Starting phenix.real_space_refine on Thu May 1 00:18:26 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9i8i_52724/05_2025/9i8i_52724.cif Found real_map, /net/cci-nas-00/data/ceres_data/9i8i_52724/05_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_52724/05_2025/9i8i_52724.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9i8i_52724/05_2025/9i8i_52724.map" model { file = "/net/cci-nas-00/data/ceres_data/9i8i_52724/05_2025/9i8i_52724.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9i8i_52724/05_2025/9i8i_52724.cif" } resolution = 2.75 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/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: 6.31, per 1000 atoms: 0.61 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: 2.58 Conformation dependent library (CDL) restraints added in 1.3 seconds 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: 1.09 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: 2.79 Time building geometry restraints manager: 3.07 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: 0.02 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: 1.150 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: 0.500 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 25.790 Find NCS groups from input model: 0.370 Set up NCS constraints: 0.050 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:13.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.120 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.018 0.002 TRP E 184 HIS 0.008 0.002 HIS D 12 PHE 0.012 0.001 PHE F 32 TYR 0.016 0.002 TYR F 169 ARG 0.004 0.001 ARG F 143 Details of bonding type rmsd hydrogen bonds : bond 0.19266 ( 590) hydrogen bonds : angle 5.33825 ( 1731) covalent geometry : bond 0.00346 (10608) covalent geometry : angle 0.94185 (14424) *********************** 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 : 1.156 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: 1.2955 time to fit residues: 463.3390 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 : 1.069 ------------------------------------------------------------------------------- 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 111 optimal weight: 7.9990 chunk 100 optimal weight: 2.9990 chunk 55 optimal weight: 4.9990 chunk 34 optimal weight: 3.9990 chunk 67 optimal weight: 4.9990 chunk 53 optimal weight: 2.9990 chunk 103 optimal weight: 1.9990 chunk 40 optimal weight: 4.9990 chunk 62 optimal weight: 5.9990 chunk 77 optimal weight: 0.7980 chunk 119 optimal weight: 1.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 192 GLN B 13 GLN B 67 GLN B 84 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4197 r_free = 0.4197 target = 0.157820 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.139598 restraints weight = 15974.798| |-----------------------------------------------------------------------------| r_work (start): 0.3978 rms_B_bonded: 2.63 r_work: 0.3853 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.3853 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7517 moved from start: 0.1993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 10608 Z= 0.224 Angle : 0.774 12.337 14424 Z= 0.382 Chirality : 0.051 0.304 1608 Planarity : 0.006 0.046 1890 Dihedral : 5.551 49.785 1443 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 10.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.96 % Favored : 94.04 % Rotamer: Outliers : 8.47 % Allowed : 33.96 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.09 (0.23), residues: 1326 helix: 1.21 (0.17), residues: 882 sheet: None (None), residues: 0 loop : -2.79 (0.27), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP E 80 HIS 0.006 0.001 HIS D 12 PHE 0.015 0.002 PHE C 168 TYR 0.024 0.003 TYR A 169 ARG 0.004 0.001 ARG C 97 Details of bonding type rmsd hydrogen bonds : bond 0.05489 ( 590) hydrogen bonds : angle 4.35233 ( 1731) covalent geometry : bond 0.00511 (10608) covalent geometry : angle 0.77387 (14424) *********************** 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 416 residues out of total 1122 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 321 time to evaluate : 2.323 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 173 ARG cc_start: 0.8362 (OUTLIER) cc_final: 0.6823 (ttp80) REVERT: A 213 GLU cc_start: 0.7536 (OUTLIER) cc_final: 0.7259 (mt-10) REVERT: F 35 GLU cc_start: 0.7653 (pm20) cc_final: 0.7406 (pm20) REVERT: F 76 GLU cc_start: 0.7921 (mm-30) cc_final: 0.7582 (mm-30) REVERT: F 97 ARG cc_start: 0.6174 (OUTLIER) cc_final: 0.5483 (ptm-80) REVERT: F 153 ILE cc_start: 0.6688 (tp) cc_final: 0.6412 (OUTLIER) REVERT: F 173 ARG cc_start: 0.8370 (OUTLIER) cc_final: 0.7810 (ttt180) REVERT: E 79 GLU cc_start: 0.7662 (mm-30) cc_final: 0.7389 (tp30) REVERT: E 97 ARG cc_start: 0.5958 (OUTLIER) cc_final: 0.5689 (ptm160) REVERT: E 113 GLU cc_start: 0.7526 (OUTLIER) cc_final: 0.7301 (mt-10) REVERT: E 143 ARG cc_start: 0.7850 (OUTLIER) cc_final: 0.7486 (ttm170) REVERT: E 191 VAL cc_start: 0.8341 (OUTLIER) cc_final: 0.8071 (p) REVERT: E 192 GLN cc_start: 0.8300 (tp-100) cc_final: 0.8018 (tp-100) REVERT: D 75 GLU cc_start: 0.7876 (mt-10) cc_final: 0.7568 (mt-10) REVERT: D 97 ARG cc_start: 0.6159 (OUTLIER) cc_final: 0.5407 (ptm-80) REVERT: D 143 ARG cc_start: 0.7852 (OUTLIER) cc_final: 0.7553 (ttm170) REVERT: C 192 GLN cc_start: 0.8096 (tp-100) cc_final: 0.7834 (tp-100) REVERT: B 37 ILE cc_start: 0.8525 (mm) cc_final: 0.8253 (mt) REVERT: B 39 MET cc_start: 0.8392 (mmm) cc_final: 0.8189 (mmm) REVERT: B 82 ARG cc_start: 0.8167 (OUTLIER) cc_final: 0.7927 (mtm110) REVERT: B 97 ARG cc_start: 0.6162 (OUTLIER) cc_final: 0.5486 (ptm-80) REVERT: B 173 ARG cc_start: 0.8536 (OUTLIER) cc_final: 0.7451 (ttp80) REVERT: B 175 GLU cc_start: 0.7371 (mt-10) cc_final: 0.7062 (mt-10) REVERT: B 213 GLU cc_start: 0.7277 (OUTLIER) cc_final: 0.7074 (mt-10) REVERT: B 215 MET cc_start: 0.7694 (OUTLIER) cc_final: 0.7325 (tpp) outliers start: 95 outliers final: 33 residues processed: 371 average time/residue: 1.6696 time to fit residues: 660.2259 Evaluate side-chains 361 residues out of total 1122 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 314 time to evaluate : 2.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 LEU Chi-restraints excluded: chain A residue 97 ARG 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 135 ILE Chi-restraints excluded: chain A residue 144 MET Chi-restraints excluded: chain A residue 173 ARG Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 213 GLU 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 173 ARG Chi-restraints excluded: chain E residue 24 VAL Chi-restraints excluded: chain E residue 30 LYS Chi-restraints excluded: chain E residue 97 ARG Chi-restraints excluded: chain E residue 113 GLU Chi-restraints excluded: chain E residue 143 ARG 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 143 ARG Chi-restraints excluded: chain D residue 144 MET 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 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 191 VAL Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 54 THR 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 110 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 Chi-restraints excluded: chain B residue 213 GLU Chi-restraints excluded: chain B residue 215 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 78 optimal weight: 0.9980 chunk 71 optimal weight: 0.9980 chunk 100 optimal weight: 5.9990 chunk 11 optimal weight: 4.9990 chunk 104 optimal weight: 1.9990 chunk 113 optimal weight: 1.9990 chunk 66 optimal weight: 6.9990 chunk 51 optimal weight: 5.9990 chunk 53 optimal weight: 0.9980 chunk 96 optimal weight: 7.9990 chunk 69 optimal weight: 0.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 67 GLN F 84 HIS E 84 HIS D 84 HIS C 67 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: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4203 r_free = 0.4203 target = 0.158949 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.140650 restraints weight = 16383.517| |-----------------------------------------------------------------------------| r_work (start): 0.3987 rms_B_bonded: 2.67 r_work: 0.3865 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3865 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7502 moved from start: 0.2651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 10608 Z= 0.151 Angle : 0.707 14.378 14424 Z= 0.335 Chirality : 0.045 0.262 1608 Planarity : 0.006 0.047 1890 Dihedral : 4.984 50.702 1426 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.56 % Favored : 93.44 % Rotamer: Outliers : 7.04 % Allowed : 34.85 % Favored : 58.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.18 (0.23), residues: 1326 helix: 1.35 (0.18), residues: 888 sheet: None (None), residues: 0 loop : -2.60 (0.27), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 80 HIS 0.009 0.001 HIS D 12 PHE 0.011 0.002 PHE B 168 TYR 0.019 0.002 TYR A 169 ARG 0.004 0.000 ARG C 143 Details of bonding type rmsd hydrogen bonds : bond 0.04481 ( 590) hydrogen bonds : angle 4.08898 ( 1731) covalent geometry : bond 0.00350 (10608) covalent geometry : angle 0.70717 (14424) *********************** 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 386 residues out of total 1122 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 307 time to evaluate : 1.164 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 173 ARG cc_start: 0.8264 (OUTLIER) cc_final: 0.7003 (ttp-170) REVERT: A 187 GLU cc_start: 0.6944 (OUTLIER) cc_final: 0.6412 (pp20) REVERT: A 213 GLU cc_start: 0.7514 (OUTLIER) cc_final: 0.7107 (mt-10) REVERT: F 35 GLU cc_start: 0.7631 (pm20) cc_final: 0.7399 (pm20) REVERT: F 97 ARG cc_start: 0.6199 (OUTLIER) cc_final: 0.5504 (ptm-80) REVERT: F 153 ILE cc_start: 0.6804 (tp) cc_final: 0.6015 (mp) REVERT: F 173 ARG cc_start: 0.8285 (OUTLIER) cc_final: 0.7080 (ttt90) REVERT: E 79 GLU cc_start: 0.7656 (mm-30) cc_final: 0.7353 (tp30) REVERT: E 113 GLU cc_start: 0.7442 (OUTLIER) cc_final: 0.7215 (mt-10) REVERT: E 187 GLU cc_start: 0.6847 (OUTLIER) cc_final: 0.6266 (pp20) REVERT: E 192 GLN cc_start: 0.8264 (tp-100) cc_final: 0.7985 (tp-100) REVERT: D 75 GLU cc_start: 0.7859 (mt-10) cc_final: 0.7534 (mt-10) REVERT: D 97 ARG cc_start: 0.6102 (OUTLIER) cc_final: 0.5392 (ptm-80) REVERT: D 179 GLN cc_start: 0.8637 (mm110) cc_final: 0.8423 (tp40) REVERT: C 143 ARG cc_start: 0.7889 (ttm-80) cc_final: 0.7623 (ttm-80) REVERT: C 180 GLU cc_start: 0.4818 (OUTLIER) cc_final: 0.3187 (mm-30) REVERT: C 192 GLN cc_start: 0.8157 (tp-100) cc_final: 0.7815 (tp-100) REVERT: B 37 ILE cc_start: 0.8520 (mm) cc_final: 0.8271 (mt) REVERT: B 97 ARG cc_start: 0.5991 (OUTLIER) cc_final: 0.5443 (ptm160) REVERT: B 143 ARG cc_start: 0.7855 (OUTLIER) cc_final: 0.7517 (ttm170) REVERT: B 173 ARG cc_start: 0.8459 (OUTLIER) cc_final: 0.7420 (ttp80) REVERT: B 175 GLU cc_start: 0.7269 (mt-10) cc_final: 0.6990 (mt-10) REVERT: B 192 GLN cc_start: 0.8305 (tp-100) cc_final: 0.8050 (tp-100) REVERT: B 213 GLU cc_start: 0.7279 (mt-10) cc_final: 0.6955 (mp0) REVERT: B 215 MET cc_start: 0.7615 (OUTLIER) cc_final: 0.7047 (tpp) outliers start: 79 outliers final: 31 residues processed: 346 average time/residue: 1.2463 time to fit residues: 461.0257 Evaluate side-chains 338 residues out of total 1122 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 294 time to evaluate : 1.036 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 LEU Chi-restraints excluded: chain A residue 97 ARG 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 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 30 LYS Chi-restraints excluded: chain F residue 97 ARG Chi-restraints excluded: chain F residue 119 THR 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 113 GLU Chi-restraints excluded: chain E residue 187 GLU Chi-restraints excluded: chain D residue 3 VAL Chi-restraints excluded: chain D residue 54 THR Chi-restraints excluded: chain D residue 97 ARG Chi-restraints excluded: chain D residue 119 THR 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 71 GLU Chi-restraints excluded: chain C residue 97 ARG Chi-restraints excluded: chain C residue 98 GLU Chi-restraints excluded: chain C residue 180 GLU Chi-restraints excluded: chain C residue 191 VAL Chi-restraints excluded: chain B residue 20 LEU Chi-restraints excluded: chain B residue 30 LYS 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 143 ARG Chi-restraints excluded: chain B residue 173 ARG Chi-restraints excluded: chain B residue 191 VAL 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 118 optimal weight: 8.9990 chunk 72 optimal weight: 3.9990 chunk 52 optimal weight: 10.0000 chunk 77 optimal weight: 4.9990 chunk 23 optimal weight: 0.0970 chunk 34 optimal weight: 2.9990 chunk 71 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 92 optimal weight: 0.9980 chunk 31 optimal weight: 0.9990 chunk 73 optimal weight: 5.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 193 ASN F 63 GLN F 155 GLN E 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: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4198 r_free = 0.4198 target = 0.158279 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.140147 restraints weight = 15921.033| |-----------------------------------------------------------------------------| r_work (start): 0.3968 rms_B_bonded: 2.58 r_work: 0.3848 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.3848 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7529 moved from start: 0.3096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 10608 Z= 0.160 Angle : 0.697 15.270 14424 Z= 0.328 Chirality : 0.046 0.307 1608 Planarity : 0.006 0.050 1890 Dihedral : 4.763 51.004 1423 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.56 % Favored : 93.44 % Rotamer: Outliers : 8.11 % Allowed : 33.78 % Favored : 58.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.19 (0.23), residues: 1326 helix: 1.32 (0.18), residues: 888 sheet: None (None), residues: 0 loop : -2.48 (0.27), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 133 HIS 0.008 0.001 HIS B 12 PHE 0.012 0.002 PHE C 168 TYR 0.020 0.002 TYR A 169 ARG 0.004 0.000 ARG D 143 Details of bonding type rmsd hydrogen bonds : bond 0.04383 ( 590) hydrogen bonds : angle 4.06646 ( 1731) covalent geometry : bond 0.00376 (10608) covalent geometry : angle 0.69672 (14424) *********************** 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 396 residues out of total 1122 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 305 time to evaluate : 1.068 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 173 ARG cc_start: 0.8327 (OUTLIER) cc_final: 0.6896 (ttp80) REVERT: A 187 GLU cc_start: 0.6946 (OUTLIER) cc_final: 0.6393 (pp20) REVERT: A 213 GLU cc_start: 0.7721 (OUTLIER) cc_final: 0.7381 (mt-10) REVERT: F 97 ARG cc_start: 0.6043 (OUTLIER) cc_final: 0.5414 (ptm-80) REVERT: F 173 ARG cc_start: 0.8318 (OUTLIER) cc_final: 0.7789 (ttt180) REVERT: F 187 GLU cc_start: 0.6858 (OUTLIER) cc_final: 0.6349 (pp20) REVERT: E 79 GLU cc_start: 0.7674 (mm-30) cc_final: 0.7403 (tp30) REVERT: E 187 GLU cc_start: 0.6889 (OUTLIER) cc_final: 0.6303 (pp20) REVERT: E 191 VAL cc_start: 0.8471 (OUTLIER) cc_final: 0.8109 (p) REVERT: E 192 GLN cc_start: 0.8226 (tp-100) cc_final: 0.7965 (tp-100) REVERT: D 69 LEU cc_start: 0.8108 (tt) cc_final: 0.7851 (tp) REVERT: D 75 GLU cc_start: 0.7870 (mt-10) cc_final: 0.7551 (mt-10) REVERT: D 97 ARG cc_start: 0.6148 (OUTLIER) cc_final: 0.5429 (ptm-80) REVERT: C 30 LYS cc_start: 0.8800 (mtpp) cc_final: 0.8541 (mttp) REVERT: C 143 ARG cc_start: 0.7854 (ttm-80) cc_final: 0.7632 (ttm-80) REVERT: C 144 MET cc_start: 0.8307 (OUTLIER) cc_final: 0.8010 (ttm) REVERT: C 180 GLU cc_start: 0.5073 (OUTLIER) cc_final: 0.3126 (mp0) REVERT: C 187 GLU cc_start: 0.6749 (OUTLIER) cc_final: 0.6298 (pp20) REVERT: C 192 GLN cc_start: 0.8127 (tp-100) cc_final: 0.7716 (tp-100) REVERT: B 97 ARG cc_start: 0.6124 (OUTLIER) cc_final: 0.5558 (ptm160) REVERT: B 143 ARG cc_start: 0.7892 (OUTLIER) cc_final: 0.7569 (ttm170) REVERT: B 173 ARG cc_start: 0.8533 (OUTLIER) cc_final: 0.7420 (ttp80) REVERT: B 175 GLU cc_start: 0.7310 (mt-10) cc_final: 0.7067 (mt-10) REVERT: B 192 GLN cc_start: 0.8212 (tp-100) cc_final: 0.7973 (tp-100) REVERT: B 213 GLU cc_start: 0.7217 (mt-10) cc_final: 0.6744 (mp0) REVERT: B 215 MET cc_start: 0.7548 (OUTLIER) cc_final: 0.7281 (tpp) outliers start: 91 outliers final: 46 residues processed: 362 average time/residue: 1.1986 time to fit residues: 463.9573 Evaluate side-chains 372 residues out of total 1122 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 310 time to evaluate : 1.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 ARG 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 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 10 MET 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 108 THR Chi-restraints excluded: chain F residue 119 THR 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 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 54 THR 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 178 SER 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 11 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 144 MET Chi-restraints excluded: chain C residue 180 GLU Chi-restraints excluded: chain C residue 187 GLU Chi-restraints excluded: chain C residue 191 VAL Chi-restraints excluded: chain B residue 28 GLU 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 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 191 VAL Chi-restraints excluded: chain B residue 210 THR Chi-restraints excluded: chain B residue 215 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 130 optimal weight: 0.9990 chunk 63 optimal weight: 4.9990 chunk 19 optimal weight: 7.9990 chunk 44 optimal weight: 6.9990 chunk 45 optimal weight: 2.9990 chunk 14 optimal weight: 1.9990 chunk 101 optimal weight: 0.9990 chunk 97 optimal weight: 8.9990 chunk 31 optimal weight: 7.9990 chunk 81 optimal weight: 7.9990 chunk 82 optimal weight: 0.8980 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4169 r_free = 0.4169 target = 0.156207 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.138146 restraints weight = 16134.660| |-----------------------------------------------------------------------------| r_work (start): 0.3956 rms_B_bonded: 2.59 r_work: 0.3832 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.3832 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7553 moved from start: 0.3442 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= 0.168 Angle : 0.725 15.979 14424 Z= 0.335 Chirality : 0.046 0.260 1608 Planarity : 0.006 0.054 1890 Dihedral : 4.875 52.859 1423 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.71 % Favored : 93.29 % Rotamer: Outliers : 7.58 % Allowed : 35.29 % Favored : 57.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.18 (0.23), residues: 1326 helix: 1.27 (0.17), residues: 888 sheet: None (None), residues: 0 loop : -2.40 (0.27), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 133 HIS 0.007 0.001 HIS D 12 PHE 0.011 0.002 PHE C 168 TYR 0.021 0.002 TYR A 169 ARG 0.005 0.000 ARG D 143 Details of bonding type rmsd hydrogen bonds : bond 0.04383 ( 590) hydrogen bonds : angle 4.11831 ( 1731) covalent geometry : bond 0.00393 (10608) covalent geometry : angle 0.72506 (14424) *********************** 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 411 residues out of total 1122 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 326 time to evaluate : 1.138 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 173 ARG cc_start: 0.8353 (OUTLIER) cc_final: 0.6918 (ttp80) REVERT: A 187 GLU cc_start: 0.6974 (OUTLIER) cc_final: 0.6455 (pp20) REVERT: A 213 GLU cc_start: 0.7664 (OUTLIER) cc_final: 0.7313 (mt-10) REVERT: F 97 ARG cc_start: 0.6027 (OUTLIER) cc_final: 0.5419 (ptm-80) REVERT: F 152 ASP cc_start: 0.5861 (OUTLIER) cc_final: 0.5600 (m-30) REVERT: F 173 ARG cc_start: 0.8340 (OUTLIER) cc_final: 0.7814 (ttt180) REVERT: F 187 GLU cc_start: 0.6883 (OUTLIER) cc_final: 0.6356 (pp20) REVERT: E 79 GLU cc_start: 0.7750 (mm-30) cc_final: 0.7479 (tp30) REVERT: E 187 GLU cc_start: 0.6916 (OUTLIER) cc_final: 0.6306 (pp20) REVERT: E 192 GLN cc_start: 0.8244 (tp-100) cc_final: 0.7907 (tp-100) REVERT: D 69 LEU cc_start: 0.8164 (tt) cc_final: 0.7955 (tp) REVERT: D 75 GLU cc_start: 0.7999 (mt-10) cc_final: 0.7674 (mt-10) REVERT: D 97 ARG cc_start: 0.6179 (OUTLIER) cc_final: 0.5468 (ptm-80) REVERT: D 111 LEU cc_start: 0.8287 (tm) cc_final: 0.8076 (tt) REVERT: C 29 GLU cc_start: 0.7815 (mp0) cc_final: 0.7589 (mp0) REVERT: C 30 LYS cc_start: 0.8786 (mtpp) cc_final: 0.8547 (mttp) REVERT: C 143 ARG cc_start: 0.7907 (ttm-80) cc_final: 0.7691 (ttm-80) REVERT: C 180 GLU cc_start: 0.5211 (OUTLIER) cc_final: 0.2976 (mm-30) REVERT: C 187 GLU cc_start: 0.6835 (OUTLIER) cc_final: 0.6366 (pp20) REVERT: C 192 GLN cc_start: 0.8163 (tp-100) cc_final: 0.7761 (tp-100) REVERT: B 35 GLU cc_start: 0.7306 (pm20) cc_final: 0.7012 (pm20) REVERT: B 37 ILE cc_start: 0.8569 (mm) cc_final: 0.8330 (mt) REVERT: B 97 ARG cc_start: 0.6150 (OUTLIER) cc_final: 0.5539 (ptm160) REVERT: B 112 GLN cc_start: 0.8109 (OUTLIER) cc_final: 0.7868 (mm110) REVERT: B 143 ARG cc_start: 0.7975 (OUTLIER) cc_final: 0.7638 (ttm170) REVERT: B 173 ARG cc_start: 0.8518 (OUTLIER) cc_final: 0.7399 (ttp80) REVERT: B 175 GLU cc_start: 0.7432 (mt-10) cc_final: 0.7177 (mt-10) REVERT: B 192 GLN cc_start: 0.8250 (tp-100) cc_final: 0.7935 (tp-100) REVERT: B 213 GLU cc_start: 0.7188 (OUTLIER) cc_final: 0.6581 (mp0) outliers start: 85 outliers final: 50 residues processed: 371 average time/residue: 1.1868 time to fit residues: 471.9019 Evaluate side-chains 378 residues out of total 1122 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 312 time to evaluate : 1.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 10 MET Chi-restraints excluded: chain F residue 12 HIS Chi-restraints excluded: chain F residue 54 THR 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 141 ILE Chi-restraints excluded: chain F residue 152 ASP Chi-restraints excluded: chain F residue 159 GLU Chi-restraints excluded: chain F residue 173 ARG 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 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 54 THR 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 178 SER 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 D residue 216 THR Chi-restraints excluded: chain C residue 3 VAL 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 97 ARG Chi-restraints excluded: chain C residue 98 GLU Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 180 GLU Chi-restraints excluded: chain C residue 187 GLU Chi-restraints excluded: chain C residue 191 VAL Chi-restraints excluded: chain B residue 24 VAL 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 148 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 210 THR 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 126 optimal weight: 2.9990 chunk 101 optimal weight: 0.9990 chunk 100 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 71 optimal weight: 0.9990 chunk 85 optimal weight: 6.9990 chunk 65 optimal weight: 5.9990 chunk 95 optimal weight: 1.9990 chunk 103 optimal weight: 10.0000 chunk 64 optimal weight: 4.9990 chunk 75 optimal weight: 0.0670 overall best weight: 1.2126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 155 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4175 r_free = 0.4175 target = 0.156715 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.138823 restraints weight = 16168.431| |-----------------------------------------------------------------------------| r_work (start): 0.3967 rms_B_bonded: 2.58 r_work: 0.3844 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3844 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7539 moved from start: 0.3654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 10608 Z= 0.149 Angle : 0.724 16.480 14424 Z= 0.329 Chirality : 0.046 0.378 1608 Planarity : 0.005 0.059 1890 Dihedral : 4.851 59.388 1423 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.49 % Favored : 93.51 % Rotamer: Outliers : 7.13 % Allowed : 36.19 % Favored : 56.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.23), residues: 1326 helix: 1.42 (0.18), residues: 852 sheet: None (None), residues: 0 loop : -2.36 (0.25), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 133 HIS 0.009 0.001 HIS C 12 PHE 0.015 0.002 PHE A 32 TYR 0.017 0.002 TYR D 169 ARG 0.005 0.000 ARG D 143 Details of bonding type rmsd hydrogen bonds : bond 0.04078 ( 590) hydrogen bonds : angle 4.02223 ( 1731) covalent geometry : bond 0.00357 (10608) covalent geometry : angle 0.72431 (14424) *********************** 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 397 residues out of total 1122 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 317 time to evaluate : 1.135 Fit side-chains revert: symmetry clash REVERT: A 24 VAL cc_start: 0.8656 (t) cc_final: 0.8449 (t) REVERT: A 173 ARG cc_start: 0.8383 (OUTLIER) cc_final: 0.7054 (ttp80) REVERT: A 187 GLU cc_start: 0.6852 (OUTLIER) cc_final: 0.6300 (pp20) REVERT: A 213 GLU cc_start: 0.7637 (OUTLIER) cc_final: 0.7296 (mt-10) REVERT: F 30 LYS cc_start: 0.8976 (OUTLIER) cc_final: 0.8589 (mtmm) REVERT: F 97 ARG cc_start: 0.6077 (OUTLIER) cc_final: 0.5508 (ptm-80) REVERT: F 152 ASP cc_start: 0.5822 (OUTLIER) cc_final: 0.5494 (m-30) REVERT: F 173 ARG cc_start: 0.8310 (OUTLIER) cc_final: 0.6860 (ttt90) REVERT: F 187 GLU cc_start: 0.6872 (OUTLIER) cc_final: 0.6315 (pp20) REVERT: E 79 GLU cc_start: 0.7661 (mm-30) cc_final: 0.7430 (tp30) REVERT: E 187 GLU cc_start: 0.6965 (OUTLIER) cc_final: 0.6323 (pp20) REVERT: E 192 GLN cc_start: 0.8222 (tp-100) cc_final: 0.7934 (tp-100) REVERT: D 75 GLU cc_start: 0.7952 (mt-10) cc_final: 0.7638 (mt-10) REVERT: D 97 ARG cc_start: 0.6214 (OUTLIER) cc_final: 0.5560 (ptm-80) REVERT: D 111 LEU cc_start: 0.8280 (tm) cc_final: 0.8050 (tt) REVERT: C 143 ARG cc_start: 0.7833 (ttm-80) cc_final: 0.7622 (ttm-80) REVERT: C 152 ASP cc_start: 0.6618 (OUTLIER) cc_final: 0.6336 (m-30) REVERT: C 180 GLU cc_start: 0.5213 (OUTLIER) cc_final: 0.2894 (mm-30) REVERT: C 187 GLU cc_start: 0.6821 (OUTLIER) cc_final: 0.6338 (pp20) REVERT: C 192 GLN cc_start: 0.8131 (tp-100) cc_final: 0.7700 (tp-100) REVERT: B 35 GLU cc_start: 0.7145 (pm20) cc_final: 0.6871 (pm20) REVERT: B 37 ILE cc_start: 0.8559 (mm) cc_final: 0.8332 (mt) REVERT: B 97 ARG cc_start: 0.6127 (OUTLIER) cc_final: 0.5544 (ptm160) REVERT: B 112 GLN cc_start: 0.8109 (OUTLIER) cc_final: 0.7872 (mm110) REVERT: B 143 ARG cc_start: 0.7944 (OUTLIER) cc_final: 0.7642 (ttm170) REVERT: B 152 ASP cc_start: 0.6416 (OUTLIER) cc_final: 0.6051 (m-30) REVERT: B 173 ARG cc_start: 0.8492 (OUTLIER) cc_final: 0.7607 (ttp-170) REVERT: B 175 GLU cc_start: 0.7343 (mt-10) cc_final: 0.7098 (mt-10) REVERT: B 192 GLN cc_start: 0.8237 (tp-100) cc_final: 0.7967 (tp-100) REVERT: B 213 GLU cc_start: 0.7095 (OUTLIER) cc_final: 0.6319 (mp0) outliers start: 80 outliers final: 43 residues processed: 362 average time/residue: 1.2360 time to fit residues: 478.9357 Evaluate side-chains 376 residues out of total 1122 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 314 time to evaluate : 1.038 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 LEU Chi-restraints excluded: chain A residue 48 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 10 MET Chi-restraints excluded: chain F residue 12 HIS 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 119 THR Chi-restraints excluded: chain F residue 141 ILE 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 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 56 LEU Chi-restraints excluded: chain E residue 148 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 119 THR Chi-restraints excluded: chain D residue 175 GLU Chi-restraints excluded: chain D residue 178 SER 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 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 152 ASP Chi-restraints excluded: chain C residue 180 GLU Chi-restraints excluded: chain C residue 187 GLU Chi-restraints excluded: chain C residue 191 VAL Chi-restraints excluded: chain B residue 28 GLU 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 210 THR Chi-restraints excluded: chain B residue 213 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 75 optimal weight: 0.1980 chunk 115 optimal weight: 3.9990 chunk 88 optimal weight: 4.9990 chunk 33 optimal weight: 5.9990 chunk 77 optimal weight: 0.7980 chunk 49 optimal weight: 0.9980 chunk 95 optimal weight: 0.7980 chunk 58 optimal weight: 1.9990 chunk 32 optimal weight: 3.9990 chunk 28 optimal weight: 2.9990 chunk 48 optimal weight: 0.0770 overall best weight: 0.5738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 193 ASN C 67 GLN B 67 GLN ** B 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4197 r_free = 0.4197 target = 0.158786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.140776 restraints weight = 16406.058| |-----------------------------------------------------------------------------| r_work (start): 0.3979 rms_B_bonded: 2.59 r_work: 0.3854 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3854 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7508 moved from start: 0.3810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 10608 Z= 0.123 Angle : 0.731 17.087 14424 Z= 0.325 Chirality : 0.045 0.244 1608 Planarity : 0.005 0.061 1890 Dihedral : 4.737 59.482 1423 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.33 % Favored : 93.67 % Rotamer: Outliers : 6.68 % Allowed : 37.34 % Favored : 55.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.32 (0.23), residues: 1326 helix: 1.48 (0.18), residues: 852 sheet: None (None), residues: 0 loop : -2.27 (0.26), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP F 133 HIS 0.010 0.001 HIS C 12 PHE 0.012 0.002 PHE A 32 TYR 0.016 0.001 TYR D 169 ARG 0.003 0.000 ARG D 143 Details of bonding type rmsd hydrogen bonds : bond 0.03685 ( 590) hydrogen bonds : angle 3.95449 ( 1731) covalent geometry : bond 0.00290 (10608) covalent geometry : angle 0.73089 (14424) *********************** 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 400 residues out of total 1122 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 325 time to evaluate : 1.200 Fit side-chains revert: symmetry clash REVERT: A 15 ILE cc_start: 0.9157 (mm) cc_final: 0.8945 (mp) REVERT: A 24 VAL cc_start: 0.8600 (t) cc_final: 0.8365 (t) REVERT: A 97 ARG cc_start: 0.5981 (OUTLIER) cc_final: 0.5679 (ptm160) REVERT: A 173 ARG cc_start: 0.8309 (OUTLIER) cc_final: 0.7051 (ttp80) REVERT: A 187 GLU cc_start: 0.6840 (OUTLIER) cc_final: 0.6290 (pp20) REVERT: A 213 GLU cc_start: 0.7632 (OUTLIER) cc_final: 0.7299 (mt-10) REVERT: F 30 LYS cc_start: 0.8991 (OUTLIER) cc_final: 0.8714 (mtmm) REVERT: F 72 THR cc_start: 0.8294 (m) cc_final: 0.7894 (t) REVERT: F 76 GLU cc_start: 0.8233 (OUTLIER) cc_final: 0.7636 (mp0) REVERT: F 97 ARG cc_start: 0.6018 (OUTLIER) cc_final: 0.5506 (ptm-80) REVERT: F 152 ASP cc_start: 0.5561 (OUTLIER) cc_final: 0.5261 (m-30) REVERT: F 187 GLU cc_start: 0.6814 (OUTLIER) cc_final: 0.6241 (pp20) REVERT: E 187 GLU cc_start: 0.6903 (OUTLIER) cc_final: 0.6278 (pp20) REVERT: E 192 GLN cc_start: 0.8218 (tp-100) cc_final: 0.7876 (tp-100) REVERT: D 75 GLU cc_start: 0.7940 (mt-10) cc_final: 0.7625 (mt-10) REVERT: D 97 ARG cc_start: 0.6167 (OUTLIER) cc_final: 0.5604 (ptm160) REVERT: D 152 ASP cc_start: 0.5846 (OUTLIER) cc_final: 0.5534 (m-30) REVERT: C 97 ARG cc_start: 0.6236 (OUTLIER) cc_final: 0.5680 (ptm-80) REVERT: C 143 ARG cc_start: 0.7846 (ttm-80) cc_final: 0.7602 (ttm-80) REVERT: C 152 ASP cc_start: 0.6573 (OUTLIER) cc_final: 0.6270 (m-30) REVERT: C 180 GLU cc_start: 0.5197 (OUTLIER) cc_final: 0.2892 (mm-30) REVERT: C 187 GLU cc_start: 0.6802 (OUTLIER) cc_final: 0.6331 (pp20) REVERT: C 192 GLN cc_start: 0.8093 (tp-100) cc_final: 0.7615 (tp-100) REVERT: B 35 GLU cc_start: 0.7127 (pm20) cc_final: 0.6864 (pm20) REVERT: B 37 ILE cc_start: 0.8569 (mm) cc_final: 0.8336 (mt) REVERT: B 97 ARG cc_start: 0.6060 (OUTLIER) cc_final: 0.5630 (ptm160) REVERT: B 112 GLN cc_start: 0.8105 (OUTLIER) cc_final: 0.7796 (mm110) REVERT: B 143 ARG cc_start: 0.7962 (OUTLIER) cc_final: 0.7724 (ttm170) REVERT: B 152 ASP cc_start: 0.6232 (OUTLIER) cc_final: 0.5875 (m-30) REVERT: B 173 ARG cc_start: 0.8424 (OUTLIER) cc_final: 0.7610 (ttp-170) REVERT: B 175 GLU cc_start: 0.7252 (mt-10) cc_final: 0.6978 (mt-10) REVERT: B 192 GLN cc_start: 0.8228 (tp-100) cc_final: 0.7911 (tp-100) REVERT: B 213 GLU cc_start: 0.7077 (OUTLIER) cc_final: 0.6277 (mp0) outliers start: 75 outliers final: 38 residues processed: 366 average time/residue: 1.1887 time to fit residues: 466.2009 Evaluate side-chains 374 residues out of total 1122 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 314 time to evaluate : 1.041 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 LEU Chi-restraints excluded: chain A residue 48 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 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 76 GLU Chi-restraints excluded: chain F residue 97 ARG Chi-restraints excluded: chain F residue 141 ILE 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 24 VAL Chi-restraints excluded: chain E residue 30 LYS Chi-restraints excluded: chain E residue 148 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 54 THR Chi-restraints excluded: chain D residue 97 ARG Chi-restraints excluded: chain D residue 119 THR Chi-restraints excluded: chain D residue 152 ASP Chi-restraints excluded: chain D residue 175 GLU Chi-restraints excluded: chain D residue 178 SER 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 56 LEU Chi-restraints excluded: chain C residue 97 ARG Chi-restraints excluded: chain C residue 98 GLU Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 152 ASP Chi-restraints excluded: chain C residue 180 GLU Chi-restraints excluded: chain C residue 187 GLU Chi-restraints excluded: chain C residue 191 VAL 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 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 90 optimal weight: 4.9990 chunk 17 optimal weight: 5.9990 chunk 102 optimal weight: 0.8980 chunk 61 optimal weight: 6.9990 chunk 63 optimal weight: 1.9990 chunk 7 optimal weight: 9.9990 chunk 37 optimal weight: 3.9990 chunk 79 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 chunk 112 optimal weight: 6.9990 chunk 41 optimal weight: 0.9980 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4157 r_free = 0.4157 target = 0.155222 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.137448 restraints weight = 16259.246| |-----------------------------------------------------------------------------| r_work (start): 0.3942 rms_B_bonded: 2.58 r_work: 0.3814 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3814 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7575 moved from start: 0.4008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 10608 Z= 0.184 Angle : 0.772 17.384 14424 Z= 0.350 Chirality : 0.048 0.262 1608 Planarity : 0.005 0.060 1890 Dihedral : 4.846 59.430 1423 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.94 % Favored : 93.06 % Rotamer: Outliers : 7.22 % Allowed : 37.25 % Favored : 55.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.18 (0.23), residues: 1326 helix: 1.34 (0.18), residues: 852 sheet: None (None), residues: 0 loop : -2.25 (0.26), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP F 133 HIS 0.010 0.001 HIS B 12 PHE 0.014 0.002 PHE C 40 TYR 0.018 0.002 TYR D 169 ARG 0.003 0.000 ARG E 82 Details of bonding type rmsd hydrogen bonds : bond 0.04393 ( 590) hydrogen bonds : angle 4.17511 ( 1731) covalent geometry : bond 0.00438 (10608) covalent geometry : angle 0.77210 (14424) *********************** 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 407 residues out of total 1122 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 326 time to evaluate : 1.059 Fit side-chains revert: symmetry clash REVERT: A 24 VAL cc_start: 0.8624 (t) cc_final: 0.8402 (t) REVERT: A 173 ARG cc_start: 0.8436 (OUTLIER) cc_final: 0.7054 (ttp80) REVERT: A 187 GLU cc_start: 0.6883 (OUTLIER) cc_final: 0.6355 (pp20) REVERT: A 213 GLU cc_start: 0.7674 (OUTLIER) cc_final: 0.7349 (mt-10) REVERT: F 30 LYS cc_start: 0.9013 (OUTLIER) cc_final: 0.8549 (mtmm) REVERT: F 76 GLU cc_start: 0.8254 (OUTLIER) cc_final: 0.7658 (mp0) REVERT: F 97 ARG cc_start: 0.6067 (OUTLIER) cc_final: 0.5478 (ptm-80) REVERT: F 152 ASP cc_start: 0.5826 (OUTLIER) cc_final: 0.5453 (m-30) REVERT: F 187 GLU cc_start: 0.6902 (OUTLIER) cc_final: 0.6322 (pp20) REVERT: E 79 GLU cc_start: 0.7706 (mm-30) cc_final: 0.7415 (tp30) REVERT: E 143 ARG cc_start: 0.7903 (ttm170) cc_final: 0.7700 (ttm170) REVERT: E 173 ARG cc_start: 0.8488 (OUTLIER) cc_final: 0.7985 (ttt180) REVERT: E 187 GLU cc_start: 0.6939 (OUTLIER) cc_final: 0.6315 (pp20) REVERT: E 192 GLN cc_start: 0.8224 (tp-100) cc_final: 0.7952 (tp-100) REVERT: D 75 GLU cc_start: 0.7956 (mt-10) cc_final: 0.7645 (mt-10) REVERT: D 97 ARG cc_start: 0.6261 (OUTLIER) cc_final: 0.5624 (ptm-80) REVERT: D 111 LEU cc_start: 0.8274 (tm) cc_final: 0.8061 (tt) REVERT: D 152 ASP cc_start: 0.6035 (OUTLIER) cc_final: 0.5683 (m-30) REVERT: D 175 GLU cc_start: 0.7533 (OUTLIER) cc_final: 0.7183 (mt-10) REVERT: C 143 ARG cc_start: 0.7886 (ttm-80) cc_final: 0.7657 (ttm-80) REVERT: C 152 ASP cc_start: 0.6714 (OUTLIER) cc_final: 0.6432 (m-30) REVERT: C 180 GLU cc_start: 0.5222 (OUTLIER) cc_final: 0.2740 (mp0) REVERT: C 187 GLU cc_start: 0.6890 (OUTLIER) cc_final: 0.6442 (pp20) REVERT: C 192 GLN cc_start: 0.8126 (tp-100) cc_final: 0.7648 (tp-100) REVERT: B 37 ILE cc_start: 0.8587 (mm) cc_final: 0.8374 (mt) REVERT: B 97 ARG cc_start: 0.6109 (OUTLIER) cc_final: 0.5557 (ptm-80) REVERT: B 112 GLN cc_start: 0.8118 (OUTLIER) cc_final: 0.7874 (mm110) REVERT: B 152 ASP cc_start: 0.6491 (OUTLIER) cc_final: 0.6148 (m-30) REVERT: B 173 ARG cc_start: 0.8525 (OUTLIER) cc_final: 0.7155 (ttp80) REVERT: B 175 GLU cc_start: 0.7473 (mt-10) cc_final: 0.7170 (mt-10) REVERT: B 192 GLN cc_start: 0.8257 (tp-100) cc_final: 0.7942 (tp-100) REVERT: B 213 GLU cc_start: 0.7053 (OUTLIER) cc_final: 0.6260 (mp0) outliers start: 81 outliers final: 42 residues processed: 369 average time/residue: 1.3702 time to fit residues: 541.5388 Evaluate side-chains 385 residues out of total 1122 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 322 time to evaluate : 1.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 GLU Chi-restraints excluded: chain A residue 48 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 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 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 141 ILE 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 30 LYS Chi-restraints excluded: chain E residue 119 THR Chi-restraints excluded: chain E residue 148 THR Chi-restraints excluded: chain E residue 173 ARG 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 11 VAL 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 178 SER 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 108 THR Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 152 ASP Chi-restraints excluded: chain C residue 180 GLU 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 103 optimal weight: 7.9990 chunk 104 optimal weight: 0.6980 chunk 119 optimal weight: 0.9980 chunk 93 optimal weight: 0.9990 chunk 101 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 100 optimal weight: 0.7980 chunk 75 optimal weight: 0.6980 chunk 92 optimal weight: 0.7980 chunk 55 optimal weight: 2.9990 chunk 14 optimal weight: 0.8980 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 13 GLN A 67 GLN D 13 GLN D 114 GLN C 67 GLN B 67 GLN B 95 GLN B 176 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4183 r_free = 0.4183 target = 0.157735 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.139704 restraints weight = 16390.468| |-----------------------------------------------------------------------------| r_work (start): 0.3971 rms_B_bonded: 2.58 r_work: 0.3847 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3847 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7503 moved from start: 0.4126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 10608 Z= 0.130 Angle : 0.759 17.628 14424 Z= 0.336 Chirality : 0.046 0.290 1608 Planarity : 0.005 0.061 1890 Dihedral : 4.675 56.393 1423 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.26 % Favored : 93.74 % Rotamer: Outliers : 5.88 % Allowed : 39.39 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.34 (0.23), residues: 1326 helix: 1.46 (0.18), residues: 852 sheet: None (None), residues: 0 loop : -2.18 (0.26), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP F 133 HIS 0.009 0.001 HIS B 12 PHE 0.011 0.002 PHE A 168 TYR 0.015 0.002 TYR D 169 ARG 0.006 0.000 ARG D 143 Details of bonding type rmsd hydrogen bonds : bond 0.03803 ( 590) hydrogen bonds : angle 4.07647 ( 1731) covalent geometry : bond 0.00313 (10608) covalent geometry : angle 0.75875 (14424) *********************** 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 375 residues out of total 1122 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 309 time to evaluate : 1.067 Fit side-chains revert: symmetry clash REVERT: A 9 GLN cc_start: 0.5634 (OUTLIER) cc_final: 0.5341 (mp10) REVERT: A 24 VAL cc_start: 0.8549 (t) cc_final: 0.8324 (t) REVERT: A 173 ARG cc_start: 0.8335 (OUTLIER) cc_final: 0.7099 (ttp80) REVERT: A 187 GLU cc_start: 0.6804 (OUTLIER) cc_final: 0.6313 (pp20) REVERT: A 213 GLU cc_start: 0.7521 (OUTLIER) cc_final: 0.7220 (mt-10) REVERT: F 30 LYS cc_start: 0.8935 (OUTLIER) cc_final: 0.8640 (mtmm) REVERT: F 72 THR cc_start: 0.8272 (m) cc_final: 0.7931 (t) REVERT: F 76 GLU cc_start: 0.8186 (OUTLIER) cc_final: 0.7612 (mp0) REVERT: F 97 ARG cc_start: 0.6096 (OUTLIER) cc_final: 0.5576 (ptm-80) REVERT: F 152 ASP cc_start: 0.5524 (OUTLIER) cc_final: 0.5176 (m-30) REVERT: F 187 GLU cc_start: 0.6877 (OUTLIER) cc_final: 0.6298 (pp20) REVERT: E 187 GLU cc_start: 0.6906 (OUTLIER) cc_final: 0.6291 (pp20) REVERT: E 192 GLN cc_start: 0.8210 (tp-100) cc_final: 0.7929 (tp-100) REVERT: D 75 GLU cc_start: 0.7821 (mt-10) cc_final: 0.7557 (mt-10) REVERT: D 97 ARG cc_start: 0.6234 (OUTLIER) cc_final: 0.5721 (ptm160) REVERT: D 111 LEU cc_start: 0.8278 (tm) cc_final: 0.8035 (tt) REVERT: D 152 ASP cc_start: 0.5853 (OUTLIER) cc_final: 0.5563 (m-30) REVERT: D 175 GLU cc_start: 0.7239 (OUTLIER) cc_final: 0.6922 (mt-10) REVERT: C 97 ARG cc_start: 0.6341 (OUTLIER) cc_final: 0.5810 (ptm-80) REVERT: C 152 ASP cc_start: 0.6555 (OUTLIER) cc_final: 0.6256 (m-30) REVERT: C 180 GLU cc_start: 0.5228 (OUTLIER) cc_final: 0.2756 (mp0) REVERT: C 187 GLU cc_start: 0.6831 (OUTLIER) cc_final: 0.6399 (pp20) REVERT: B 37 ILE cc_start: 0.8530 (mm) cc_final: 0.8305 (mt) REVERT: B 97 ARG cc_start: 0.6075 (OUTLIER) cc_final: 0.5610 (ptm160) REVERT: B 112 GLN cc_start: 0.8045 (OUTLIER) cc_final: 0.7597 (mp-120) REVERT: B 143 ARG cc_start: 0.8087 (ttp-170) cc_final: 0.7759 (ttm170) REVERT: B 152 ASP cc_start: 0.6254 (OUTLIER) cc_final: 0.5891 (m-30) REVERT: B 173 ARG cc_start: 0.8428 (OUTLIER) cc_final: 0.7592 (ttp-170) REVERT: B 175 GLU cc_start: 0.7154 (mt-10) cc_final: 0.6940 (mt-10) REVERT: B 192 GLN cc_start: 0.8193 (tp-100) cc_final: 0.7929 (tp-100) REVERT: B 213 GLU cc_start: 0.7063 (OUTLIER) cc_final: 0.6425 (mp0) outliers start: 66 outliers final: 35 residues processed: 351 average time/residue: 1.2091 time to fit residues: 454.3260 Evaluate side-chains 368 residues out of total 1122 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 311 time to evaluate : 1.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 GLN Chi-restraints excluded: chain A residue 48 THR 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 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 76 GLU Chi-restraints excluded: chain F residue 97 ARG 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 30 LYS Chi-restraints excluded: chain E residue 119 THR Chi-restraints excluded: chain E residue 148 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 11 VAL Chi-restraints excluded: chain D residue 56 LEU Chi-restraints excluded: chain D residue 96 MET 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 178 SER 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 56 LEU Chi-restraints excluded: chain C residue 97 ARG Chi-restraints excluded: chain C residue 98 GLU Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 152 ASP Chi-restraints excluded: chain C residue 180 GLU Chi-restraints excluded: chain C residue 187 GLU Chi-restraints excluded: chain C residue 191 VAL 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 25 optimal weight: 0.4980 chunk 1 optimal weight: 4.9990 chunk 2 optimal weight: 1.9990 chunk 112 optimal weight: 0.0770 chunk 53 optimal weight: 0.8980 chunk 99 optimal weight: 1.9990 chunk 14 optimal weight: 0.0970 chunk 74 optimal weight: 0.9990 chunk 113 optimal weight: 0.7980 chunk 15 optimal weight: 0.0970 chunk 83 optimal weight: 4.9990 overall best weight: 0.3134 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 67 GLN D 13 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 = 0.4206 r_free = 0.4206 target = 0.159428 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.141306 restraints weight = 16418.989| |-----------------------------------------------------------------------------| r_work (start): 0.3999 rms_B_bonded: 2.60 r_work: 0.3879 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3879 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7459 moved from start: 0.4252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 10608 Z= 0.124 Angle : 0.773 18.338 14424 Z= 0.340 Chirality : 0.044 0.235 1608 Planarity : 0.005 0.061 1890 Dihedral : 4.497 55.018 1423 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer: Outliers : 5.26 % Allowed : 40.20 % Favored : 54.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.43 (0.23), residues: 1326 helix: 1.53 (0.18), residues: 852 sheet: None (None), residues: 0 loop : -2.15 (0.26), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 133 HIS 0.009 0.001 HIS B 12 PHE 0.010 0.001 PHE A 32 TYR 0.014 0.001 TYR D 169 ARG 0.014 0.000 ARG C 143 Details of bonding type rmsd hydrogen bonds : bond 0.03542 ( 590) hydrogen bonds : angle 4.03820 ( 1731) covalent geometry : bond 0.00294 (10608) covalent geometry : angle 0.77281 (14424) ********************** 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 380 residues out of total 1122 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 321 time to evaluate : 1.372 Fit side-chains revert: symmetry clash REVERT: A 9 GLN cc_start: 0.5623 (OUTLIER) cc_final: 0.5332 (mp10) REVERT: A 173 ARG cc_start: 0.8246 (OUTLIER) cc_final: 0.7919 (ttt180) REVERT: A 187 GLU cc_start: 0.6749 (OUTLIER) cc_final: 0.6233 (pp20) REVERT: A 213 GLU cc_start: 0.7557 (OUTLIER) cc_final: 0.7236 (mt-10) REVERT: F 30 LYS cc_start: 0.8897 (OUTLIER) cc_final: 0.8526 (mtmm) REVERT: F 76 GLU cc_start: 0.8155 (OUTLIER) cc_final: 0.7570 (mp0) REVERT: F 97 ARG cc_start: 0.6020 (OUTLIER) cc_final: 0.5571 (ptm-80) REVERT: F 152 ASP cc_start: 0.5524 (OUTLIER) cc_final: 0.5196 (m-30) REVERT: F 187 GLU cc_start: 0.6796 (OUTLIER) cc_final: 0.6225 (pp20) REVERT: E 72 THR cc_start: 0.8512 (t) cc_final: 0.8244 (p) REVERT: E 173 ARG cc_start: 0.8394 (OUTLIER) cc_final: 0.7103 (ttt90) REVERT: E 187 GLU cc_start: 0.6922 (OUTLIER) cc_final: 0.6338 (pp20) REVERT: E 192 GLN cc_start: 0.8198 (tp-100) cc_final: 0.7892 (tp-100) REVERT: D 75 GLU cc_start: 0.7770 (mt-10) cc_final: 0.7512 (mt-10) REVERT: D 97 ARG cc_start: 0.6144 (OUTLIER) cc_final: 0.5782 (ptm160) REVERT: D 152 ASP cc_start: 0.5857 (OUTLIER) cc_final: 0.5562 (m-30) REVERT: D 175 GLU cc_start: 0.7099 (OUTLIER) cc_final: 0.6770 (mt-10) REVERT: D 213 GLU cc_start: 0.7729 (mm-30) cc_final: 0.7482 (mm-30) REVERT: C 97 ARG cc_start: 0.6292 (OUTLIER) cc_final: 0.5823 (ptm-80) REVERT: C 152 ASP cc_start: 0.6530 (OUTLIER) cc_final: 0.6225 (m-30) REVERT: C 180 GLU cc_start: 0.5231 (OUTLIER) cc_final: 0.2702 (mp0) REVERT: C 187 GLU cc_start: 0.6765 (OUTLIER) cc_final: 0.6337 (pp20) REVERT: B 82 ARG cc_start: 0.8145 (mtm110) cc_final: 0.7889 (mtm110) REVERT: B 97 ARG cc_start: 0.5910 (OUTLIER) cc_final: 0.5553 (ptm160) REVERT: B 112 GLN cc_start: 0.8033 (OUTLIER) cc_final: 0.7609 (mp10) REVERT: B 143 ARG cc_start: 0.8036 (ttp-170) cc_final: 0.7731 (ttm170) REVERT: B 152 ASP cc_start: 0.6170 (OUTLIER) cc_final: 0.5813 (m-30) REVERT: B 192 GLN cc_start: 0.8188 (tp-100) cc_final: 0.7834 (tp-100) outliers start: 59 outliers final: 27 residues processed: 356 average time/residue: 1.2048 time to fit residues: 460.4224 Evaluate side-chains 364 residues out of total 1122 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 316 time to evaluate : 1.037 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 GLN Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 97 ARG 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 76 GLU Chi-restraints excluded: chain F residue 97 ARG 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 30 LYS Chi-restraints excluded: chain E residue 173 ARG 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 11 VAL Chi-restraints excluded: chain D residue 69 LEU Chi-restraints excluded: chain D residue 96 MET Chi-restraints excluded: chain D residue 97 ARG Chi-restraints excluded: chain D residue 110 THR Chi-restraints excluded: chain D residue 152 ASP Chi-restraints excluded: chain D residue 175 GLU Chi-restraints excluded: chain D residue 178 SER Chi-restraints excluded: chain D residue 182 LYS Chi-restraints excluded: chain D residue 189 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 148 THR Chi-restraints excluded: chain C residue 152 ASP Chi-restraints excluded: chain C residue 180 GLU Chi-restraints excluded: chain C residue 187 GLU Chi-restraints excluded: chain C residue 191 VAL Chi-restraints excluded: chain B residue 97 ARG Chi-restraints excluded: chain B residue 112 GLN Chi-restraints excluded: chain B residue 152 ASP Chi-restraints excluded: chain B residue 191 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 104 optimal weight: 0.8980 chunk 13 optimal weight: 0.7980 chunk 21 optimal weight: 0.9980 chunk 44 optimal weight: 0.8980 chunk 105 optimal weight: 3.9990 chunk 9 optimal weight: 6.9990 chunk 80 optimal weight: 3.9990 chunk 7 optimal weight: 0.9990 chunk 96 optimal weight: 0.0060 chunk 0 optimal weight: 10.0000 chunk 123 optimal weight: 0.0570 overall best weight: 0.5314 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 67 GLN D 114 GLN C 63 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4202 r_free = 0.4202 target = 0.158883 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.140871 restraints weight = 16270.618| |-----------------------------------------------------------------------------| r_work (start): 0.3995 rms_B_bonded: 2.57 r_work: 0.3874 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3874 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7465 moved from start: 0.4336 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= 0.125 Angle : 0.769 17.918 14424 Z= 0.339 Chirality : 0.045 0.259 1608 Planarity : 0.005 0.060 1890 Dihedral : 4.092 49.342 1420 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer: Outliers : 5.08 % Allowed : 40.82 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.48 (0.23), residues: 1326 helix: 1.56 (0.18), residues: 852 sheet: None (None), residues: 0 loop : -2.09 (0.26), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 133 HIS 0.008 0.001 HIS C 12 PHE 0.011 0.002 PHE A 32 TYR 0.015 0.001 TYR C 169 ARG 0.009 0.000 ARG C 143 Details of bonding type rmsd hydrogen bonds : bond 0.03558 ( 590) hydrogen bonds : angle 4.03758 ( 1731) covalent geometry : bond 0.00304 (10608) covalent geometry : angle 0.76936 (14424) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9497.74 seconds wall clock time: 164 minutes 46.21 seconds (9886.21 seconds total)