (tt) REVERT: C 214 MET cc_start: 0.8331 (mtt) cc_final: 0.8110 (mtp) REVERT: C 218 CYS cc_start: 0.7357 (t) cc_final: 0.6924 (m) REVERT: D 162 ARG cc_start: 0.6962 (OUTLIER) cc_final: 0.6257 (ttm-80) REVERT: D 180 GLU cc_start: 0.6168 (OUTLIER) cc_final: 0.5829 (pm20) REVERT: D 199 LYS cc_start: 0.7983 (tptp) cc_final: 0.7467 (mmtt) REVERT: D 203 LYS cc_start: 0.7193 (OUTLIER) cc_final: 0.6781 (mppt) REVERT: D 214 MET cc_start: 0.7828 (OUTLIER) cc_final: 0.7267 (mtp) REVERT: D 218 CYS cc_start: 0.7615 (t) cc_final: 0.7138 (m) REVERT: E 29 GLU cc_start: 0.7002 (OUTLIER) cc_final: 0.6589 (mp0) REVERT: E 55 MET cc_start: 0.8589 (OUTLIER) cc_final: 0.8020 (mtp) REVERT: E 132 ARG cc_start: 0.7542 (ttp80) cc_final: 0.7249 (mtm110) REVERT: E 136 LEU cc_start: 0.8705 (OUTLIER) cc_final: 0.8424 (tt) REVERT: E 167 ARG cc_start: 0.7463 (ptm-80) cc_final: 0.7189 (ptm160) REVERT: E 210 THR cc_start: 0.6006 (OUTLIER) cc_final: 0.5665 (t) REVERT: E 213 GLU cc_start: 0.7133 (mm-30) cc_final: 0.6635 (mm-30) REVERT: E 218 CYS cc_start: 0.7429 (t) cc_final: 0.7062 (m) REVERT: F 29 GLU cc_start: 0.7425 (OUTLIER) cc_final: 0.6959 (mp0) REVERT: F 67 GLN cc_start: 0.9011 (tp40) cc_final: 0.8412 (tp40) REVERT: F 79 GLU cc_start: 0.5959 (tm-30) cc_final: 0.5652 (tm-30) REVERT: F 180 GLU cc_start: 0.5891 (OUTLIER) cc_final: 0.5664 (pm20) REVERT: F 215 MET cc_start: 0.7196 (OUTLIER) cc_final: 0.6892 (mtp) outliers start: 70 outliers final: 38 residues processed: 326 average time/residue: 0.7460 time to fit residues: 257.0465 Evaluate side-chains 341 residues out of total 1128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 282 time to evaluate : 0.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 GLU Chi-restraints excluded: chain A residue 30 LYS Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain A residue 120 HIS Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 203 LYS Chi-restraints excluded: chain B residue 29 GLU Chi-restraints excluded: chain B residue 30 LYS Chi-restraints excluded: chain B residue 41 SER Chi-restraints excluded: chain B residue 58 THR Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain B residue 110 THR Chi-restraints excluded: chain B residue 120 HIS Chi-restraints excluded: chain B residue 192 GLN Chi-restraints excluded: chain B residue 203 LYS Chi-restraints excluded: chain B residue 210 THR Chi-restraints excluded: chain C residue 29 GLU Chi-restraints excluded: chain C residue 55 MET Chi-restraints excluded: chain C residue 58 THR Chi-restraints excluded: chain C residue 71 GLU Chi-restraints excluded: chain C residue 83 LEU Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain C residue 120 HIS Chi-restraints excluded: chain C residue 170 LYS Chi-restraints excluded: chain C residue 192 GLN Chi-restraints excluded: chain C residue 210 THR Chi-restraints excluded: chain C residue 211 LEU Chi-restraints excluded: chain D residue 83 LEU Chi-restraints excluded: chain D residue 110 THR Chi-restraints excluded: chain D residue 120 HIS Chi-restraints excluded: chain D residue 162 ARG Chi-restraints excluded: chain D residue 175 GLU Chi-restraints excluded: chain D residue 180 GLU Chi-restraints excluded: chain D residue 200 THR Chi-restraints excluded: chain D residue 203 LYS Chi-restraints excluded: chain D residue 214 MET Chi-restraints excluded: chain E residue 29 GLU Chi-restraints excluded: chain E residue 30 LYS Chi-restraints excluded: chain E residue 55 MET Chi-restraints excluded: chain E residue 69 LEU Chi-restraints excluded: chain E residue 71 GLU Chi-restraints excluded: chain E residue 83 LEU Chi-restraints excluded: chain E residue 110 THR Chi-restraints excluded: chain E residue 119 THR Chi-restraints excluded: chain E residue 120 HIS Chi-restraints excluded: chain E residue 136 LEU Chi-restraints excluded: chain E residue 192 GLN Chi-restraints excluded: chain E residue 210 THR Chi-restraints excluded: chain F residue 12 HIS Chi-restraints excluded: chain F residue 29 GLU Chi-restraints excluded: chain F residue 30 LYS Chi-restraints excluded: chain F residue 71 GLU Chi-restraints excluded: chain F residue 83 LEU Chi-restraints excluded: chain F residue 110 THR Chi-restraints excluded: chain F residue 120 HIS Chi-restraints excluded: chain F residue 180 GLU Chi-restraints excluded: chain F residue 192 GLN Chi-restraints excluded: chain F residue 215 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 72 optimal weight: 0.9980 chunk 86 optimal weight: 7.9990 chunk 92 optimal weight: 0.9990 chunk 107 optimal weight: 4.9990 chunk 90 optimal weight: 0.5980 chunk 104 optimal weight: 0.5980 chunk 14 optimal weight: 0.4980 chunk 9 optimal weight: 9.9990 chunk 6 optimal weight: 0.8980 chunk 36 optimal weight: 1.9990 chunk 52 optimal weight: 10.0000 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 155 GLN ** A 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 183 ASN ** D 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4362 r_free = 0.4362 target = 0.185221 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.155407 restraints weight = 14965.322| |-----------------------------------------------------------------------------| r_work (start): 0.3999 rms_B_bonded: 2.52 r_work: 0.3860 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3860 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7196 moved from start: 0.4096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 10584 Z= 0.151 Angle : 0.661 9.741 14388 Z= 0.330 Chirality : 0.044 0.213 1608 Planarity : 0.005 0.049 1878 Dihedral : 4.173 17.944 1404 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 10.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.09 % Favored : 93.91 % Rotamer: Outliers : 5.23 % Allowed : 37.32 % Favored : 57.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: 0.82 (0.24), residues: 1314 helix: 1.40 (0.18), residues: 834 sheet: None (None), residues: 0 loop : -0.97 (0.31), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 154 TYR 0.013 0.002 TYR B 169 PHE 0.009 0.001 PHE A 32 TRP 0.052 0.002 TRP A 184 HIS 0.002 0.001 HIS D 12 Details of bonding type rmsd covalent geometry : bond 0.00371 (10584) covalent geometry : angle 0.66109 (14388) hydrogen bonds : bond 0.03935 ( 612) hydrogen bonds : angle 4.52930 ( 1836) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 1128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 275 time to evaluate : 0.422 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 GLU cc_start: 0.6894 (OUTLIER) cc_final: 0.6525 (mp0) REVERT: A 30 LYS cc_start: 0.8653 (tppp) cc_final: 0.8339 (mmmm) REVERT: A 35 GLU cc_start: 0.7621 (pm20) cc_final: 0.6847 (pm20) REVERT: A 75 GLU cc_start: 0.7988 (mt-10) cc_final: 0.7753 (mt-10) REVERT: A 76 GLU cc_start: 0.7815 (mm-30) cc_final: 0.7482 (mp0) REVERT: A 83 LEU cc_start: 0.6139 (OUTLIER) cc_final: 0.5806 (mm) REVERT: A 203 LYS cc_start: 0.7499 (OUTLIER) cc_final: 0.7225 (mppt) REVERT: A 213 GLU cc_start: 0.7197 (mm-30) cc_final: 0.6878 (mm-30) REVERT: A 219 GLN cc_start: 0.6367 (tp-100) cc_final: 0.6157 (tp-100) REVERT: B 29 GLU cc_start: 0.7261 (OUTLIER) cc_final: 0.6866 (mp0) REVERT: B 39 MET cc_start: 0.8068 (tpp) cc_final: 0.7703 (tpt) REVERT: B 44 SER cc_start: 0.8303 (p) cc_final: 0.7885 (m) REVERT: B 128 GLU cc_start: 0.7663 (mm-30) cc_final: 0.7379 (mm-30) REVERT: B 173 ARG cc_start: 0.7726 (ttt-90) cc_final: 0.7473 (ttt180) REVERT: B 203 LYS cc_start: 0.7548 (OUTLIER) cc_final: 0.7121 (mptt) REVERT: C 29 GLU cc_start: 0.6766 (OUTLIER) cc_final: 0.6389 (mp0) REVERT: C 55 MET cc_start: 0.8483 (OUTLIER) cc_final: 0.7756 (mtp) REVERT: C 113 GLU cc_start: 0.6179 (mt-10) cc_final: 0.5908 (mt-10) REVERT: C 210 THR cc_start: 0.6560 (OUTLIER) cc_final: 0.6275 (t) REVERT: C 211 LEU cc_start: 0.6530 (OUTLIER) cc_final: 0.6047 (tt) REVERT: C 218 CYS cc_start: 0.7131 (t) cc_final: 0.6817 (m) REVERT: D 83 LEU cc_start: 0.6287 (OUTLIER) cc_final: 0.5844 (mm) REVERT: D 162 ARG cc_start: 0.6922 (OUTLIER) cc_final: 0.6130 (ttm-80) REVERT: D 173 ARG cc_start: 0.7728 (OUTLIER) cc_final: 0.6547 (ttp-170) REVERT: D 180 GLU cc_start: 0.6094 (OUTLIER) cc_final: 0.5783 (pm20) REVERT: D 181 VAL cc_start: 0.8140 (p) cc_final: 0.7617 (t) REVERT: D 199 LYS cc_start: 0.7967 (tptp) cc_final: 0.7459 (mmtt) REVERT: D 203 LYS cc_start: 0.7135 (OUTLIER) cc_final: 0.6750 (mppt) REVERT: D 214 MET cc_start: 0.7771 (OUTLIER) cc_final: 0.7218 (mtp) REVERT: D 218 CYS cc_start: 0.7390 (t) cc_final: 0.6990 (m) REVERT: E 29 GLU cc_start: 0.6923 (OUTLIER) cc_final: 0.6537 (mp0) REVERT: E 35 GLU cc_start: 0.7812 (pm20) cc_final: 0.7581 (pm20) REVERT: E 55 MET cc_start: 0.8538 (OUTLIER) cc_final: 0.7889 (mtp) REVERT: E 132 ARG cc_start: 0.7521 (ttp80) cc_final: 0.7249 (mtm110) REVERT: E 136 LEU cc_start: 0.8687 (OUTLIER) cc_final: 0.8413 (tt) REVERT: E 167 ARG cc_start: 0.7459 (ptm-80) cc_final: 0.7179 (ptm160) REVERT: E 210 THR cc_start: 0.6640 (OUTLIER) cc_final: 0.6401 (t) REVERT: E 218 CYS cc_start: 0.7272 (t) cc_final: 0.6965 (m) REVERT: F 29 GLU cc_start: 0.7429 (OUTLIER) cc_final: 0.6948 (mp0) REVERT: F 35 GLU cc_start: 0.7837 (pm20) cc_final: 0.7592 (pm20) REVERT: F 67 GLN cc_start: 0.9012 (tp40) cc_final: 0.8411 (tp40) REVERT: F 79 GLU cc_start: 0.5957 (tm-30) cc_final: 0.5646 (tm-30) REVERT: F 215 MET cc_start: 0.7134 (OUTLIER) cc_final: 0.6849 (mtp) outliers start: 59 outliers final: 30 residues processed: 309 average time/residue: 0.7554 time to fit residues: 246.0606 Evaluate side-chains 323 residues out of total 1128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 272 time to evaluate : 0.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 GLU Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 120 HIS Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 203 LYS Chi-restraints excluded: chain B residue 29 GLU Chi-restraints excluded: chain B residue 30 LYS Chi-restraints excluded: chain B residue 41 SER Chi-restraints excluded: chain B residue 58 THR Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain B residue 110 THR Chi-restraints excluded: chain B residue 120 HIS Chi-restraints excluded: chain B residue 192 GLN Chi-restraints excluded: chain B residue 203 LYS Chi-restraints excluded: chain C residue 29 GLU Chi-restraints excluded: chain C residue 55 MET Chi-restraints excluded: chain C residue 58 THR Chi-restraints excluded: chain C residue 71 GLU Chi-restraints excluded: chain C residue 83 LEU Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain C residue 120 HIS Chi-restraints excluded: chain C residue 170 LYS Chi-restraints excluded: chain C residue 192 GLN Chi-restraints excluded: chain C residue 210 THR Chi-restraints excluded: chain C residue 211 LEU Chi-restraints excluded: chain D residue 83 LEU Chi-restraints excluded: chain D residue 120 HIS Chi-restraints excluded: chain D residue 162 ARG Chi-restraints excluded: chain D residue 173 ARG Chi-restraints excluded: chain D residue 175 GLU Chi-restraints excluded: chain D residue 180 GLU Chi-restraints excluded: chain D residue 200 THR Chi-restraints excluded: chain D residue 203 LYS Chi-restraints excluded: chain D residue 214 MET Chi-restraints excluded: chain E residue 29 GLU Chi-restraints excluded: chain E residue 30 LYS Chi-restraints excluded: chain E residue 55 MET Chi-restraints excluded: chain E residue 69 LEU Chi-restraints excluded: chain E residue 71 GLU Chi-restraints excluded: chain E residue 83 LEU Chi-restraints excluded: chain E residue 110 THR Chi-restraints excluded: chain E residue 136 LEU Chi-restraints excluded: chain E residue 192 GLN Chi-restraints excluded: chain E residue 210 THR Chi-restraints excluded: chain F residue 29 GLU Chi-restraints excluded: chain F residue 30 LYS Chi-restraints excluded: chain F residue 83 LEU Chi-restraints excluded: chain F residue 110 THR Chi-restraints excluded: chain F residue 120 HIS Chi-restraints excluded: chain F residue 192 GLN Chi-restraints excluded: chain F residue 215 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 26 optimal weight: 1.9990 chunk 120 optimal weight: 0.5980 chunk 45 optimal weight: 4.9990 chunk 131 optimal weight: 2.9990 chunk 56 optimal weight: 0.2980 chunk 23 optimal weight: 0.8980 chunk 47 optimal weight: 0.5980 chunk 57 optimal weight: 0.9990 chunk 129 optimal weight: 0.6980 chunk 104 optimal weight: 0.5980 chunk 102 optimal weight: 0.5980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 57 ASN A 183 ASN ** B 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4368 r_free = 0.4368 target = 0.185073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.154730 restraints weight = 14753.533| |-----------------------------------------------------------------------------| r_work (start): 0.4012 rms_B_bonded: 2.54 r_work: 0.3875 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3875 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7182 moved from start: 0.4157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 10584 Z= 0.138 Angle : 0.660 11.414 14388 Z= 0.328 Chirality : 0.043 0.200 1608 Planarity : 0.005 0.049 1878 Dihedral : 4.114 17.440 1404 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 10.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.32 % Favored : 93.68 % Rotamer: Outliers : 5.05 % Allowed : 37.15 % Favored : 57.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: 0.82 (0.24), residues: 1314 helix: 1.40 (0.18), residues: 834 sheet: None (None), residues: 0 loop : -0.97 (0.31), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 167 TYR 0.011 0.001 TYR B 169 PHE 0.009 0.001 PHE C 32 TRP 0.042 0.002 TRP D 184 HIS 0.002 0.000 HIS F 12 Details of bonding type rmsd covalent geometry : bond 0.00338 (10584) covalent geometry : angle 0.66034 (14388) hydrogen bonds : bond 0.03812 ( 612) hydrogen bonds : angle 4.60036 ( 1836) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 1128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 268 time to evaluate : 0.417 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 GLU cc_start: 0.6900 (OUTLIER) cc_final: 0.6529 (mp0) REVERT: A 30 LYS cc_start: 0.8675 (tppp) cc_final: 0.8329 (mmmm) REVERT: A 35 GLU cc_start: 0.7611 (pm20) cc_final: 0.6784 (pm20) REVERT: A 75 GLU cc_start: 0.7937 (mt-10) cc_final: 0.7729 (mt-10) REVERT: A 76 GLU cc_start: 0.7740 (mm-30) cc_final: 0.7452 (mp0) REVERT: A 83 LEU cc_start: 0.6174 (OUTLIER) cc_final: 0.5837 (mm) REVERT: A 203 LYS cc_start: 0.7448 (OUTLIER) cc_final: 0.7189 (mppt) REVERT: A 213 GLU cc_start: 0.7210 (mm-30) cc_final: 0.6805 (mm-30) REVERT: B 29 GLU cc_start: 0.7279 (OUTLIER) cc_final: 0.6864 (mp0) REVERT: B 35 GLU cc_start: 0.7829 (pm20) cc_final: 0.7609 (pm20) REVERT: B 39 MET cc_start: 0.7946 (tpp) cc_final: 0.7576 (tpt) REVERT: B 128 GLU cc_start: 0.7614 (mm-30) cc_final: 0.7308 (mm-30) REVERT: B 173 ARG cc_start: 0.7716 (ttt-90) cc_final: 0.7473 (ttt180) REVERT: B 203 LYS cc_start: 0.7504 (OUTLIER) cc_final: 0.7089 (mptt) REVERT: C 29 GLU cc_start: 0.6754 (OUTLIER) cc_final: 0.6397 (mp0) REVERT: C 58 THR cc_start: 0.8796 (OUTLIER) cc_final: 0.8527 (m) REVERT: C 76 GLU cc_start: 0.7899 (mm-30) cc_final: 0.7698 (mp0) REVERT: C 113 GLU cc_start: 0.6154 (mt-10) cc_final: 0.5867 (mt-10) REVERT: C 175 GLU cc_start: 0.6805 (tp30) cc_final: 0.6547 (tp30) REVERT: C 211 LEU cc_start: 0.6519 (OUTLIER) cc_final: 0.6193 (tt) REVERT: C 213 GLU cc_start: 0.7121 (mm-30) cc_final: 0.6784 (mm-30) REVERT: D 1 PRO cc_start: 0.8026 (Cg_exo) cc_final: 0.7723 (Cg_endo) REVERT: D 83 LEU cc_start: 0.6271 (OUTLIER) cc_final: 0.5834 (mm) REVERT: D 162 ARG cc_start: 0.7048 (OUTLIER) cc_final: 0.6157 (ttm-80) REVERT: D 173 ARG cc_start: 0.7707 (OUTLIER) cc_final: 0.6515 (ttp-170) REVERT: D 180 GLU cc_start: 0.6150 (OUTLIER) cc_final: 0.5808 (pm20) REVERT: D 203 LYS cc_start: 0.7047 (OUTLIER) cc_final: 0.6729 (mmtm) REVERT: D 214 MET cc_start: 0.7745 (OUTLIER) cc_final: 0.7249 (mtp) REVERT: E 29 GLU cc_start: 0.6905 (OUTLIER) cc_final: 0.6535 (mp0) REVERT: E 35 GLU cc_start: 0.7757 (pm20) cc_final: 0.7494 (pm20) REVERT: E 55 MET cc_start: 0.8478 (OUTLIER) cc_final: 0.7832 (mtp) REVERT: E 118 MET cc_start: 0.7412 (ptm) cc_final: 0.7143 (ptt) REVERT: E 132 ARG cc_start: 0.7487 (ttp80) cc_final: 0.7220 (mtm110) REVERT: E 136 LEU cc_start: 0.8644 (OUTLIER) cc_final: 0.8407 (tt) REVERT: E 167 ARG cc_start: 0.7462 (ptm-80) cc_final: 0.7188 (ptm160) REVERT: E 210 THR cc_start: 0.6632 (OUTLIER) cc_final: 0.6419 (t) REVERT: E 218 CYS cc_start: 0.7205 (t) cc_final: 0.6993 (m) REVERT: F 29 GLU cc_start: 0.7430 (OUTLIER) cc_final: 0.6949 (mp0) REVERT: F 67 GLN cc_start: 0.9020 (tp40) cc_final: 0.8422 (tp40) REVERT: F 79 GLU cc_start: 0.5947 (tm-30) cc_final: 0.5634 (tm-30) REVERT: F 215 MET cc_start: 0.7058 (OUTLIER) cc_final: 0.6768 (mtp) outliers start: 57 outliers final: 33 residues processed: 303 average time/residue: 0.7936 time to fit residues: 253.4380 Evaluate side-chains 321 residues out of total 1128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 268 time to evaluate : 0.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 GLU Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain A residue 120 HIS Chi-restraints excluded: chain A residue 183 ASN Chi-restraints excluded: chain A residue 203 LYS Chi-restraints excluded: chain B residue 29 GLU Chi-restraints excluded: chain B residue 30 LYS Chi-restraints excluded: chain B residue 41 SER Chi-restraints excluded: chain B residue 58 THR Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain B residue 120 HIS Chi-restraints excluded: chain B residue 192 GLN Chi-restraints excluded: chain B residue 203 LYS Chi-restraints excluded: chain C residue 29 GLU Chi-restraints excluded: chain C residue 58 THR Chi-restraints excluded: chain C residue 59 VAL Chi-restraints excluded: chain C residue 83 LEU Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain C residue 120 HIS Chi-restraints excluded: chain C residue 170 LYS Chi-restraints excluded: chain C residue 192 GLN Chi-restraints excluded: chain C residue 211 LEU Chi-restraints excluded: chain D residue 83 LEU Chi-restraints excluded: chain D residue 110 THR Chi-restraints excluded: chain D residue 120 HIS Chi-restraints excluded: chain D residue 162 ARG Chi-restraints excluded: chain D residue 173 ARG Chi-restraints excluded: chain D residue 175 GLU Chi-restraints excluded: chain D residue 180 GLU Chi-restraints excluded: chain D residue 200 THR Chi-restraints excluded: chain D residue 203 LYS Chi-restraints excluded: chain D residue 214 MET Chi-restraints excluded: chain E residue 29 GLU Chi-restraints excluded: chain E residue 30 LYS Chi-restraints excluded: chain E residue 55 MET Chi-restraints excluded: chain E residue 69 LEU Chi-restraints excluded: chain E residue 71 GLU Chi-restraints excluded: chain E residue 83 LEU Chi-restraints excluded: chain E residue 110 THR Chi-restraints excluded: chain E residue 119 THR Chi-restraints excluded: chain E residue 120 HIS Chi-restraints excluded: chain E residue 136 LEU Chi-restraints excluded: chain E residue 192 GLN Chi-restraints excluded: chain E residue 210 THR Chi-restraints excluded: chain F residue 29 GLU Chi-restraints excluded: chain F residue 30 LYS Chi-restraints excluded: chain F residue 83 LEU Chi-restraints excluded: chain F residue 110 THR Chi-restraints excluded: chain F residue 120 HIS Chi-restraints excluded: chain F residue 180 GLU Chi-restraints excluded: chain F residue 192 GLN Chi-restraints excluded: chain F residue 215 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 58 optimal weight: 0.7980 chunk 104 optimal weight: 0.5980 chunk 9 optimal weight: 9.9990 chunk 86 optimal weight: 5.9990 chunk 46 optimal weight: 0.5980 chunk 106 optimal weight: 0.8980 chunk 89 optimal weight: 2.9990 chunk 53 optimal weight: 6.9990 chunk 55 optimal weight: 2.9990 chunk 68 optimal weight: 0.8980 chunk 84 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 183 ASN ** E 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4361 r_free = 0.4361 target = 0.184544 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.154085 restraints weight = 14988.153| |-----------------------------------------------------------------------------| r_work (start): 0.4012 rms_B_bonded: 2.55 r_work: 0.3876 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3876 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7184 moved from start: 0.4254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 10584 Z= 0.158 Angle : 0.692 11.181 14388 Z= 0.345 Chirality : 0.044 0.233 1608 Planarity : 0.005 0.049 1878 Dihedral : 4.138 17.398 1404 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 10.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.16 % Favored : 93.84 % Rotamer: Outliers : 5.50 % Allowed : 37.15 % Favored : 57.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: 0.77 (0.24), residues: 1314 helix: 1.28 (0.18), residues: 840 sheet: None (None), residues: 0 loop : -0.83 (0.31), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 154 TYR 0.015 0.002 TYR B 169 PHE 0.008 0.001 PHE A 32 TRP 0.058 0.003 TRP A 184 HIS 0.001 0.001 HIS F 12 Details of bonding type rmsd covalent geometry : bond 0.00387 (10584) covalent geometry : angle 0.69169 (14388) hydrogen bonds : bond 0.04104 ( 612) hydrogen bonds : angle 4.63919 ( 1836) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4492.34 seconds wall clock time: 77 minutes 10.54 seconds (4630.54 seconds total)