Starting phenix.real_space_refine on Sat Aug 23 05:40:04 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9i8i_52724/08_2025/9i8i_52724.cif Found real_map, /net/cci-nas-00/data/ceres_data/9i8i_52724/08_2025/9i8i_52724.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.75 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9i8i_52724/08_2025/9i8i_52724.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9i8i_52724/08_2025/9i8i_52724.map" model { file = "/net/cci-nas-00/data/ceres_data/9i8i_52724/08_2025/9i8i_52724.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9i8i_52724/08_2025/9i8i_52724.cif" } resolution = 2.75 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= 0.006 sd= 0.054 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 6534 2.51 5 N 1812 2.21 5 O 1950 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 23 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 10374 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1729 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1729 Classifications: {'peptide': 223} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 206} Chain: "F" Number of atoms: 1729 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1729 Classifications: {'peptide': 223} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 206} Chain: "E" Number of atoms: 1729 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1729 Classifications: {'peptide': 223} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 206} Chain: "D" Number of atoms: 1729 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1729 Classifications: {'peptide': 223} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 206} Chain: "C" Number of atoms: 1729 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1729 Classifications: {'peptide': 223} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 206} Chain: "B" Number of atoms: 1729 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1729 Classifications: {'peptide': 223} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 206} Time building chain proxies: 2.13, per 1000 atoms: 0.21 Number of scatterers: 10374 At special positions: 0 Unit cell: (113.23, 113.23, 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 1950 8.00 N 1812 7.00 C 6534 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: 0.78 Conformation dependent library (CDL) restraints added in 271.3 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 2652 Ramachandran restraints generated. 1326 Oldfield, 0 Emsley, 1326 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 5 sheets defined 67.6% alpha, 0.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.28 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: 4.155A pdb=" N VAL A 59 " --> pdb=" O MET A 55 " (cutoff:3.500A) Processing helix chain 'A' and resid 62 through 84 removed outlier: 3.528A pdb=" N ARG A 82 " --> pdb=" O ALA A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 100 through 105 removed outlier: 3.617A pdb=" N ALA A 105 " --> pdb=" O GLY A 101 " (cutoff:3.500A) Processing helix chain 'A' and resid 110 through 118 Processing helix chain 'A' and resid 125 through 145 removed outlier: 3.693A pdb=" N LYS A 140 " --> pdb=" O LEU A 136 " (cutoff:3.500A) Processing helix chain 'A' and resid 149 through 153 Processing helix chain 'A' and resid 160 through 175 Processing helix chain 'A' and resid 178 through 189 Processing helix chain 'A' and resid 195 through 206 Processing helix chain 'A' and resid 210 through 219 Processing helix chain 'F' and resid 16 through 30 removed outlier: 3.594A pdb=" N LEU F 20 " --> pdb=" O SER F 16 " (cutoff:3.500A) Processing helix chain 'F' and resid 35 through 44 Processing helix chain 'F' and resid 48 through 58 Processing helix chain 'F' and resid 62 through 84 removed outlier: 3.530A pdb=" N ARG F 82 " --> pdb=" O ALA F 78 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N HIS F 84 " --> pdb=" O TRP F 80 " (cutoff:3.500A) Processing helix chain 'F' and resid 100 through 105 removed outlier: 3.548A pdb=" N ALA F 105 " --> pdb=" O GLY F 101 " (cutoff:3.500A) Processing helix chain 'F' and resid 110 through 118 Processing helix chain 'F' and resid 125 through 145 removed outlier: 3.817A pdb=" N LYS F 140 " --> pdb=" O LEU F 136 " (cutoff:3.500A) Processing helix chain 'F' and resid 149 through 153 removed outlier: 3.558A pdb=" N ILE F 153 " --> pdb=" O ILE F 150 " (cutoff:3.500A) Processing helix chain 'F' and resid 160 through 175 Processing helix chain 'F' and resid 178 through 189 Processing helix chain 'F' and resid 195 through 206 Processing helix chain 'F' and resid 210 through 218 Processing helix chain 'E' and resid 16 through 30 removed outlier: 3.512A pdb=" N LEU E 20 " --> pdb=" O SER E 16 " (cutoff:3.500A) Processing helix chain 'E' and resid 35 through 44 Processing helix chain 'E' and resid 48 through 59 removed outlier: 4.197A pdb=" N VAL E 59 " --> pdb=" O MET E 55 " (cutoff:3.500A) Processing helix chain 'E' and resid 62 through 84 removed outlier: 3.531A pdb=" N ARG E 82 " --> pdb=" O ALA E 78 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N HIS E 84 " --> pdb=" O TRP E 80 " (cutoff:3.500A) Processing helix chain 'E' and resid 100 through 105 removed outlier: 3.681A pdb=" N ALA E 105 " --> pdb=" O GLY E 101 " (cutoff:3.500A) Processing helix chain 'E' and resid 110 through 118 Processing helix chain 'E' and resid 125 through 145 removed outlier: 4.218A pdb=" N LYS E 140 " --> pdb=" O LEU E 136 " (cutoff:3.500A) Processing helix chain 'E' and resid 149 through 153 removed outlier: 3.692A pdb=" N ILE E 153 " --> pdb=" O ILE E 150 " (cutoff:3.500A) Processing helix chain 'E' and resid 160 through 175 Processing helix chain 'E' and resid 178 through 189 Processing helix chain 'E' and resid 195 through 206 Processing helix chain 'E' and resid 210 through 218 removed outlier: 3.510A pdb=" N CYS E 218 " --> pdb=" O MET E 214 " (cutoff:3.500A) 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: 3.928A pdb=" N VAL D 59 " --> pdb=" O MET D 55 " (cutoff:3.500A) Processing helix chain 'D' and resid 62 through 84 removed outlier: 3.532A pdb=" N ARG D 82 " --> pdb=" O ALA D 78 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N HIS D 84 " --> pdb=" O TRP D 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 100 through 105 removed outlier: 3.725A pdb=" N ALA D 105 " --> pdb=" O GLY D 101 " (cutoff:3.500A) Processing helix chain 'D' and resid 110 through 118 Processing helix chain 'D' and resid 125 through 145 removed outlier: 3.859A pdb=" N LYS D 140 " --> pdb=" O LEU D 136 " (cutoff:3.500A) Processing helix chain 'D' and resid 149 through 153 removed outlier: 3.764A pdb=" N ILE D 153 " --> pdb=" O ILE D 150 " (cutoff:3.500A) Processing helix chain 'D' and resid 160 through 175 removed outlier: 3.514A pdb=" N TYR D 164 " --> pdb=" O PRO D 160 " (cutoff:3.500A) Processing helix chain 'D' and resid 178 through 193 removed outlier: 4.057A pdb=" N LEU D 190 " --> pdb=" O THR D 186 " (cutoff:3.500A) removed outlier: 5.880A pdb=" N VAL D 191 " --> pdb=" O GLU D 187 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N GLN D 192 " --> pdb=" O THR D 188 " (cutoff:3.500A) Processing helix chain 'D' and resid 195 through 206 Processing helix chain 'D' and resid 210 through 218 Processing helix chain 'C' and resid 16 through 30 removed outlier: 3.638A pdb=" N LEU C 20 " --> pdb=" O SER C 16 " (cutoff:3.500A) Processing helix chain 'C' and resid 35 through 44 Processing helix chain 'C' and resid 48 through 59 removed outlier: 4.144A pdb=" N VAL C 59 " --> pdb=" O MET C 55 " (cutoff:3.500A) Processing helix chain 'C' and resid 62 through 84 removed outlier: 3.505A pdb=" N ARG C 82 " --> pdb=" O ALA C 78 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N HIS C 84 " --> pdb=" O TRP C 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 100 through 105 removed outlier: 3.689A 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 145 removed outlier: 3.718A pdb=" N LYS C 140 " --> pdb=" O LEU C 136 " (cutoff:3.500A) Processing helix chain 'C' and resid 149 through 153 Processing helix chain 'C' and resid 160 through 175 removed outlier: 3.504A pdb=" N TYR C 164 " --> pdb=" O PRO C 160 " (cutoff:3.500A) Processing helix chain 'C' and resid 178 through 189 Processing helix chain 'C' and resid 195 through 206 Processing helix chain 'C' and resid 210 through 218 removed outlier: 3.503A pdb=" N CYS C 218 " --> pdb=" O MET C 214 " (cutoff:3.500A) 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 58 Processing helix chain 'B' and resid 62 through 84 removed outlier: 3.504A pdb=" N ARG B 82 " --> pdb=" O ALA B 78 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N HIS B 84 " --> pdb=" O TRP B 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 100 through 105 removed outlier: 3.606A pdb=" N ALA B 105 " --> pdb=" O GLY B 101 " (cutoff:3.500A) Processing helix chain 'B' and resid 110 through 118 Processing helix chain 'B' and resid 125 through 145 removed outlier: 3.801A pdb=" N LYS B 140 " --> pdb=" O LEU B 136 " (cutoff:3.500A) Processing helix chain 'B' and resid 149 through 153 removed outlier: 3.634A pdb=" N ILE B 153 " --> pdb=" O ILE B 150 " (cutoff:3.500A) Processing helix chain 'B' and resid 160 through 175 removed outlier: 3.514A pdb=" N TYR B 164 " --> pdb=" O PRO B 160 " (cutoff:3.500A) Processing helix chain 'B' and resid 178 through 189 Processing helix chain 'B' and resid 195 through 206 Processing helix chain 'B' and resid 210 through 218 removed outlier: 3.687A pdb=" N MET B 214 " --> pdb=" O THR B 210 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 2 through 3 Processing sheet with id=AA2, first strand: chain 'E' and resid 2 through 3 Processing sheet with id=AA3, first strand: chain 'D' and resid 2 through 3 Processing sheet with id=AA4, first strand: chain 'C' and resid 2 through 3 Processing sheet with id=AA5, first strand: chain 'B' and resid 2 through 3 590 hydrogen bonds defined for protein. 1731 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: 1.39 Time building geometry restraints manager: 0.99 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3465 1.34 - 1.46: 1594 1.46 - 1.58: 5405 1.58 - 1.70: 0 1.70 - 1.82: 144 Bond restraints: 10608 Sorted by residual: bond pdb=" C ILE D 37 " pdb=" N PRO D 38 " ideal model delta sigma weight residual 1.335 1.359 -0.024 1.28e-02 6.10e+03 3.50e+00 bond pdb=" C ILE B 37 " pdb=" N PRO B 38 " ideal model delta sigma weight residual 1.335 1.361 -0.025 1.36e-02 5.41e+03 3.45e+00 bond pdb=" C ILE A 37 " pdb=" N PRO A 38 " ideal model delta sigma weight residual 1.335 1.358 -0.024 1.28e-02 6.10e+03 3.42e+00 bond pdb=" C ILE E 37 " pdb=" N PRO E 38 " ideal model delta sigma weight residual 1.335 1.358 -0.024 1.28e-02 6.10e+03 3.37e+00 bond pdb=" C ILE F 37 " pdb=" N PRO F 38 " ideal model delta sigma weight residual 1.335 1.356 -0.022 1.28e-02 6.10e+03 2.91e+00 ... (remaining 10603 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.13: 13927 2.13 - 4.26: 411 4.26 - 6.40: 49 6.40 - 8.53: 16 8.53 - 10.66: 21 Bond angle restraints: 14424 Sorted by residual: angle pdb=" N GLN E 192 " pdb=" CA GLN E 192 " pdb=" C GLN E 192 " ideal model delta sigma weight residual 112.72 104.60 8.12 1.14e+00 7.69e-01 5.07e+01 angle pdb=" C TYR A 145 " pdb=" N SER A 146 " pdb=" CA SER A 146 " ideal model delta sigma weight residual 121.61 112.06 9.55 1.39e+00 5.18e-01 4.72e+01 angle pdb=" C TYR D 145 " pdb=" N SER D 146 " pdb=" CA SER D 146 " ideal model delta sigma weight residual 121.61 112.27 9.34 1.39e+00 5.18e-01 4.52e+01 angle pdb=" C TYR B 145 " pdb=" N SER B 146 " pdb=" CA SER B 146 " ideal model delta sigma weight residual 121.61 112.36 9.25 1.39e+00 5.18e-01 4.43e+01 angle pdb=" C TYR E 145 " pdb=" N SER E 146 " pdb=" CA SER E 146 " ideal model delta sigma weight residual 121.61 112.39 9.22 1.39e+00 5.18e-01 4.40e+01 ... (remaining 14419 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 5465 17.98 - 35.96: 700 35.96 - 53.94: 233 53.94 - 71.91: 46 71.91 - 89.89: 30 Dihedral angle restraints: 6474 sinusoidal: 2646 harmonic: 3828 Sorted by residual: dihedral pdb=" CA MET F 10 " pdb=" C MET F 10 " pdb=" N VAL F 11 " pdb=" CA VAL F 11 " ideal model delta harmonic sigma weight residual -180.00 -162.24 -17.76 0 5.00e+00 4.00e-02 1.26e+01 dihedral pdb=" CA LEU F 189 " pdb=" C LEU F 189 " pdb=" N LEU F 190 " pdb=" CA LEU F 190 " ideal model delta harmonic sigma weight residual 180.00 164.18 15.82 0 5.00e+00 4.00e-02 1.00e+01 dihedral pdb=" CA GLN F 192 " pdb=" C GLN F 192 " pdb=" N ASN F 193 " pdb=" CA ASN F 193 " ideal model delta harmonic sigma weight residual 180.00 164.36 15.64 0 5.00e+00 4.00e-02 9.78e+00 ... (remaining 6471 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 1264 0.053 - 0.106: 291 0.106 - 0.158: 48 0.158 - 0.211: 2 0.211 - 0.264: 3 Chirality restraints: 1608 Sorted by residual: chirality pdb=" CG LEU F 205 " pdb=" CB LEU F 205 " pdb=" CD1 LEU F 205 " pdb=" CD2 LEU F 205 " both_signs ideal model delta sigma weight residual False -2.59 -2.33 -0.26 2.00e-01 2.50e+01 1.74e+00 chirality pdb=" CG LEU E 205 " pdb=" CB LEU E 205 " pdb=" CD1 LEU E 205 " pdb=" CD2 LEU E 205 " both_signs ideal model delta sigma weight residual False -2.59 -2.33 -0.26 2.00e-01 2.50e+01 1.65e+00 chirality pdb=" CG LEU C 205 " pdb=" CB LEU C 205 " pdb=" CD1 LEU C 205 " pdb=" CD2 LEU C 205 " both_signs ideal model delta sigma weight residual False -2.59 -2.38 -0.21 2.00e-01 2.50e+01 1.12e+00 ... (remaining 1605 not shown) Planarity restraints: 1890 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU D 98 " -0.031 5.00e-02 4.00e+02 4.75e-02 3.61e+00 pdb=" N PRO D 99 " 0.082 5.00e-02 4.00e+02 pdb=" CA PRO D 99 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO D 99 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN B 195 " -0.031 5.00e-02 4.00e+02 4.64e-02 3.44e+00 pdb=" N PRO B 196 " 0.080 5.00e-02 4.00e+02 pdb=" CA PRO B 196 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO B 196 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR F 48 " -0.029 5.00e-02 4.00e+02 4.36e-02 3.05e+00 pdb=" N PRO F 49 " 0.075 5.00e-02 4.00e+02 pdb=" CA PRO F 49 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO F 49 " -0.024 5.00e-02 4.00e+02 ... (remaining 1887 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 135 2.62 - 3.19: 9673 3.19 - 3.76: 16495 3.76 - 4.33: 20749 4.33 - 4.90: 33352 Nonbonded interactions: 80404 Sorted by model distance: nonbonded pdb=" O TRP A 184 " pdb=" OG1 THR A 188 " model vdw 2.054 3.040 nonbonded pdb=" O TRP E 184 " pdb=" OG1 THR E 188 " model vdw 2.070 3.040 nonbonded pdb=" OG SER F 149 " pdb=" OD1 ASP F 152 " model vdw 2.084 3.040 nonbonded pdb=" OG SER C 149 " pdb=" OD1 ASP C 152 " model vdw 2.085 3.040 nonbonded pdb=" OG SER B 149 " pdb=" OD1 ASP B 152 " model vdw 2.092 3.040 ... (remaining 80399 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain '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: 1.530 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.200 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 8.770 Find NCS groups from input model: 0.160 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:7.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7253 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 10608 Z= 0.179 Angle : 0.942 10.660 14424 Z= 0.560 Chirality : 0.046 0.264 1608 Planarity : 0.005 0.047 1890 Dihedral : 18.875 89.893 4002 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 12.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer: Outliers : 2.32 % Allowed : 41.27 % Favored : 56.42 % 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 aren not related in a simple way. whole: 0.11 (0.24), residues: 1326 helix: 1.50 (0.18), residues: 810 sheet: None (None), residues: 0 loop : -2.40 (0.27), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG F 143 TYR 0.016 0.002 TYR F 169 PHE 0.012 0.001 PHE F 32 TRP 0.018 0.002 TRP E 184 HIS 0.008 0.002 HIS D 12 Details of bonding type rmsd covalent geometry : bond 0.00346 (10608) covalent geometry : angle 0.94185 (14424) hydrogen bonds : bond 0.19266 ( 590) hydrogen bonds : angle 5.33825 ( 1731) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2652 Ramachandran restraints generated. 1326 Oldfield, 0 Emsley, 1326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2652 Ramachandran restraints generated. 1326 Oldfield, 0 Emsley, 1326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 348 residues out of total 1122 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 322 time to evaluate : 0.260 Fit side-chains revert: symmetry clash REVERT: A 59 VAL cc_start: 0.8795 (OUTLIER) cc_final: 0.8540 (m) REVERT: A 97 ARG cc_start: 0.5849 (OUTLIER) cc_final: 0.5525 (ptm160) REVERT: A 135 ILE cc_start: 0.8439 (mm) cc_final: 0.8223 (mp) REVERT: F 35 GLU cc_start: 0.7655 (pm20) cc_final: 0.7337 (pm20) REVERT: F 111 LEU cc_start: 0.8199 (tm) cc_final: 0.7962 (tt) REVERT: E 3 VAL cc_start: 0.7421 (t) cc_final: 0.7215 (m) REVERT: E 10 MET cc_start: 0.6172 (mmm) cc_final: 0.5560 (mmm) REVERT: D 27 VAL cc_start: 0.8428 (t) cc_final: 0.8186 (t) REVERT: D 75 GLU cc_start: 0.7804 (mt-10) cc_final: 0.7523 (mt-10) REVERT: D 143 ARG cc_start: 0.7554 (ttm110) cc_final: 0.7294 (ttm170) REVERT: C 180 GLU cc_start: 0.6494 (OUTLIER) cc_final: 0.6101 (pm20) REVERT: C 187 GLU cc_start: 0.6701 (OUTLIER) cc_final: 0.6416 (pp20) REVERT: B 37 ILE cc_start: 0.8494 (mm) cc_final: 0.8203 (mt) REVERT: B 71 GLU cc_start: 0.6620 (mt-10) cc_final: 0.6396 (mp0) REVERT: B 135 ILE cc_start: 0.8540 (mm) cc_final: 0.8316 (mp) REVERT: B 143 ARG cc_start: 0.7548 (ttm-80) cc_final: 0.7253 (ttm170) REVERT: B 175 GLU cc_start: 0.6922 (mt-10) cc_final: 0.6613 (mt-10) outliers start: 26 outliers final: 7 residues processed: 335 average time/residue: 0.5051 time to fit residues: 180.7724 Evaluate side-chains 299 residues out of total 1122 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 288 time to evaluate : 0.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 97 ARG Chi-restraints excluded: chain F residue 124 ILE Chi-restraints excluded: chain F residue 135 ILE Chi-restraints excluded: chain E residue 13 GLN Chi-restraints excluded: chain E residue 135 ILE Chi-restraints excluded: chain D residue 178 SER Chi-restraints excluded: chain D residue 180 GLU Chi-restraints excluded: chain D residue 185 MET Chi-restraints excluded: chain C residue 180 GLU Chi-restraints excluded: chain C residue 187 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 98 optimal weight: 10.0000 chunk 107 optimal weight: 0.5980 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 0.0170 chunk 130 optimal weight: 0.7980 chunk 124 optimal weight: 0.0020 chunk 103 optimal weight: 0.9990 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 3.9990 chunk 91 optimal weight: 0.3980 chunk 55 optimal weight: 4.9990 overall best weight: 0.3626 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 63 GLN ** F 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 84 HIS E 12 HIS ** E 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 84 HIS E 155 GLN D 84 HIS C 13 GLN C 84 HIS C 192 GLN B 13 GLN B 67 GLN B 84 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4257 r_free = 0.4257 target = 0.162959 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.145228 restraints weight = 16076.409| |-----------------------------------------------------------------------------| r_work (start): 0.4054 rms_B_bonded: 2.63 r_work: 0.3930 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3930 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7388 moved from start: 0.1796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 10608 Z= 0.142 Angle : 0.736 12.034 14424 Z= 0.356 Chirality : 0.047 0.273 1608 Planarity : 0.006 0.044 1890 Dihedral : 5.347 51.901 1443 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer: Outliers : 7.66 % Allowed : 34.49 % Favored : 57.84 % 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 aren not related in a simple way. whole: 0.12 (0.24), residues: 1326 helix: 1.53 (0.18), residues: 846 sheet: None (None), residues: 0 loop : -2.75 (0.25), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 143 TYR 0.015 0.002 TYR E 164 PHE 0.009 0.001 PHE C 32 TRP 0.009 0.001 TRP D 133 HIS 0.005 0.001 HIS D 12 Details of bonding type rmsd covalent geometry : bond 0.00311 (10608) covalent geometry : angle 0.73551 (14424) hydrogen bonds : bond 0.04755 ( 590) hydrogen bonds : angle 4.07596 ( 1731) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2652 Ramachandran restraints generated. 1326 Oldfield, 0 Emsley, 1326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2652 Ramachandran restraints generated. 1326 Oldfield, 0 Emsley, 1326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 376 residues out of total 1122 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 290 time to evaluate : 0.436 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 144 MET cc_start: 0.8170 (OUTLIER) cc_final: 0.7907 (ttm) REVERT: A 173 ARG cc_start: 0.8195 (OUTLIER) cc_final: 0.7063 (ttp-170) REVERT: A 187 GLU cc_start: 0.6805 (OUTLIER) cc_final: 0.6353 (pp20) REVERT: A 213 GLU cc_start: 0.7518 (OUTLIER) cc_final: 0.7214 (mt-10) REVERT: F 35 GLU cc_start: 0.7607 (pm20) cc_final: 0.7316 (pm20) REVERT: F 97 ARG cc_start: 0.6060 (OUTLIER) cc_final: 0.5578 (ptm-80) REVERT: E 119 THR cc_start: 0.8820 (m) cc_final: 0.8507 (p) REVERT: E 143 ARG cc_start: 0.7765 (OUTLIER) cc_final: 0.7518 (ttm170) REVERT: E 187 GLU cc_start: 0.6675 (OUTLIER) cc_final: 0.6126 (pp20) REVERT: E 192 GLN cc_start: 0.8208 (tp-100) cc_final: 0.7955 (tp-100) REVERT: D 75 GLU cc_start: 0.7850 (mt-10) cc_final: 0.7527 (mt-10) REVERT: D 97 ARG cc_start: 0.6069 (OUTLIER) cc_final: 0.5533 (ptm160) REVERT: D 111 LEU cc_start: 0.8181 (tm) cc_final: 0.7918 (tt) REVERT: C 56 LEU cc_start: 0.8591 (OUTLIER) cc_final: 0.8339 (mp) REVERT: B 37 ILE cc_start: 0.8462 (mm) cc_final: 0.8168 (mt) REVERT: B 82 ARG cc_start: 0.8105 (OUTLIER) cc_final: 0.7888 (mtm110) REVERT: B 97 ARG cc_start: 0.6109 (OUTLIER) cc_final: 0.5675 (ptm160) REVERT: B 108 THR cc_start: 0.8785 (OUTLIER) cc_final: 0.8549 (p) REVERT: B 143 ARG cc_start: 0.7705 (ttm-80) cc_final: 0.7436 (ttm170) REVERT: B 173 ARG cc_start: 0.8373 (OUTLIER) cc_final: 0.7410 (ttp80) REVERT: B 175 GLU cc_start: 0.7036 (mt-10) cc_final: 0.6671 (mt-10) REVERT: B 210 THR cc_start: 0.8100 (OUTLIER) cc_final: 0.7802 (p) REVERT: B 213 GLU cc_start: 0.7206 (mt-10) cc_final: 0.6849 (mp0) outliers start: 86 outliers final: 23 residues processed: 334 average time/residue: 0.5314 time to fit residues: 189.4672 Evaluate side-chains 332 residues out of total 1122 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 295 time to evaluate : 0.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 LEU Chi-restraints excluded: chain A residue 98 GLU Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain A residue 141 ILE Chi-restraints excluded: chain A residue 144 MET Chi-restraints excluded: chain A residue 173 ARG Chi-restraints excluded: chain A residue 187 GLU Chi-restraints excluded: chain A residue 213 GLU Chi-restraints excluded: chain F residue 24 VAL Chi-restraints excluded: chain F residue 30 LYS Chi-restraints excluded: chain F residue 97 ARG Chi-restraints excluded: chain F residue 115 ILE Chi-restraints excluded: chain F residue 119 THR Chi-restraints excluded: chain F residue 190 LEU Chi-restraints excluded: chain E residue 24 VAL Chi-restraints excluded: chain E residue 30 LYS Chi-restraints excluded: chain E residue 143 ARG Chi-restraints excluded: chain E residue 180 GLU Chi-restraints excluded: chain E residue 187 GLU Chi-restraints excluded: chain D residue 97 ARG Chi-restraints excluded: chain D residue 119 THR Chi-restraints excluded: chain D residue 180 GLU Chi-restraints excluded: chain D residue 182 LYS Chi-restraints excluded: chain D residue 185 MET Chi-restraints excluded: chain D residue 189 LEU Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain C residue 98 GLU Chi-restraints excluded: chain C residue 221 VAL Chi-restraints excluded: chain B residue 82 ARG Chi-restraints excluded: chain B residue 97 ARG Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 173 ARG Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 210 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 95 optimal weight: 1.9990 chunk 46 optimal weight: 0.8980 chunk 25 optimal weight: 1.9990 chunk 63 optimal weight: 8.9990 chunk 91 optimal weight: 2.9990 chunk 8 optimal weight: 10.0000 chunk 84 optimal weight: 10.0000 chunk 60 optimal weight: 0.8980 chunk 57 optimal weight: 0.9980 chunk 81 optimal weight: 7.9990 chunk 22 optimal weight: 4.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 155 GLN ** F 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 84 HIS ** E 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 84 HIS D 84 HIS C 84 HIS C 192 GLN B 13 GLN B 67 GLN B 84 HIS ** B 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 112 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4213 r_free = 0.4213 target = 0.159855 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.141627 restraints weight = 16307.079| |-----------------------------------------------------------------------------| r_work (start): 0.3990 rms_B_bonded: 2.64 r_work: 0.3864 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3864 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7498 moved from start: 0.2628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 10608 Z= 0.158 Angle : 0.710 15.268 14424 Z= 0.336 Chirality : 0.045 0.151 1608 Planarity : 0.005 0.047 1890 Dihedral : 4.693 51.442 1422 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.11 % Favored : 93.89 % Rotamer: Outliers : 7.40 % Allowed : 33.87 % Favored : 58.73 % 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 aren not related in a simple way. whole: 0.14 (0.23), residues: 1326 helix: 1.30 (0.18), residues: 888 sheet: None (None), residues: 0 loop : -2.55 (0.27), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 82 TYR 0.022 0.003 TYR A 169 PHE 0.011 0.002 PHE B 168 TRP 0.010 0.001 TRP E 80 HIS 0.009 0.001 HIS B 12 Details of bonding type rmsd covalent geometry : bond 0.00361 (10608) covalent geometry : angle 0.70984 (14424) hydrogen bonds : bond 0.04574 ( 590) hydrogen bonds : angle 4.02035 ( 1731) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2652 Ramachandran restraints generated. 1326 Oldfield, 0 Emsley, 1326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2652 Ramachandran restraints generated. 1326 Oldfield, 0 Emsley, 1326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 389 residues out of total 1122 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 306 time to evaluate : 0.392 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 144 MET cc_start: 0.8285 (OUTLIER) cc_final: 0.8040 (ttm) REVERT: A 173 ARG cc_start: 0.8323 (OUTLIER) cc_final: 0.7050 (ttp-170) REVERT: A 187 GLU cc_start: 0.6906 (OUTLIER) cc_final: 0.6393 (pp20) REVERT: A 213 GLU cc_start: 0.7547 (OUTLIER) cc_final: 0.7228 (mt-10) REVERT: F 35 GLU cc_start: 0.7669 (pm20) cc_final: 0.7454 (pm20) REVERT: F 97 ARG cc_start: 0.6170 (OUTLIER) cc_final: 0.5509 (ptm-80) REVERT: F 173 ARG cc_start: 0.8309 (OUTLIER) cc_final: 0.7732 (ttt180) REVERT: F 187 GLU cc_start: 0.6813 (OUTLIER) cc_final: 0.6374 (pp20) REVERT: E 143 ARG cc_start: 0.7847 (ttm170) cc_final: 0.7641 (ttm170) REVERT: E 187 GLU cc_start: 0.6695 (OUTLIER) cc_final: 0.6159 (pp20) REVERT: E 191 VAL cc_start: 0.8444 (OUTLIER) cc_final: 0.8071 (p) REVERT: E 192 GLN cc_start: 0.8285 (tp-100) cc_final: 0.7980 (tp-100) REVERT: D 69 LEU cc_start: 0.8102 (tt) cc_final: 0.7594 (tp) REVERT: D 72 THR cc_start: 0.8457 (m) cc_final: 0.8246 (p) REVERT: D 75 GLU cc_start: 0.7906 (mt-10) cc_final: 0.7592 (mt-10) REVERT: D 97 ARG cc_start: 0.6093 (OUTLIER) cc_final: 0.5405 (ptm-80) REVERT: C 97 ARG cc_start: 0.5903 (OUTLIER) cc_final: 0.5679 (ptm-80) REVERT: C 192 GLN cc_start: 0.8133 (tp-100) cc_final: 0.7693 (tp-100) REVERT: B 97 ARG cc_start: 0.5925 (OUTLIER) cc_final: 0.5398 (ptm160) REVERT: B 143 ARG cc_start: 0.7857 (ttm-80) cc_final: 0.7632 (ttm170) REVERT: B 173 ARG cc_start: 0.8487 (OUTLIER) cc_final: 0.7398 (ttp80) REVERT: B 175 GLU cc_start: 0.7255 (mt-10) cc_final: 0.6999 (mt-10) REVERT: B 213 GLU cc_start: 0.7235 (OUTLIER) cc_final: 0.6801 (mp0) REVERT: B 215 MET cc_start: 0.7599 (OUTLIER) cc_final: 0.7332 (tpp) outliers start: 83 outliers final: 32 residues processed: 343 average time/residue: 0.5353 time to fit residues: 195.9914 Evaluate side-chains 345 residues out of total 1122 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 298 time to evaluate : 0.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 LEU Chi-restraints excluded: chain A residue 98 GLU Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain A residue 141 ILE Chi-restraints excluded: chain A residue 144 MET Chi-restraints excluded: chain A residue 173 ARG Chi-restraints excluded: chain A residue 187 GLU Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 213 GLU Chi-restraints excluded: chain A residue 216 THR Chi-restraints excluded: chain F residue 12 HIS Chi-restraints excluded: chain F residue 24 VAL Chi-restraints excluded: chain F residue 30 LYS Chi-restraints excluded: chain F residue 97 ARG Chi-restraints excluded: chain F residue 173 ARG Chi-restraints excluded: chain F residue 187 GLU Chi-restraints excluded: chain E residue 24 VAL Chi-restraints excluded: chain E residue 30 LYS Chi-restraints excluded: chain E residue 187 GLU Chi-restraints excluded: chain E residue 191 VAL Chi-restraints excluded: chain D residue 3 VAL Chi-restraints excluded: chain D residue 97 ARG Chi-restraints excluded: chain D residue 119 THR Chi-restraints excluded: chain D residue 180 GLU Chi-restraints excluded: chain D residue 182 LYS Chi-restraints excluded: chain D residue 185 MET Chi-restraints excluded: chain D residue 189 LEU Chi-restraints excluded: chain D residue 191 VAL Chi-restraints excluded: chain C residue 3 VAL Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain C residue 97 ARG Chi-restraints excluded: chain C residue 98 GLU Chi-restraints excluded: chain C residue 191 VAL Chi-restraints excluded: chain C residue 216 THR Chi-restraints excluded: chain B residue 20 LEU Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 96 MET Chi-restraints excluded: chain B residue 97 ARG Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 173 ARG Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 213 GLU Chi-restraints excluded: chain B residue 215 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 82 optimal weight: 3.9990 chunk 37 optimal weight: 7.9990 chunk 128 optimal weight: 5.9990 chunk 87 optimal weight: 0.8980 chunk 46 optimal weight: 0.9990 chunk 13 optimal weight: 1.9990 chunk 91 optimal weight: 2.9990 chunk 121 optimal weight: 4.9990 chunk 72 optimal weight: 4.9990 chunk 25 optimal weight: 2.9990 chunk 39 optimal weight: 3.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 193 ASN F 63 GLN E 13 GLN D 67 GLN C 13 GLN C 67 GLN B 13 GLN B 67 GLN ** B 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4184 r_free = 0.4184 target = 0.157042 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.138771 restraints weight = 16015.140| |-----------------------------------------------------------------------------| r_work (start): 0.3955 rms_B_bonded: 2.59 r_work: 0.3828 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.3828 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7559 moved from start: 0.3197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 10608 Z= 0.195 Angle : 0.718 15.538 14424 Z= 0.339 Chirality : 0.046 0.198 1608 Planarity : 0.006 0.051 1890 Dihedral : 4.696 50.559 1422 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.86 % Favored : 93.14 % Rotamer: Outliers : 7.93 % Allowed : 34.49 % Favored : 57.58 % 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 aren not related in a simple way. whole: 0.07 (0.23), residues: 1326 helix: 1.20 (0.17), residues: 888 sheet: None (None), residues: 0 loop : -2.48 (0.27), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG F 82 TYR 0.022 0.003 TYR A 169 PHE 0.012 0.002 PHE B 168 TRP 0.011 0.001 TRP E 80 HIS 0.008 0.001 HIS B 12 Details of bonding type rmsd covalent geometry : bond 0.00449 (10608) covalent geometry : angle 0.71797 (14424) hydrogen bonds : bond 0.04720 ( 590) hydrogen bonds : angle 4.11850 ( 1731) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2652 Ramachandran restraints generated. 1326 Oldfield, 0 Emsley, 1326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2652 Ramachandran restraints generated. 1326 Oldfield, 0 Emsley, 1326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 426 residues out of total 1122 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 337 time to evaluate : 0.371 Fit side-chains revert: symmetry clash REVERT: A 173 ARG cc_start: 0.8386 (OUTLIER) cc_final: 0.6930 (ttp80) REVERT: A 187 GLU cc_start: 0.6960 (OUTLIER) cc_final: 0.6426 (pp20) REVERT: A 213 GLU cc_start: 0.7526 (OUTLIER) cc_final: 0.7217 (mt-10) REVERT: F 59 VAL cc_start: 0.8886 (t) cc_final: 0.8672 (m) REVERT: F 97 ARG cc_start: 0.6175 (OUTLIER) cc_final: 0.5609 (ptm-80) REVERT: F 173 ARG cc_start: 0.8369 (OUTLIER) cc_final: 0.7830 (ttt180) REVERT: E 187 GLU cc_start: 0.6789 (OUTLIER) cc_final: 0.6230 (pp20) REVERT: E 191 VAL cc_start: 0.8515 (OUTLIER) cc_final: 0.8175 (p) REVERT: E 192 GLN cc_start: 0.8225 (tp-100) cc_final: 0.7941 (tp-100) REVERT: D 72 THR cc_start: 0.8502 (m) cc_final: 0.8238 (p) REVERT: D 75 GLU cc_start: 0.7917 (mt-10) cc_final: 0.7608 (mt-10) REVERT: C 30 LYS cc_start: 0.8872 (OUTLIER) cc_final: 0.8616 (mttp) REVERT: C 97 ARG cc_start: 0.6006 (OUTLIER) cc_final: 0.5579 (ptm-80) REVERT: C 187 GLU cc_start: 0.6850 (OUTLIER) cc_final: 0.6382 (pp20) REVERT: C 192 GLN cc_start: 0.8169 (tp-100) cc_final: 0.7683 (tp-100) REVERT: B 97 ARG cc_start: 0.6139 (OUTLIER) cc_final: 0.5479 (ptm160) REVERT: B 112 GLN cc_start: 0.8113 (OUTLIER) cc_final: 0.7872 (mm110) REVERT: B 152 ASP cc_start: 0.6536 (OUTLIER) cc_final: 0.6188 (m-30) REVERT: B 173 ARG cc_start: 0.8552 (OUTLIER) cc_final: 0.7348 (ttp80) REVERT: B 175 GLU cc_start: 0.7448 (mt-10) cc_final: 0.7179 (mt-10) REVERT: B 213 GLU cc_start: 0.7169 (OUTLIER) cc_final: 0.6678 (mp0) outliers start: 89 outliers final: 41 residues processed: 381 average time/residue: 0.4979 time to fit residues: 203.4565 Evaluate side-chains 379 residues out of total 1122 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 323 time to evaluate : 0.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain A residue 141 ILE Chi-restraints excluded: chain A residue 173 ARG Chi-restraints excluded: chain A residue 185 MET Chi-restraints excluded: chain A residue 187 GLU Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 213 GLU Chi-restraints excluded: chain F residue 12 HIS Chi-restraints excluded: chain F residue 30 LYS Chi-restraints excluded: chain F residue 56 LEU Chi-restraints excluded: chain F residue 97 ARG Chi-restraints excluded: chain F residue 119 THR Chi-restraints excluded: chain F residue 144 MET Chi-restraints excluded: chain F residue 173 ARG Chi-restraints excluded: chain E residue 24 VAL Chi-restraints excluded: chain E residue 30 LYS Chi-restraints excluded: chain E residue 54 THR Chi-restraints excluded: chain E residue 108 THR Chi-restraints excluded: chain E residue 119 THR Chi-restraints excluded: chain E residue 185 MET Chi-restraints excluded: chain E residue 187 GLU Chi-restraints excluded: chain E residue 191 VAL Chi-restraints excluded: chain D residue 3 VAL Chi-restraints excluded: chain D residue 12 HIS Chi-restraints excluded: chain D residue 54 THR Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 175 GLU Chi-restraints excluded: chain D residue 182 LYS Chi-restraints excluded: chain D residue 185 MET Chi-restraints excluded: chain D residue 189 LEU Chi-restraints excluded: chain D residue 191 VAL Chi-restraints excluded: chain C residue 3 VAL Chi-restraints excluded: chain C residue 12 HIS Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 30 LYS Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain C residue 97 ARG Chi-restraints excluded: chain C residue 98 GLU Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 187 GLU Chi-restraints excluded: chain C residue 191 VAL Chi-restraints excluded: chain B residue 12 HIS Chi-restraints excluded: chain B residue 20 LEU Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 97 ARG Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 112 GLN Chi-restraints excluded: chain B residue 119 THR Chi-restraints excluded: chain B residue 152 ASP Chi-restraints excluded: chain B residue 173 ARG Chi-restraints excluded: chain B residue 185 MET Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 210 THR Chi-restraints excluded: chain B residue 213 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 2 optimal weight: 3.9990 chunk 39 optimal weight: 6.9990 chunk 40 optimal weight: 0.9980 chunk 118 optimal weight: 7.9990 chunk 94 optimal weight: 3.9990 chunk 70 optimal weight: 4.9990 chunk 98 optimal weight: 0.5980 chunk 60 optimal weight: 0.7980 chunk 63 optimal weight: 2.9990 chunk 112 optimal weight: 4.9990 chunk 103 optimal weight: 8.9990 overall best weight: 1.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 155 GLN D 67 GLN C 67 GLN B 67 GLN ** B 95 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 = 0.4160 r_free = 0.4160 target = 0.155261 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.137353 restraints weight = 16206.501| |-----------------------------------------------------------------------------| r_work (start): 0.3940 rms_B_bonded: 2.58 r_work: 0.3811 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3811 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7579 moved from start: 0.3571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 10608 Z= 0.188 Angle : 0.721 15.703 14424 Z= 0.338 Chirality : 0.046 0.169 1608 Planarity : 0.005 0.053 1890 Dihedral : 4.522 51.053 1419 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.18 % Favored : 93.82 % Rotamer: Outliers : 7.58 % Allowed : 35.65 % Favored : 56.77 % 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 aren not related in a simple way. whole: 0.11 (0.23), residues: 1326 helix: 1.23 (0.17), residues: 888 sheet: None (None), residues: 0 loop : -2.45 (0.27), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 143 TYR 0.020 0.003 TYR A 169 PHE 0.013 0.002 PHE A 32 TRP 0.010 0.001 TRP A 133 HIS 0.008 0.001 HIS B 12 Details of bonding type rmsd covalent geometry : bond 0.00434 (10608) covalent geometry : angle 0.72099 (14424) hydrogen bonds : bond 0.04570 ( 590) hydrogen bonds : angle 4.08318 ( 1731) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2652 Ramachandran restraints generated. 1326 Oldfield, 0 Emsley, 1326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2652 Ramachandran restraints generated. 1326 Oldfield, 0 Emsley, 1326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 409 residues out of total 1122 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 324 time to evaluate : 0.265 Fit side-chains revert: symmetry clash REVERT: A 173 ARG cc_start: 0.8443 (OUTLIER) cc_final: 0.7018 (ttp80) REVERT: A 187 GLU cc_start: 0.6986 (OUTLIER) cc_final: 0.6491 (pp20) REVERT: A 213 GLU cc_start: 0.7602 (OUTLIER) cc_final: 0.7282 (mt-10) REVERT: F 97 ARG cc_start: 0.6127 (OUTLIER) cc_final: 0.5479 (ptm-80) REVERT: F 152 ASP cc_start: 0.5937 (OUTLIER) cc_final: 0.5656 (m-30) REVERT: F 173 ARG cc_start: 0.8338 (OUTLIER) cc_final: 0.7783 (ttt180) REVERT: F 187 GLU cc_start: 0.6863 (OUTLIER) cc_final: 0.6294 (pp20) REVERT: E 187 GLU cc_start: 0.6871 (OUTLIER) cc_final: 0.6276 (pp20) REVERT: E 192 GLN cc_start: 0.8246 (tp-100) cc_final: 0.7887 (tp-100) REVERT: D 35 GLU cc_start: 0.7658 (mp0) cc_final: 0.7329 (mp0) REVERT: D 69 LEU cc_start: 0.8278 (OUTLIER) cc_final: 0.7936 (tp) REVERT: D 75 GLU cc_start: 0.8026 (mt-10) cc_final: 0.7713 (mt-10) REVERT: D 97 ARG cc_start: 0.6230 (OUTLIER) cc_final: 0.5615 (ptm160) REVERT: C 187 GLU cc_start: 0.6867 (OUTLIER) cc_final: 0.6404 (pp20) REVERT: C 192 GLN cc_start: 0.8146 (tp-100) cc_final: 0.7694 (tp-100) REVERT: B 35 GLU cc_start: 0.7320 (pm20) cc_final: 0.7102 (pm20) REVERT: B 37 ILE cc_start: 0.8557 (mm) cc_final: 0.8338 (mt) REVERT: B 97 ARG cc_start: 0.6146 (OUTLIER) cc_final: 0.5465 (ptm160) REVERT: B 112 GLN cc_start: 0.8176 (OUTLIER) cc_final: 0.7959 (mm110) REVERT: B 143 ARG cc_start: 0.8009 (OUTLIER) cc_final: 0.7674 (ttm170) REVERT: B 152 ASP cc_start: 0.6481 (OUTLIER) cc_final: 0.6021 (m-30) REVERT: B 173 ARG cc_start: 0.8534 (OUTLIER) cc_final: 0.7094 (ttp80) REVERT: B 175 GLU cc_start: 0.7416 (mt-10) cc_final: 0.7158 (mt-10) REVERT: B 213 GLU cc_start: 0.7214 (OUTLIER) cc_final: 0.6744 (mp0) outliers start: 85 outliers final: 43 residues processed: 365 average time/residue: 0.5106 time to fit residues: 199.6483 Evaluate side-chains 390 residues out of total 1122 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 330 time to evaluate : 0.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain A residue 159 GLU Chi-restraints excluded: chain A residue 173 ARG Chi-restraints excluded: chain A residue 185 MET Chi-restraints excluded: chain A residue 187 GLU Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 213 GLU Chi-restraints excluded: chain A residue 216 THR Chi-restraints excluded: chain F residue 12 HIS Chi-restraints excluded: chain F residue 20 LEU Chi-restraints excluded: chain F residue 54 THR Chi-restraints excluded: chain F residue 97 ARG Chi-restraints excluded: chain F residue 152 ASP Chi-restraints excluded: chain F residue 173 ARG Chi-restraints excluded: chain F residue 178 SER Chi-restraints excluded: chain F residue 187 GLU Chi-restraints excluded: chain E residue 24 VAL Chi-restraints excluded: chain E residue 30 LYS Chi-restraints excluded: chain E residue 54 THR Chi-restraints excluded: chain E residue 56 LEU Chi-restraints excluded: chain E residue 119 THR Chi-restraints excluded: chain E residue 185 MET Chi-restraints excluded: chain E residue 187 GLU Chi-restraints excluded: chain E residue 191 VAL Chi-restraints excluded: chain D residue 3 VAL Chi-restraints excluded: chain D residue 12 HIS Chi-restraints excluded: chain D residue 24 VAL Chi-restraints excluded: chain D residue 54 THR Chi-restraints excluded: chain D residue 69 LEU Chi-restraints excluded: chain D residue 97 ARG Chi-restraints excluded: chain D residue 119 THR Chi-restraints excluded: chain D residue 175 GLU Chi-restraints excluded: chain D residue 182 LYS Chi-restraints excluded: chain D residue 185 MET Chi-restraints excluded: chain D residue 189 LEU Chi-restraints excluded: chain D residue 191 VAL Chi-restraints excluded: chain C residue 12 HIS Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain C residue 98 GLU Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 187 GLU Chi-restraints excluded: chain C residue 191 VAL Chi-restraints excluded: chain B residue 12 HIS Chi-restraints excluded: chain B residue 20 LEU Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 97 ARG Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 112 GLN Chi-restraints excluded: chain B residue 119 THR Chi-restraints excluded: chain B residue 143 ARG Chi-restraints excluded: chain B residue 152 ASP Chi-restraints excluded: chain B residue 173 ARG Chi-restraints excluded: chain B residue 185 MET Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 213 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 122 optimal weight: 1.9990 chunk 24 optimal weight: 5.9990 chunk 55 optimal weight: 0.7980 chunk 97 optimal weight: 0.0470 chunk 10 optimal weight: 6.9990 chunk 63 optimal weight: 0.2980 chunk 36 optimal weight: 0.9990 chunk 57 optimal weight: 0.9990 chunk 40 optimal weight: 3.9990 chunk 41 optimal weight: 0.3980 chunk 119 optimal weight: 6.9990 overall best weight: 0.5080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 67 GLN D 13 GLN C 67 GLN B 67 GLN B 95 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4206 r_free = 0.4206 target = 0.159242 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.141346 restraints weight = 16314.925| |-----------------------------------------------------------------------------| r_work (start): 0.3991 rms_B_bonded: 2.60 r_work: 0.3864 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3864 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7505 moved from start: 0.3712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10608 Z= 0.119 Angle : 0.700 16.624 14424 Z= 0.316 Chirality : 0.044 0.144 1608 Planarity : 0.005 0.043 1890 Dihedral : 4.274 53.510 1419 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.58 % Favored : 94.42 % Rotamer: Outliers : 6.24 % Allowed : 37.70 % Favored : 56.06 % 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 aren not related in a simple way. whole: 0.30 (0.23), residues: 1326 helix: 1.48 (0.18), residues: 852 sheet: None (None), residues: 0 loop : -2.31 (0.26), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 143 TYR 0.013 0.002 TYR C 169 PHE 0.015 0.002 PHE A 32 TRP 0.016 0.001 TRP A 133 HIS 0.007 0.001 HIS B 12 Details of bonding type rmsd covalent geometry : bond 0.00275 (10608) covalent geometry : angle 0.70045 (14424) hydrogen bonds : bond 0.03643 ( 590) hydrogen bonds : angle 3.84744 ( 1731) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2652 Ramachandran restraints generated. 1326 Oldfield, 0 Emsley, 1326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2652 Ramachandran restraints generated. 1326 Oldfield, 0 Emsley, 1326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 396 residues out of total 1122 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 326 time to evaluate : 0.326 Fit side-chains revert: symmetry clash REVERT: A 9 GLN cc_start: 0.5568 (OUTLIER) cc_final: 0.5268 (mp10) REVERT: A 97 ARG cc_start: 0.5625 (OUTLIER) cc_final: 0.5335 (ptm160) REVERT: A 173 ARG cc_start: 0.8328 (OUTLIER) cc_final: 0.7098 (ttp80) REVERT: A 187 GLU cc_start: 0.6841 (OUTLIER) cc_final: 0.6319 (pp20) REVERT: A 213 GLU cc_start: 0.7544 (OUTLIER) cc_final: 0.7198 (mt-10) REVERT: F 30 LYS cc_start: 0.8932 (OUTLIER) cc_final: 0.8625 (mtmm) REVERT: F 97 ARG cc_start: 0.6011 (OUTLIER) cc_final: 0.5479 (ptm-80) REVERT: F 152 ASP cc_start: 0.5792 (OUTLIER) cc_final: 0.5390 (m-30) REVERT: F 187 GLU cc_start: 0.6793 (OUTLIER) cc_final: 0.6246 (pp20) REVERT: E 187 GLU cc_start: 0.6847 (OUTLIER) cc_final: 0.6236 (pp20) REVERT: E 192 GLN cc_start: 0.8216 (tp-100) cc_final: 0.7885 (tp-100) REVERT: D 75 GLU cc_start: 0.7953 (mt-10) cc_final: 0.7655 (mt-10) REVERT: D 97 ARG cc_start: 0.6260 (OUTLIER) cc_final: 0.5561 (ptm-80) REVERT: D 152 ASP cc_start: 0.5834 (OUTLIER) cc_final: 0.5524 (m-30) REVERT: C 97 ARG cc_start: 0.6202 (OUTLIER) cc_final: 0.5494 (ptm-80) REVERT: C 187 GLU cc_start: 0.6736 (OUTLIER) cc_final: 0.6269 (pp20) REVERT: B 37 ILE cc_start: 0.8555 (mm) cc_final: 0.8326 (mt) REVERT: B 97 ARG cc_start: 0.6116 (OUTLIER) cc_final: 0.5520 (ptm160) REVERT: B 143 ARG cc_start: 0.8007 (OUTLIER) cc_final: 0.7793 (ttm170) REVERT: B 152 ASP cc_start: 0.6269 (OUTLIER) cc_final: 0.5898 (m-30) REVERT: B 173 ARG cc_start: 0.8415 (OUTLIER) cc_final: 0.7557 (ttp-170) REVERT: B 175 GLU cc_start: 0.7220 (mt-10) cc_final: 0.6962 (mt-10) REVERT: B 192 GLN cc_start: 0.8265 (tp-100) cc_final: 0.7940 (mm-40) outliers start: 70 outliers final: 33 residues processed: 360 average time/residue: 0.5164 time to fit residues: 198.7095 Evaluate side-chains 377 residues out of total 1122 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 326 time to evaluate : 0.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 GLN Chi-restraints excluded: chain A residue 20 LEU Chi-restraints excluded: chain A residue 45 GLU Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 97 ARG Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain A residue 159 GLU Chi-restraints excluded: chain A residue 173 ARG Chi-restraints excluded: chain A residue 187 GLU Chi-restraints excluded: chain A residue 213 GLU Chi-restraints excluded: chain A residue 216 THR Chi-restraints excluded: chain F residue 12 HIS Chi-restraints excluded: chain F residue 20 LEU Chi-restraints excluded: chain F residue 30 LYS Chi-restraints excluded: chain F residue 97 ARG Chi-restraints excluded: chain F residue 119 THR Chi-restraints excluded: chain F residue 152 ASP Chi-restraints excluded: chain F residue 187 GLU Chi-restraints excluded: chain E residue 24 VAL Chi-restraints excluded: chain E residue 30 LYS Chi-restraints excluded: chain E residue 108 THR Chi-restraints excluded: chain E residue 185 MET Chi-restraints excluded: chain E residue 187 GLU Chi-restraints excluded: chain D residue 3 VAL Chi-restraints excluded: chain D residue 13 GLN Chi-restraints excluded: chain D residue 54 THR Chi-restraints excluded: chain D residue 97 ARG Chi-restraints excluded: chain D residue 152 ASP Chi-restraints excluded: chain D residue 175 GLU Chi-restraints excluded: chain D residue 182 LYS Chi-restraints excluded: chain D residue 185 MET Chi-restraints excluded: chain D residue 189 LEU Chi-restraints excluded: chain C residue 12 HIS Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain C residue 97 ARG Chi-restraints excluded: chain C residue 98 GLU Chi-restraints excluded: chain C residue 187 GLU Chi-restraints excluded: chain B residue 20 LEU Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 58 THR Chi-restraints excluded: chain B residue 97 ARG Chi-restraints excluded: chain B residue 119 THR Chi-restraints excluded: chain B residue 143 ARG Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 152 ASP Chi-restraints excluded: chain B residue 173 ARG Chi-restraints excluded: chain B residue 185 MET Chi-restraints excluded: chain B residue 210 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 12 optimal weight: 0.8980 chunk 17 optimal weight: 4.9990 chunk 120 optimal weight: 1.9990 chunk 99 optimal weight: 0.9980 chunk 1 optimal weight: 6.9990 chunk 82 optimal weight: 3.9990 chunk 115 optimal weight: 4.9990 chunk 48 optimal weight: 0.7980 chunk 69 optimal weight: 0.8980 chunk 14 optimal weight: 0.2980 chunk 70 optimal weight: 0.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 67 GLN F 193 ASN C 67 GLN B 13 GLN B 67 GLN ** B 95 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 = 0.4198 r_free = 0.4198 target = 0.158469 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.140895 restraints weight = 16216.669| |-----------------------------------------------------------------------------| r_work (start): 0.3984 rms_B_bonded: 2.56 r_work: 0.3858 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3858 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7516 moved from start: 0.3841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 10608 Z= 0.128 Angle : 0.721 16.999 14424 Z= 0.323 Chirality : 0.045 0.274 1608 Planarity : 0.005 0.046 1890 Dihedral : 4.220 54.151 1419 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.88 % Favored : 94.12 % Rotamer: Outliers : 5.88 % Allowed : 39.13 % Favored : 54.99 % 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 aren not related in a simple way. whole: 0.36 (0.23), residues: 1326 helix: 1.49 (0.18), residues: 852 sheet: None (None), residues: 0 loop : -2.20 (0.26), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 143 TYR 0.013 0.002 TYR A 169 PHE 0.012 0.002 PHE A 32 TRP 0.016 0.001 TRP A 133 HIS 0.007 0.001 HIS B 12 Details of bonding type rmsd covalent geometry : bond 0.00307 (10608) covalent geometry : angle 0.72108 (14424) hydrogen bonds : bond 0.03747 ( 590) hydrogen bonds : angle 3.87095 ( 1731) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2652 Ramachandran restraints generated. 1326 Oldfield, 0 Emsley, 1326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2652 Ramachandran restraints generated. 1326 Oldfield, 0 Emsley, 1326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 394 residues out of total 1122 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 328 time to evaluate : 0.345 Fit side-chains revert: symmetry clash REVERT: A 9 GLN cc_start: 0.5609 (OUTLIER) cc_final: 0.5297 (mp10) REVERT: A 97 ARG cc_start: 0.5611 (OUTLIER) cc_final: 0.5306 (ptm160) REVERT: A 173 ARG cc_start: 0.8334 (OUTLIER) cc_final: 0.7042 (ttp80) REVERT: A 187 GLU cc_start: 0.6839 (OUTLIER) cc_final: 0.6332 (pp20) REVERT: A 213 GLU cc_start: 0.7677 (OUTLIER) cc_final: 0.7336 (mt-10) REVERT: F 30 LYS cc_start: 0.8901 (OUTLIER) cc_final: 0.8508 (mtmm) REVERT: F 97 ARG cc_start: 0.6014 (OUTLIER) cc_final: 0.5510 (ptm-80) REVERT: F 143 ARG cc_start: 0.7624 (ttm-80) cc_final: 0.7415 (ttm-80) REVERT: F 152 ASP cc_start: 0.5695 (OUTLIER) cc_final: 0.5301 (m-30) REVERT: F 187 GLU cc_start: 0.6803 (OUTLIER) cc_final: 0.6258 (pp20) REVERT: E 187 GLU cc_start: 0.6846 (OUTLIER) cc_final: 0.6244 (pp20) REVERT: E 192 GLN cc_start: 0.8208 (tp-100) cc_final: 0.7851 (tp-100) REVERT: D 75 GLU cc_start: 0.7933 (mt-10) cc_final: 0.7640 (mt-10) REVERT: D 97 ARG cc_start: 0.6250 (OUTLIER) cc_final: 0.5592 (ptm-80) REVERT: D 152 ASP cc_start: 0.5891 (OUTLIER) cc_final: 0.5566 (m-30) REVERT: D 213 GLU cc_start: 0.7806 (mt-10) cc_final: 0.7597 (mm-30) REVERT: C 97 ARG cc_start: 0.6218 (OUTLIER) cc_final: 0.5538 (ptm-80) REVERT: C 152 ASP cc_start: 0.6505 (OUTLIER) cc_final: 0.6214 (m-30) REVERT: C 187 GLU cc_start: 0.6769 (OUTLIER) cc_final: 0.6301 (pp20) REVERT: B 37 ILE cc_start: 0.8567 (mm) cc_final: 0.8347 (mt) REVERT: B 97 ARG cc_start: 0.6007 (OUTLIER) cc_final: 0.5500 (ptm160) REVERT: B 112 GLN cc_start: 0.8082 (OUTLIER) cc_final: 0.7787 (mm110) REVERT: B 152 ASP cc_start: 0.6283 (OUTLIER) cc_final: 0.5922 (m-30) REVERT: B 173 ARG cc_start: 0.8454 (OUTLIER) cc_final: 0.7603 (ttp-170) REVERT: B 175 GLU cc_start: 0.7271 (mt-10) cc_final: 0.7012 (mt-10) REVERT: B 192 GLN cc_start: 0.8276 (tp-100) cc_final: 0.7927 (mm-40) REVERT: B 213 GLU cc_start: 0.7047 (OUTLIER) cc_final: 0.6252 (mp0) outliers start: 66 outliers final: 32 residues processed: 360 average time/residue: 0.4991 time to fit residues: 192.3818 Evaluate side-chains 370 residues out of total 1122 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 318 time to evaluate : 0.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 GLN Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain A residue 97 ARG Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain A residue 144 MET Chi-restraints excluded: chain A residue 173 ARG Chi-restraints excluded: chain A residue 187 GLU Chi-restraints excluded: chain A residue 213 GLU Chi-restraints excluded: chain A residue 216 THR Chi-restraints excluded: chain F residue 12 HIS Chi-restraints excluded: chain F residue 20 LEU Chi-restraints excluded: chain F residue 30 LYS Chi-restraints excluded: chain F residue 54 THR Chi-restraints excluded: chain F residue 97 ARG Chi-restraints excluded: chain F residue 152 ASP Chi-restraints excluded: chain F residue 159 GLU Chi-restraints excluded: chain F residue 178 SER Chi-restraints excluded: chain F residue 187 GLU Chi-restraints excluded: chain E residue 24 VAL Chi-restraints excluded: chain E residue 30 LYS Chi-restraints excluded: chain E residue 185 MET Chi-restraints excluded: chain E residue 187 GLU Chi-restraints excluded: chain D residue 11 VAL Chi-restraints excluded: chain D residue 24 VAL Chi-restraints excluded: chain D residue 96 MET Chi-restraints excluded: chain D residue 97 ARG Chi-restraints excluded: chain D residue 108 THR Chi-restraints excluded: chain D residue 152 ASP Chi-restraints excluded: chain D residue 175 GLU Chi-restraints excluded: chain D residue 182 LYS Chi-restraints excluded: chain D residue 185 MET Chi-restraints excluded: chain D residue 189 LEU Chi-restraints excluded: chain C residue 12 HIS Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain C residue 97 ARG Chi-restraints excluded: chain C residue 98 GLU Chi-restraints excluded: chain C residue 152 ASP Chi-restraints excluded: chain C residue 187 GLU Chi-restraints excluded: chain B residue 20 LEU Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 97 ARG Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 112 GLN Chi-restraints excluded: chain B residue 119 THR Chi-restraints excluded: chain B residue 152 ASP Chi-restraints excluded: chain B residue 173 ARG Chi-restraints excluded: chain B residue 210 THR Chi-restraints excluded: chain B residue 213 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 72 optimal weight: 2.9990 chunk 61 optimal weight: 1.9990 chunk 116 optimal weight: 4.9990 chunk 59 optimal weight: 10.0000 chunk 90 optimal weight: 2.9990 chunk 63 optimal weight: 2.9990 chunk 111 optimal weight: 3.9990 chunk 28 optimal weight: 3.9990 chunk 112 optimal weight: 0.9990 chunk 42 optimal weight: 4.9990 chunk 103 optimal weight: 8.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 67 GLN F 4 GLN C 67 GLN B 67 GLN ** B 95 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 = 0.4134 r_free = 0.4134 target = 0.153404 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.135945 restraints weight = 16156.782| |-----------------------------------------------------------------------------| r_work (start): 0.3914 rms_B_bonded: 2.47 r_work: 0.3789 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work (final): 0.3789 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7600 moved from start: 0.4127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 10608 Z= 0.234 Angle : 0.787 17.499 14424 Z= 0.367 Chirality : 0.049 0.165 1608 Planarity : 0.005 0.049 1890 Dihedral : 4.627 51.625 1419 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.86 % Favored : 93.14 % Rotamer: Outliers : 7.04 % Allowed : 38.24 % Favored : 54.72 % 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 aren not related in a simple way. whole: 0.02 (0.23), residues: 1326 helix: 1.19 (0.18), residues: 852 sheet: None (None), residues: 0 loop : -2.26 (0.25), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 143 TYR 0.023 0.003 TYR B 169 PHE 0.019 0.003 PHE A 32 TRP 0.033 0.002 TRP F 133 HIS 0.007 0.001 HIS B 12 Details of bonding type rmsd covalent geometry : bond 0.00541 (10608) covalent geometry : angle 0.78744 (14424) hydrogen bonds : bond 0.04939 ( 590) hydrogen bonds : angle 4.27776 ( 1731) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2652 Ramachandran restraints generated. 1326 Oldfield, 0 Emsley, 1326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2652 Ramachandran restraints generated. 1326 Oldfield, 0 Emsley, 1326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 418 residues out of total 1122 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 339 time to evaluate : 0.414 Fit side-chains revert: symmetry clash REVERT: A 97 ARG cc_start: 0.5860 (OUTLIER) cc_final: 0.5404 (ptm160) REVERT: A 173 ARG cc_start: 0.8516 (OUTLIER) cc_final: 0.7071 (ttp80) REVERT: A 187 GLU cc_start: 0.6971 (OUTLIER) cc_final: 0.6458 (pp20) REVERT: A 213 GLU cc_start: 0.7629 (OUTLIER) cc_final: 0.7325 (mt-10) REVERT: F 30 LYS cc_start: 0.8998 (OUTLIER) cc_final: 0.8591 (mtmm) REVERT: F 76 GLU cc_start: 0.8185 (OUTLIER) cc_final: 0.7609 (mp0) REVERT: F 97 ARG cc_start: 0.6181 (OUTLIER) cc_final: 0.5557 (ptm-80) REVERT: F 152 ASP cc_start: 0.6152 (OUTLIER) cc_final: 0.5770 (m-30) REVERT: F 187 GLU cc_start: 0.6894 (OUTLIER) cc_final: 0.6317 (pp20) REVERT: E 143 ARG cc_start: 0.7945 (ttm170) cc_final: 0.7660 (ttm170) REVERT: E 187 GLU cc_start: 0.6967 (OUTLIER) cc_final: 0.6411 (pp20) REVERT: E 192 GLN cc_start: 0.8244 (tp-100) cc_final: 0.7985 (tp-100) REVERT: D 75 GLU cc_start: 0.7887 (mt-10) cc_final: 0.7616 (mt-10) REVERT: D 97 ARG cc_start: 0.6423 (OUTLIER) cc_final: 0.5804 (ptm-80) REVERT: D 175 GLU cc_start: 0.7713 (OUTLIER) cc_final: 0.7366 (mt-10) REVERT: C 152 ASP cc_start: 0.6668 (OUTLIER) cc_final: 0.6411 (m-30) REVERT: B 97 ARG cc_start: 0.6072 (OUTLIER) cc_final: 0.5419 (ptm160) REVERT: B 152 ASP cc_start: 0.6602 (OUTLIER) cc_final: 0.6266 (m-30) REVERT: B 173 ARG cc_start: 0.8563 (OUTLIER) cc_final: 0.7104 (ttp80) REVERT: B 175 GLU cc_start: 0.7366 (mt-10) cc_final: 0.7159 (mt-10) REVERT: B 192 GLN cc_start: 0.8297 (tp-100) cc_final: 0.7940 (tp-100) REVERT: B 213 GLU cc_start: 0.7170 (OUTLIER) cc_final: 0.6666 (mp0) outliers start: 79 outliers final: 44 residues processed: 381 average time/residue: 0.4857 time to fit residues: 198.1750 Evaluate side-chains 390 residues out of total 1122 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 329 time to evaluate : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 LEU Chi-restraints excluded: chain A residue 45 GLU Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain A residue 97 ARG Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain A residue 173 ARG Chi-restraints excluded: chain A residue 187 GLU Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 213 GLU Chi-restraints excluded: chain A residue 216 THR Chi-restraints excluded: chain F residue 12 HIS Chi-restraints excluded: chain F residue 20 LEU Chi-restraints excluded: chain F residue 30 LYS Chi-restraints excluded: chain F residue 54 THR Chi-restraints excluded: chain F residue 56 LEU Chi-restraints excluded: chain F residue 76 GLU Chi-restraints excluded: chain F residue 97 ARG Chi-restraints excluded: chain F residue 119 THR Chi-restraints excluded: chain F residue 152 ASP Chi-restraints excluded: chain F residue 159 GLU Chi-restraints excluded: chain F residue 178 SER Chi-restraints excluded: chain F residue 187 GLU Chi-restraints excluded: chain E residue 12 HIS Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 24 VAL Chi-restraints excluded: chain E residue 30 LYS Chi-restraints excluded: chain E residue 54 THR Chi-restraints excluded: chain E residue 56 LEU Chi-restraints excluded: chain E residue 108 THR Chi-restraints excluded: chain E residue 185 MET Chi-restraints excluded: chain E residue 187 GLU Chi-restraints excluded: chain D residue 3 VAL Chi-restraints excluded: chain D residue 11 VAL Chi-restraints excluded: chain D residue 24 VAL Chi-restraints excluded: chain D residue 54 THR Chi-restraints excluded: chain D residue 97 ARG Chi-restraints excluded: chain D residue 175 GLU Chi-restraints excluded: chain D residue 182 LYS Chi-restraints excluded: chain D residue 185 MET Chi-restraints excluded: chain D residue 189 LEU Chi-restraints excluded: chain C residue 12 HIS Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain C residue 97 ARG Chi-restraints excluded: chain C residue 98 GLU Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 152 ASP Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain B residue 20 LEU Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 97 ARG Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 119 THR Chi-restraints excluded: chain B residue 152 ASP Chi-restraints excluded: chain B residue 173 ARG Chi-restraints excluded: chain B residue 213 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 115 optimal weight: 3.9990 chunk 109 optimal weight: 6.9990 chunk 86 optimal weight: 3.9990 chunk 19 optimal weight: 6.9990 chunk 83 optimal weight: 3.9990 chunk 88 optimal weight: 3.9990 chunk 3 optimal weight: 0.0000 chunk 100 optimal weight: 0.9990 chunk 102 optimal weight: 0.0870 chunk 63 optimal weight: 6.9990 chunk 99 optimal weight: 0.8980 overall best weight: 1.1966 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 13 GLN E 179 GLN D 13 GLN D 67 GLN D 114 GLN C 12 HIS C 67 GLN B 67 GLN ** B 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4165 r_free = 0.4165 target = 0.155857 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.138035 restraints weight = 16138.184| |-----------------------------------------------------------------------------| r_work (start): 0.3947 rms_B_bonded: 2.59 r_work: 0.3823 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3823 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7560 moved from start: 0.4197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 10608 Z= 0.153 Angle : 0.781 18.279 14424 Z= 0.353 Chirality : 0.047 0.330 1608 Planarity : 0.005 0.048 1890 Dihedral : 4.447 53.771 1419 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.71 % Favored : 93.29 % Rotamer: Outliers : 5.79 % Allowed : 40.11 % Favored : 54.10 % 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 aren not related in a simple way. whole: 0.22 (0.23), residues: 1326 helix: 1.34 (0.18), residues: 852 sheet: None (None), residues: 0 loop : -2.18 (0.26), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 143 TYR 0.015 0.002 TYR F 169 PHE 0.011 0.002 PHE F 168 TRP 0.027 0.002 TRP F 133 HIS 0.011 0.001 HIS D 12 Details of bonding type rmsd covalent geometry : bond 0.00369 (10608) covalent geometry : angle 0.78121 (14424) hydrogen bonds : bond 0.04114 ( 590) hydrogen bonds : angle 4.13733 ( 1731) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2652 Ramachandran restraints generated. 1326 Oldfield, 0 Emsley, 1326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2652 Ramachandran restraints generated. 1326 Oldfield, 0 Emsley, 1326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 391 residues out of total 1122 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 326 time to evaluate : 0.242 Fit side-chains revert: symmetry clash REVERT: A 9 GLN cc_start: 0.5658 (OUTLIER) cc_final: 0.5347 (mp10) REVERT: A 97 ARG cc_start: 0.5779 (OUTLIER) cc_final: 0.5292 (ptm160) REVERT: A 173 ARG cc_start: 0.8443 (OUTLIER) cc_final: 0.7166 (ttp80) REVERT: A 187 GLU cc_start: 0.6867 (OUTLIER) cc_final: 0.6352 (pp20) REVERT: A 213 GLU cc_start: 0.7637 (OUTLIER) cc_final: 0.7308 (mt-10) REVERT: F 30 LYS cc_start: 0.8955 (OUTLIER) cc_final: 0.8545 (mtmm) REVERT: F 76 GLU cc_start: 0.8270 (OUTLIER) cc_final: 0.7672 (mp0) REVERT: F 97 ARG cc_start: 0.6087 (OUTLIER) cc_final: 0.5500 (ptm-80) REVERT: F 152 ASP cc_start: 0.6022 (OUTLIER) cc_final: 0.5613 (m-30) REVERT: F 187 GLU cc_start: 0.6788 (OUTLIER) cc_final: 0.6189 (pp20) REVERT: E 143 ARG cc_start: 0.7940 (ttm170) cc_final: 0.7632 (ttm170) REVERT: E 187 GLU cc_start: 0.6932 (OUTLIER) cc_final: 0.6361 (pp20) REVERT: E 192 GLN cc_start: 0.8236 (tp-100) cc_final: 0.7937 (tp-100) REVERT: D 43 LEU cc_start: 0.9104 (mt) cc_final: 0.8889 (mp) REVERT: D 75 GLU cc_start: 0.7898 (mt-10) cc_final: 0.7605 (mt-10) REVERT: D 97 ARG cc_start: 0.6347 (OUTLIER) cc_final: 0.5794 (ptm160) REVERT: D 175 GLU cc_start: 0.7557 (OUTLIER) cc_final: 0.7198 (mt-10) REVERT: C 152 ASP cc_start: 0.6647 (OUTLIER) cc_final: 0.6357 (m-30) REVERT: B 97 ARG cc_start: 0.6055 (OUTLIER) cc_final: 0.5452 (ptm160) REVERT: B 112 GLN cc_start: 0.8104 (OUTLIER) cc_final: 0.7810 (mm110) REVERT: B 152 ASP cc_start: 0.6471 (OUTLIER) cc_final: 0.6084 (m-30) REVERT: B 173 ARG cc_start: 0.8478 (OUTLIER) cc_final: 0.7464 (ttp-170) REVERT: B 192 GLN cc_start: 0.8318 (tp-100) cc_final: 0.8006 (tp-100) REVERT: B 213 GLU cc_start: 0.7205 (OUTLIER) cc_final: 0.6568 (mp0) outliers start: 65 outliers final: 39 residues processed: 366 average time/residue: 0.4934 time to fit residues: 193.8640 Evaluate side-chains 375 residues out of total 1122 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 317 time to evaluate : 0.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 GLN Chi-restraints excluded: chain A residue 20 LEU Chi-restraints excluded: chain A residue 45 GLU Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain A residue 97 ARG Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain A residue 173 ARG Chi-restraints excluded: chain A residue 187 GLU Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 213 GLU Chi-restraints excluded: chain A residue 216 THR Chi-restraints excluded: chain F residue 12 HIS Chi-restraints excluded: chain F residue 20 LEU Chi-restraints excluded: chain F residue 30 LYS Chi-restraints excluded: chain F residue 54 THR Chi-restraints excluded: chain F residue 76 GLU Chi-restraints excluded: chain F residue 97 ARG Chi-restraints excluded: chain F residue 108 THR Chi-restraints excluded: chain F residue 152 ASP Chi-restraints excluded: chain F residue 178 SER Chi-restraints excluded: chain F residue 187 GLU Chi-restraints excluded: chain E residue 12 HIS Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 30 LYS Chi-restraints excluded: chain E residue 54 THR Chi-restraints excluded: chain E residue 185 MET Chi-restraints excluded: chain E residue 187 GLU Chi-restraints excluded: chain D residue 3 VAL Chi-restraints excluded: chain D residue 11 VAL Chi-restraints excluded: chain D residue 13 GLN Chi-restraints excluded: chain D residue 24 VAL Chi-restraints excluded: chain D residue 69 LEU Chi-restraints excluded: chain D residue 97 ARG Chi-restraints excluded: chain D residue 119 THR Chi-restraints excluded: chain D residue 175 GLU Chi-restraints excluded: chain D residue 182 LYS Chi-restraints excluded: chain D residue 185 MET Chi-restraints excluded: chain D residue 189 LEU Chi-restraints excluded: chain C residue 12 HIS Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain C residue 97 ARG Chi-restraints excluded: chain C residue 98 GLU Chi-restraints excluded: chain C residue 141 ILE Chi-restraints excluded: chain C residue 152 ASP Chi-restraints excluded: chain B residue 20 LEU Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 97 ARG Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 112 GLN Chi-restraints excluded: chain B residue 119 THR Chi-restraints excluded: chain B residue 152 ASP Chi-restraints excluded: chain B residue 173 ARG Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 213 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 119 optimal weight: 0.0980 chunk 3 optimal weight: 0.5980 chunk 77 optimal weight: 0.7980 chunk 62 optimal weight: 5.9990 chunk 98 optimal weight: 2.9990 chunk 124 optimal weight: 1.9990 chunk 110 optimal weight: 0.9980 chunk 65 optimal weight: 0.7980 chunk 89 optimal weight: 7.9990 chunk 104 optimal weight: 0.8980 chunk 53 optimal weight: 0.0770 overall best weight: 0.4738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 67 GLN E 179 GLN D 13 GLN D 114 GLN C 67 GLN B 67 GLN ** B 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4179 r_free = 0.4179 target = 0.156963 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.138755 restraints weight = 16038.501| |-----------------------------------------------------------------------------| r_work (start): 0.3969 rms_B_bonded: 2.61 r_work: 0.3847 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3847 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7517 moved from start: 0.4253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10608 Z= 0.131 Angle : 0.775 18.651 14424 Z= 0.349 Chirality : 0.046 0.304 1608 Planarity : 0.005 0.050 1890 Dihedral : 4.300 55.070 1419 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.96 % Favored : 94.04 % Rotamer: Outliers : 5.35 % Allowed : 40.37 % Favored : 54.28 % 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 aren not related in a simple way. whole: 0.27 (0.23), residues: 1326 helix: 1.36 (0.18), residues: 852 sheet: None (None), residues: 0 loop : -2.10 (0.26), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 143 TYR 0.014 0.001 TYR C 169 PHE 0.014 0.002 PHE A 32 TRP 0.026 0.002 TRP F 133 HIS 0.019 0.001 HIS D 12 Details of bonding type rmsd covalent geometry : bond 0.00311 (10608) covalent geometry : angle 0.77548 (14424) hydrogen bonds : bond 0.03766 ( 590) hydrogen bonds : angle 4.01691 ( 1731) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2652 Ramachandran restraints generated. 1326 Oldfield, 0 Emsley, 1326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2652 Ramachandran restraints generated. 1326 Oldfield, 0 Emsley, 1326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 387 residues out of total 1122 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 327 time to evaluate : 0.353 Fit side-chains revert: symmetry clash REVERT: A 9 GLN cc_start: 0.5666 (OUTLIER) cc_final: 0.5352 (mp10) REVERT: A 97 ARG cc_start: 0.5712 (OUTLIER) cc_final: 0.5280 (ptm160) REVERT: A 173 ARG cc_start: 0.8394 (OUTLIER) cc_final: 0.7144 (ttp80) REVERT: A 187 GLU cc_start: 0.6821 (OUTLIER) cc_final: 0.6324 (pp20) REVERT: A 213 GLU cc_start: 0.7644 (OUTLIER) cc_final: 0.7312 (mt-10) REVERT: F 30 LYS cc_start: 0.8924 (OUTLIER) cc_final: 0.8521 (mtmm) REVERT: F 76 GLU cc_start: 0.8258 (OUTLIER) cc_final: 0.7658 (mp0) REVERT: F 97 ARG cc_start: 0.6059 (OUTLIER) cc_final: 0.5515 (ptm-80) REVERT: F 152 ASP cc_start: 0.5937 (OUTLIER) cc_final: 0.5539 (m-30) REVERT: F 187 GLU cc_start: 0.6724 (OUTLIER) cc_final: 0.6139 (pp20) REVERT: E 187 GLU cc_start: 0.6889 (OUTLIER) cc_final: 0.6325 (pp20) REVERT: D 75 GLU cc_start: 0.7935 (mt-10) cc_final: 0.7643 (mt-10) REVERT: D 97 ARG cc_start: 0.6316 (OUTLIER) cc_final: 0.5685 (ptm-80) REVERT: D 143 ARG cc_start: 0.7723 (ttm170) cc_final: 0.7495 (ttm170) REVERT: D 152 ASP cc_start: 0.5911 (OUTLIER) cc_final: 0.5600 (m-30) REVERT: D 175 GLU cc_start: 0.7416 (OUTLIER) cc_final: 0.7037 (mt-10) REVERT: C 97 ARG cc_start: 0.6235 (OUTLIER) cc_final: 0.5553 (ptm-80) REVERT: C 152 ASP cc_start: 0.6577 (OUTLIER) cc_final: 0.6281 (m-30) REVERT: B 82 ARG cc_start: 0.8112 (OUTLIER) cc_final: 0.7734 (mtm110) REVERT: B 97 ARG cc_start: 0.6018 (OUTLIER) cc_final: 0.5548 (ptm160) REVERT: B 152 ASP cc_start: 0.6292 (OUTLIER) cc_final: 0.5913 (m-30) REVERT: B 173 ARG cc_start: 0.8436 (OUTLIER) cc_final: 0.8134 (ttp80) REVERT: B 192 GLN cc_start: 0.8270 (tp-100) cc_final: 0.8032 (tp-100) REVERT: B 213 GLU cc_start: 0.7196 (OUTLIER) cc_final: 0.6579 (mp0) outliers start: 60 outliers final: 31 residues processed: 360 average time/residue: 0.5164 time to fit residues: 199.6013 Evaluate side-chains 369 residues out of total 1122 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 317 time to evaluate : 0.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 GLN Chi-restraints excluded: chain A residue 45 GLU Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 97 ARG Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain A residue 173 ARG Chi-restraints excluded: chain A residue 187 GLU Chi-restraints excluded: chain A residue 213 GLU Chi-restraints excluded: chain A residue 216 THR Chi-restraints excluded: chain F residue 12 HIS Chi-restraints excluded: chain F residue 20 LEU Chi-restraints excluded: chain F residue 30 LYS Chi-restraints excluded: chain F residue 76 GLU Chi-restraints excluded: chain F residue 97 ARG Chi-restraints excluded: chain F residue 108 THR Chi-restraints excluded: chain F residue 152 ASP Chi-restraints excluded: chain F residue 178 SER Chi-restraints excluded: chain F residue 187 GLU Chi-restraints excluded: chain E residue 30 LYS Chi-restraints excluded: chain E residue 54 THR Chi-restraints excluded: chain E residue 185 MET Chi-restraints excluded: chain E residue 187 GLU Chi-restraints excluded: chain D residue 3 VAL Chi-restraints excluded: chain D residue 11 VAL Chi-restraints excluded: chain D residue 13 GLN Chi-restraints excluded: chain D residue 15 ILE Chi-restraints excluded: chain D residue 97 ARG Chi-restraints excluded: chain D residue 152 ASP Chi-restraints excluded: chain D residue 175 GLU Chi-restraints excluded: chain D residue 182 LYS Chi-restraints excluded: chain D residue 189 LEU Chi-restraints excluded: chain C residue 12 HIS Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain C residue 97 ARG Chi-restraints excluded: chain C residue 98 GLU Chi-restraints excluded: chain C residue 141 ILE Chi-restraints excluded: chain C residue 152 ASP Chi-restraints excluded: chain C residue 216 THR Chi-restraints excluded: chain B residue 20 LEU Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 82 ARG Chi-restraints excluded: chain B residue 97 ARG Chi-restraints excluded: chain B residue 119 THR Chi-restraints excluded: chain B residue 152 ASP Chi-restraints excluded: chain B residue 173 ARG Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 213 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 25 optimal weight: 0.9990 chunk 36 optimal weight: 4.9990 chunk 125 optimal weight: 7.9990 chunk 4 optimal weight: 0.1980 chunk 50 optimal weight: 2.9990 chunk 32 optimal weight: 7.9990 chunk 89 optimal weight: 0.8980 chunk 69 optimal weight: 2.9990 chunk 97 optimal weight: 0.0870 chunk 45 optimal weight: 6.9990 chunk 109 optimal weight: 3.9990 overall best weight: 1.0362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 67 GLN E 179 GLN D 13 GLN D 67 GLN D 114 GLN C 67 GLN B 67 GLN ** B 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4181 r_free = 0.4181 target = 0.157610 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.140077 restraints weight = 16171.189| |-----------------------------------------------------------------------------| r_work (start): 0.3965 rms_B_bonded: 2.51 r_work: 0.3843 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.3843 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7516 moved from start: 0.4320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 10608 Z= 0.148 Angle : 0.785 18.427 14424 Z= 0.354 Chirality : 0.047 0.240 1608 Planarity : 0.005 0.071 1890 Dihedral : 3.940 14.784 1416 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.49 % Favored : 93.51 % Rotamer: Outliers : 5.17 % Allowed : 40.55 % Favored : 54.28 % 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 aren not related in a simple way. whole: 0.26 (0.23), residues: 1326 helix: 1.34 (0.18), residues: 852 sheet: None (None), residues: 0 loop : -2.07 (0.26), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 143 TYR 0.015 0.002 TYR C 169 PHE 0.014 0.002 PHE A 32 TRP 0.023 0.002 TRP A 133 HIS 0.008 0.001 HIS D 12 Details of bonding type rmsd covalent geometry : bond 0.00361 (10608) covalent geometry : angle 0.78532 (14424) hydrogen bonds : bond 0.03951 ( 590) hydrogen bonds : angle 4.12669 ( 1731) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3871.36 seconds wall clock time: 66 minutes 32.58 seconds (3992.58 seconds total)