Starting phenix.real_space_refine on Thu Jul 18 19:27:16 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j7n_36043/07_2024/8j7n_36043_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j7n_36043/07_2024/8j7n_36043.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j7n_36043/07_2024/8j7n_36043.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j7n_36043/07_2024/8j7n_36043.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j7n_36043/07_2024/8j7n_36043_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j7n_36043/07_2024/8j7n_36043_neut.cif" } resolution = 3.0 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= 0.000 sd= 0.003 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 21 5.16 5 C 2082 2.51 5 N 519 2.21 5 O 636 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 122": "OD1" <-> "OD2" Residue "A TYR 125": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 180": "NH1" <-> "NH2" Residue "A TYR 197": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 236": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 250": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 122": "OD1" <-> "OD2" Residue "B TYR 125": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 180": "NH1" <-> "NH2" Residue "B TYR 197": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 236": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 250": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 122": "OD1" <-> "OD2" Residue "C TYR 125": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 180": "NH1" <-> "NH2" Residue "C TYR 197": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 236": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 250": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 3258 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 1086 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1086 Classifications: {'peptide': 135} Link IDs: {'PTRANS': 2, 'TRANS': 132} Chain: "B" Number of atoms: 1086 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1086 Classifications: {'peptide': 135} Link IDs: {'PTRANS': 2, 'TRANS': 132} Chain: "C" Number of atoms: 1086 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1086 Classifications: {'peptide': 135} Link IDs: {'PTRANS': 2, 'TRANS': 132} Time building chain proxies: 3.34, per 1000 atoms: 1.03 Number of scatterers: 3258 At special positions: 0 Unit cell: (95.45, 104.58, 34.86, 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 21 16.00 O 636 8.00 N 519 7.00 C 2082 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 214 " - pdb=" SG CYS A 253 " distance=2.03 Simple disulfide: pdb=" SG CYS B 214 " - pdb=" SG CYS B 253 " distance=2.03 Simple disulfide: pdb=" SG CYS C 214 " - pdb=" SG CYS C 253 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.03 Conformation dependent library (CDL) restraints added in 739.9 milliseconds 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 780 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 17 sheets defined 0.0% alpha, 40.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.54 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'B' and resid 122 through 126 removed outlier: 6.344A pdb=" N VAL A 123 " --> pdb=" O LYS B 124 " (cutoff:3.500A) removed outlier: 7.597A pdb=" N ILE B 126 " --> pdb=" O VAL A 123 " (cutoff:3.500A) removed outlier: 6.020A pdb=" N TYR A 125 " --> pdb=" O ILE B 126 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 129 through 130 removed outlier: 6.669A pdb=" N LYS A 129 " --> pdb=" O SER B 130 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 133 through 138 removed outlier: 6.520A pdb=" N SER A 134 " --> pdb=" O TYR B 135 " (cutoff:3.500A) removed outlier: 8.035A pdb=" N VAL B 137 " --> pdb=" O SER A 134 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N ASP A 136 " --> pdb=" O VAL B 137 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 142 through 144 removed outlier: 6.463A pdb=" N ILE A 142 " --> pdb=" O TYR B 143 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 147 through 151 removed outlier: 6.088A pdb=" N THR A 147 " --> pdb=" O ASN B 148 " (cutoff:3.500A) removed outlier: 7.425A pdb=" N LEU B 150 " --> pdb=" O THR A 147 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N THR A 149 " --> pdb=" O LEU B 150 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 156 through 160 removed outlier: 6.315A pdb=" N TYR A 157 " --> pdb=" O TYR B 158 " (cutoff:3.500A) removed outlier: 7.543A pdb=" N VAL B 160 " --> pdb=" O TYR A 157 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N SER A 159 " --> pdb=" O VAL B 160 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 163 through 170 removed outlier: 6.198A pdb=" N ASN A 164 " --> pdb=" O ILE B 165 " (cutoff:3.500A) removed outlier: 7.727A pdb=" N ALA B 167 " --> pdb=" O ASN A 164 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N THR A 166 " --> pdb=" O ALA B 167 " (cutoff:3.500A) removed outlier: 7.891A pdb=" N VAL B 169 " --> pdb=" O THR A 166 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N GLN A 168 " --> pdb=" O VAL B 169 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 173 through 176 removed outlier: 7.994A pdb=" N LYS A 173 " --> pdb=" O THR B 174 " (cutoff:3.500A) removed outlier: 7.504A pdb=" N ILE B 176 " --> pdb=" O LYS A 173 " (cutoff:3.500A) removed outlier: 9.071A pdb=" N VAL A 175 " --> pdb=" O ILE B 176 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N VAL C 175 " --> pdb=" O THR A 174 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N ILE A 176 " --> pdb=" O VAL C 175 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 185 through 187 removed outlier: 6.755A pdb=" N ILE A 186 " --> pdb=" O ILE B 187 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 192 through 195 removed outlier: 9.217A pdb=" N MET A 192 " --> pdb=" O LYS B 193 " (cutoff:3.500A) removed outlier: 9.408A pdb=" N ILE B 195 " --> pdb=" O MET A 192 " (cutoff:3.500A) removed outlier: 5.930A pdb=" N GLN A 194 " --> pdb=" O ILE B 195 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N LYS A 193 " --> pdb=" O MET C 192 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N GLN C 194 " --> pdb=" O LYS A 193 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 202 through 203 removed outlier: 6.177A pdb=" N VAL A 202 " --> pdb=" O ILE B 203 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 206 through 207 removed outlier: 6.581A pdb=" N GLU A 206 " --> pdb=" O MET C 207 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 210 through 213 removed outlier: 6.878A pdb=" N MET A 210 " --> pdb=" O TYR C 211 " (cutoff:3.500A) removed outlier: 7.863A pdb=" N PHE C 213 " --> pdb=" O MET A 210 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N ASP A 212 " --> pdb=" O PHE C 213 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 222 through 230 removed outlier: 6.980A pdb=" N ASN B 223 " --> pdb=" O HIS A 222 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N ILE A 224 " --> pdb=" O ASN B 223 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N VAL B 225 " --> pdb=" O ILE A 224 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N LEU A 226 " --> pdb=" O VAL B 225 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N MET B 227 " --> pdb=" O LEU A 226 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N MET A 228 " --> pdb=" O MET B 227 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N GLN B 229 " --> pdb=" O MET A 228 " (cutoff:3.500A) removed outlier: 9.054A pdb=" N ASN A 223 " --> pdb=" O ILE C 224 " (cutoff:3.500A) removed outlier: 10.385A pdb=" N LEU C 226 " --> pdb=" O ASN A 223 " (cutoff:3.500A) removed outlier: 9.068A pdb=" N VAL A 225 " --> pdb=" O LEU C 226 " (cutoff:3.500A) removed outlier: 10.526A pdb=" N MET C 228 " --> pdb=" O VAL A 225 " (cutoff:3.500A) removed outlier: 9.226A pdb=" N MET A 227 " --> pdb=" O MET C 228 " (cutoff:3.500A) removed outlier: 9.113A pdb=" N VAL C 230 " --> pdb=" O MET A 227 " (cutoff:3.500A) removed outlier: 6.052A pdb=" N GLN A 229 " --> pdb=" O VAL C 230 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 236 through 239 removed outlier: 6.444A pdb=" N TYR A 236 " --> pdb=" O PHE B 237 " (cutoff:3.500A) removed outlier: 7.545A pdb=" N HIS B 239 " --> pdb=" O TYR A 236 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N GLY A 238 " --> pdb=" O HIS B 239 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 243 through 245 removed outlier: 6.423A pdb=" N SER A 244 " --> pdb=" O GLN B 245 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 251 through 253 removed outlier: 6.504A pdb=" N ASP A 252 " --> pdb=" O CYS C 253 " (cutoff:3.500A) 44 hydrogen bonds defined for protein. 132 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.84 Time building geometry restraints manager: 1.19 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 1015 1.33 - 1.45: 424 1.45 - 1.57: 1837 1.57 - 1.68: 0 1.68 - 1.80: 36 Bond restraints: 3312 Sorted by residual: bond pdb=" CB MET A 228 " pdb=" CG MET A 228 " ideal model delta sigma weight residual 1.520 1.475 0.045 3.00e-02 1.11e+03 2.24e+00 bond pdb=" CB MET C 228 " pdb=" CG MET C 228 " ideal model delta sigma weight residual 1.520 1.476 0.044 3.00e-02 1.11e+03 2.19e+00 bond pdb=" CB MET B 228 " pdb=" CG MET B 228 " ideal model delta sigma weight residual 1.520 1.476 0.044 3.00e-02 1.11e+03 2.18e+00 bond pdb=" CB THR A 235 " pdb=" CG2 THR A 235 " ideal model delta sigma weight residual 1.521 1.476 0.045 3.30e-02 9.18e+02 1.87e+00 bond pdb=" CB THR C 235 " pdb=" CG2 THR C 235 " ideal model delta sigma weight residual 1.521 1.477 0.044 3.30e-02 9.18e+02 1.82e+00 ... (remaining 3307 not shown) Histogram of bond angle deviations from ideal: 100.13 - 106.36: 70 106.36 - 112.59: 1754 112.59 - 118.81: 870 118.81 - 125.04: 1794 125.04 - 131.27: 15 Bond angle restraints: 4503 Sorted by residual: angle pdb=" N GLU B 246 " pdb=" CA GLU B 246 " pdb=" C GLU B 246 " ideal model delta sigma weight residual 110.41 114.66 -4.25 1.23e+00 6.61e-01 1.20e+01 angle pdb=" N GLU C 246 " pdb=" CA GLU C 246 " pdb=" C GLU C 246 " ideal model delta sigma weight residual 110.41 114.65 -4.24 1.23e+00 6.61e-01 1.19e+01 angle pdb=" N GLU A 246 " pdb=" CA GLU A 246 " pdb=" C GLU A 246 " ideal model delta sigma weight residual 110.41 114.65 -4.24 1.23e+00 6.61e-01 1.19e+01 angle pdb=" C LEU A 144 " pdb=" N ASN A 145 " pdb=" CA ASN A 145 " ideal model delta sigma weight residual 121.54 128.12 -6.58 1.91e+00 2.74e-01 1.19e+01 angle pdb=" C LEU C 144 " pdb=" N ASN C 145 " pdb=" CA ASN C 145 " ideal model delta sigma weight residual 121.54 128.12 -6.58 1.91e+00 2.74e-01 1.19e+01 ... (remaining 4498 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.51: 1676 11.51 - 23.01: 239 23.01 - 34.52: 47 34.52 - 46.03: 27 46.03 - 57.53: 6 Dihedral angle restraints: 1995 sinusoidal: 777 harmonic: 1218 Sorted by residual: dihedral pdb=" CA GLN B 138 " pdb=" C GLN B 138 " pdb=" N LYS B 139 " pdb=" CA LYS B 139 " ideal model delta harmonic sigma weight residual 180.00 158.19 21.81 0 5.00e+00 4.00e-02 1.90e+01 dihedral pdb=" CA GLN A 138 " pdb=" C GLN A 138 " pdb=" N LYS A 139 " pdb=" CA LYS A 139 " ideal model delta harmonic sigma weight residual 180.00 158.21 21.79 0 5.00e+00 4.00e-02 1.90e+01 dihedral pdb=" CA GLN C 138 " pdb=" C GLN C 138 " pdb=" N LYS C 139 " pdb=" CA LYS C 139 " ideal model delta harmonic sigma weight residual 180.00 158.22 21.78 0 5.00e+00 4.00e-02 1.90e+01 ... (remaining 1992 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 310 0.043 - 0.085: 141 0.085 - 0.128: 83 0.128 - 0.170: 6 0.170 - 0.213: 3 Chirality restraints: 543 Sorted by residual: chirality pdb=" CA ASN C 145 " pdb=" N ASN C 145 " pdb=" C ASN C 145 " pdb=" CB ASN C 145 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.13e+00 chirality pdb=" CA ASN B 145 " pdb=" N ASN B 145 " pdb=" C ASN B 145 " pdb=" CB ASN B 145 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.13e+00 chirality pdb=" CA ASN A 145 " pdb=" N ASN A 145 " pdb=" C ASN A 145 " pdb=" CB ASN A 145 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.11e+00 ... (remaining 540 not shown) Planarity restraints: 558 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 125 " 0.009 2.00e-02 2.50e+03 1.02e-02 2.09e+00 pdb=" CG TYR A 125 " -0.024 2.00e-02 2.50e+03 pdb=" CD1 TYR A 125 " 0.004 2.00e-02 2.50e+03 pdb=" CD2 TYR A 125 " 0.011 2.00e-02 2.50e+03 pdb=" CE1 TYR A 125 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 TYR A 125 " -0.004 2.00e-02 2.50e+03 pdb=" CZ TYR A 125 " 0.000 2.00e-02 2.50e+03 pdb=" OH TYR A 125 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR C 125 " 0.008 2.00e-02 2.50e+03 1.01e-02 2.05e+00 pdb=" CG TYR C 125 " -0.024 2.00e-02 2.50e+03 pdb=" CD1 TYR C 125 " 0.004 2.00e-02 2.50e+03 pdb=" CD2 TYR C 125 " 0.011 2.00e-02 2.50e+03 pdb=" CE1 TYR C 125 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 TYR C 125 " -0.004 2.00e-02 2.50e+03 pdb=" CZ TYR C 125 " 0.000 2.00e-02 2.50e+03 pdb=" OH TYR C 125 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 125 " 0.008 2.00e-02 2.50e+03 9.97e-03 1.99e+00 pdb=" CG TYR B 125 " -0.024 2.00e-02 2.50e+03 pdb=" CD1 TYR B 125 " 0.003 2.00e-02 2.50e+03 pdb=" CD2 TYR B 125 " 0.011 2.00e-02 2.50e+03 pdb=" CE1 TYR B 125 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 TYR B 125 " -0.003 2.00e-02 2.50e+03 pdb=" CZ TYR B 125 " 0.000 2.00e-02 2.50e+03 pdb=" OH TYR B 125 " 0.000 2.00e-02 2.50e+03 ... (remaining 555 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 782 2.80 - 3.33: 2823 3.33 - 3.85: 5283 3.85 - 4.38: 5764 4.38 - 4.90: 11828 Nonbonded interactions: 26480 Sorted by model distance: nonbonded pdb=" NE2 GLN B 229 " pdb=" O GLU B 241 " model vdw 2.276 2.520 nonbonded pdb=" NE2 GLN C 229 " pdb=" O GLU C 241 " model vdw 2.276 2.520 nonbonded pdb=" NE2 GLN A 229 " pdb=" O GLU A 241 " model vdw 2.276 2.520 nonbonded pdb=" OG1 THR A 233 " pdb=" N THR A 234 " model vdw 2.530 2.520 nonbonded pdb=" OG1 THR B 233 " pdb=" N THR B 234 " model vdw 2.531 2.520 ... (remaining 26475 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.330 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.150 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 14.820 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8667 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 : 0.008 0.045 3312 Z= 0.561 Angle : 0.820 6.584 4503 Z= 0.482 Chirality : 0.058 0.213 543 Planarity : 0.003 0.012 558 Dihedral : 12.258 57.534 1206 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 16.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.53 % Favored : 86.47 % Rotamer: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -5.22 (0.31), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.97 (0.23), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.003 HIS A 239 PHE 0.005 0.001 PHE C 213 TYR 0.024 0.003 TYR A 125 ARG 0.004 0.001 ARG B 140 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 92 time to evaluate : 0.344 Fit side-chains REVERT: A 168 GLN cc_start: 0.8781 (mt0) cc_final: 0.8520 (mt0) REVERT: B 129 LYS cc_start: 0.9171 (ptpp) cc_final: 0.8968 (ptpt) REVERT: B 168 GLN cc_start: 0.8902 (mt0) cc_final: 0.8673 (mt0) REVERT: B 180 ARG cc_start: 0.7968 (ptp-170) cc_final: 0.6442 (pmt-80) REVERT: C 168 GLN cc_start: 0.8790 (mt0) cc_final: 0.8585 (mt0) REVERT: C 180 ARG cc_start: 0.8061 (ptp-170) cc_final: 0.7838 (ptp-170) REVERT: C 196 ASP cc_start: 0.8420 (p0) cc_final: 0.8000 (p0) outliers start: 0 outliers final: 0 residues processed: 92 average time/residue: 1.2721 time to fit residues: 119.9903 Evaluate side-chains 70 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 70 time to evaluate : 0.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 32 optimal weight: 0.6980 chunk 29 optimal weight: 2.9990 chunk 16 optimal weight: 6.9990 chunk 10 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 chunk 15 optimal weight: 6.9990 chunk 30 optimal weight: 5.9990 chunk 11 optimal weight: 0.9980 chunk 18 optimal weight: 2.9990 chunk 22 optimal weight: 10.0000 chunk 35 optimal weight: 9.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 155 ASN A 156 ASN A 222 HIS ** A 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 155 ASN B 156 ASN B 222 HIS ** B 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 156 ASN C 222 HIS ** C 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8642 moved from start: 0.1718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 3312 Z= 0.237 Angle : 0.614 6.304 4503 Z= 0.337 Chirality : 0.054 0.183 543 Planarity : 0.002 0.013 558 Dihedral : 6.467 20.136 447 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.28 % Favored : 89.72 % Rotamer: Outliers : 3.97 % Allowed : 11.38 % Favored : 84.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -4.80 (0.31), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.65 (0.24), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS B 239 PHE 0.005 0.001 PHE A 213 TYR 0.015 0.002 TYR A 143 ARG 0.001 0.000 ARG C 247 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 81 time to evaluate : 0.361 Fit side-chains REVERT: A 168 GLN cc_start: 0.8784 (mt0) cc_final: 0.8515 (mt0) REVERT: A 178 LYS cc_start: 0.8385 (OUTLIER) cc_final: 0.8119 (ttpt) REVERT: B 129 LYS cc_start: 0.9125 (ptpp) cc_final: 0.8907 (ptpt) REVERT: B 168 GLN cc_start: 0.8841 (mt0) cc_final: 0.8622 (mt0) REVERT: B 180 ARG cc_start: 0.7946 (ptp-170) cc_final: 0.6125 (pmt-80) REVERT: B 190 LEU cc_start: 0.8928 (OUTLIER) cc_final: 0.8408 (tt) REVERT: C 180 ARG cc_start: 0.7942 (ptp-170) cc_final: 0.7687 (ptp90) REVERT: C 250 TYR cc_start: 0.7106 (t80) cc_final: 0.6897 (t80) outliers start: 15 outliers final: 4 residues processed: 85 average time/residue: 1.1870 time to fit residues: 103.5559 Evaluate side-chains 80 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 74 time to evaluate : 0.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 178 LYS Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 240 SER Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 217 ILE Chi-restraints excluded: chain C residue 240 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 19 optimal weight: 0.0570 chunk 10 optimal weight: 8.9990 chunk 29 optimal weight: 2.9990 chunk 24 optimal weight: 4.9990 chunk 9 optimal weight: 7.9990 chunk 35 optimal weight: 3.9990 chunk 38 optimal weight: 0.9990 chunk 31 optimal weight: 6.9990 chunk 12 optimal weight: 0.9980 chunk 28 optimal weight: 4.9990 chunk 26 optimal weight: 8.9990 overall best weight: 1.8104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 223 ASN ** A 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 223 ASN ** B 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 168 GLN ** C 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8636 moved from start: 0.2066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 3312 Z= 0.201 Angle : 0.575 6.745 4503 Z= 0.317 Chirality : 0.053 0.178 543 Planarity : 0.002 0.012 558 Dihedral : 6.214 19.058 447 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.53 % Favored : 89.47 % Rotamer: Outliers : 3.44 % Allowed : 14.81 % Favored : 81.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -4.55 (0.32), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.46 (0.24), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.002 HIS B 239 PHE 0.006 0.001 PHE A 213 TYR 0.014 0.002 TYR A 143 ARG 0.001 0.000 ARG B 247 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 84 time to evaluate : 0.403 Fit side-chains REVERT: A 168 GLN cc_start: 0.8794 (mt0) cc_final: 0.8491 (mt0) REVERT: A 178 LYS cc_start: 0.8300 (OUTLIER) cc_final: 0.8039 (ttpt) REVERT: A 208 SER cc_start: 0.8574 (m) cc_final: 0.8373 (t) REVERT: B 168 GLN cc_start: 0.8819 (mt0) cc_final: 0.8595 (mt0) REVERT: B 180 ARG cc_start: 0.7901 (ptp-170) cc_final: 0.6044 (pmt-80) REVERT: B 190 LEU cc_start: 0.8882 (OUTLIER) cc_final: 0.8391 (tt) REVERT: C 180 ARG cc_start: 0.7905 (ptp-170) cc_final: 0.7700 (ptp-170) REVERT: C 250 TYR cc_start: 0.7257 (t80) cc_final: 0.6973 (t80) outliers start: 13 outliers final: 6 residues processed: 88 average time/residue: 1.1316 time to fit residues: 102.2724 Evaluate side-chains 87 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 79 time to evaluate : 0.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 178 LYS Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 240 SER Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 217 ILE Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain C residue 190 LEU Chi-restraints excluded: chain C residue 240 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 18 optimal weight: 4.9990 chunk 3 optimal weight: 10.0000 chunk 16 optimal weight: 2.9990 chunk 23 optimal weight: 10.0000 chunk 35 optimal weight: 10.0000 chunk 37 optimal weight: 6.9990 chunk 33 optimal weight: 7.9990 chunk 10 optimal weight: 0.9980 chunk 31 optimal weight: 9.9990 chunk 21 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 overall best weight: 4.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 168 GLN C 229 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8720 moved from start: 0.2068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.041 3312 Z= 0.464 Angle : 0.686 6.359 4503 Z= 0.382 Chirality : 0.055 0.207 543 Planarity : 0.003 0.016 558 Dihedral : 6.750 20.213 447 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.28 % Favored : 88.72 % Rotamer: Outliers : 4.76 % Allowed : 15.08 % Favored : 80.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -4.45 (0.32), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.38 (0.24), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.003 HIS B 239 PHE 0.007 0.001 PHE A 213 TYR 0.028 0.003 TYR C 158 ARG 0.001 0.000 ARG B 180 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 75 time to evaluate : 0.389 Fit side-chains REVERT: A 168 GLN cc_start: 0.8818 (mt0) cc_final: 0.8539 (mt0) REVERT: A 178 LYS cc_start: 0.8549 (OUTLIER) cc_final: 0.8321 (ttpt) REVERT: B 168 GLN cc_start: 0.8889 (mt0) cc_final: 0.8658 (mt0) REVERT: B 180 ARG cc_start: 0.7964 (ptp-170) cc_final: 0.6107 (pmt-80) REVERT: B 190 LEU cc_start: 0.8926 (OUTLIER) cc_final: 0.8458 (tt) REVERT: C 180 ARG cc_start: 0.8000 (ptp-170) cc_final: 0.7711 (ptp90) outliers start: 18 outliers final: 9 residues processed: 82 average time/residue: 1.2325 time to fit residues: 103.7179 Evaluate side-chains 84 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 73 time to evaluate : 0.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 178 LYS Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 192 MET Chi-restraints excluded: chain A residue 240 SER Chi-restraints excluded: chain B residue 134 SER Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 217 ILE Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain C residue 190 LEU Chi-restraints excluded: chain C residue 240 SER Chi-restraints excluded: chain C residue 250 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 28 optimal weight: 6.9990 chunk 15 optimal weight: 5.9990 chunk 32 optimal weight: 1.9990 chunk 26 optimal weight: 3.9990 chunk 0 optimal weight: 0.7980 chunk 19 optimal weight: 0.3980 chunk 33 optimal weight: 6.9990 chunk 9 optimal weight: 8.9990 chunk 12 optimal weight: 2.9990 chunk 7 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8640 moved from start: 0.2440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.017 3312 Z= 0.178 Angle : 0.579 6.663 4503 Z= 0.317 Chirality : 0.053 0.179 543 Planarity : 0.002 0.011 558 Dihedral : 6.193 18.546 447 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.77 % Favored : 91.23 % Rotamer: Outliers : 3.97 % Allowed : 16.40 % Favored : 79.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -4.30 (0.32), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.27 (0.25), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS C 239 PHE 0.006 0.001 PHE A 213 TYR 0.014 0.001 TYR A 143 ARG 0.001 0.000 ARG B 140 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 88 time to evaluate : 0.290 Fit side-chains REVERT: A 168 GLN cc_start: 0.8791 (mt0) cc_final: 0.8497 (mt0) REVERT: A 178 LYS cc_start: 0.8296 (OUTLIER) cc_final: 0.8032 (ttpt) REVERT: B 168 GLN cc_start: 0.8832 (mt0) cc_final: 0.8616 (mt0) REVERT: B 180 ARG cc_start: 0.7920 (ptp-170) cc_final: 0.6045 (pmt-80) REVERT: B 190 LEU cc_start: 0.8897 (OUTLIER) cc_final: 0.8442 (tt) REVERT: C 178 LYS cc_start: 0.8316 (OUTLIER) cc_final: 0.8108 (ttpt) REVERT: C 250 TYR cc_start: 0.7527 (OUTLIER) cc_final: 0.7228 (t80) outliers start: 15 outliers final: 7 residues processed: 90 average time/residue: 1.1045 time to fit residues: 102.2312 Evaluate side-chains 93 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 82 time to evaluate : 0.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 178 LYS Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 228 MET Chi-restraints excluded: chain A residue 240 SER Chi-restraints excluded: chain B residue 134 SER Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 217 ILE Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain C residue 178 LYS Chi-restraints excluded: chain C residue 190 LEU Chi-restraints excluded: chain C residue 250 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 9 optimal weight: 8.9990 chunk 37 optimal weight: 5.9990 chunk 31 optimal weight: 8.9990 chunk 17 optimal weight: 10.0000 chunk 3 optimal weight: 9.9990 chunk 12 optimal weight: 9.9990 chunk 19 optimal weight: 6.9990 chunk 36 optimal weight: 4.9990 chunk 4 optimal weight: 9.9990 chunk 21 optimal weight: 7.9990 chunk 27 optimal weight: 0.9980 overall best weight: 5.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 168 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8736 moved from start: 0.2277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.044 3312 Z= 0.528 Angle : 0.719 6.732 4503 Z= 0.399 Chirality : 0.056 0.215 543 Planarity : 0.003 0.015 558 Dihedral : 6.808 19.116 447 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.28 % Favored : 88.72 % Rotamer: Outliers : 6.08 % Allowed : 15.87 % Favored : 78.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -4.29 (0.33), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.26 (0.25), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.003 HIS B 239 PHE 0.007 0.001 PHE A 213 TYR 0.032 0.003 TYR C 158 ARG 0.002 0.000 ARG B 180 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 69 time to evaluate : 0.379 Fit side-chains REVERT: A 168 GLN cc_start: 0.8829 (mt0) cc_final: 0.8592 (mt0) REVERT: A 178 LYS cc_start: 0.8560 (OUTLIER) cc_final: 0.8342 (ttpt) REVERT: B 168 GLN cc_start: 0.8887 (mt0) cc_final: 0.8663 (mt0) REVERT: B 180 ARG cc_start: 0.7962 (ptp-170) cc_final: 0.6050 (pmt-80) REVERT: B 190 LEU cc_start: 0.8924 (OUTLIER) cc_final: 0.8486 (tt) REVERT: C 217 ILE cc_start: 0.8953 (OUTLIER) cc_final: 0.8666 (mp) outliers start: 23 outliers final: 11 residues processed: 80 average time/residue: 1.2914 time to fit residues: 106.0469 Evaluate side-chains 81 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 67 time to evaluate : 0.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 178 LYS Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 240 SER Chi-restraints excluded: chain B residue 134 SER Chi-restraints excluded: chain B residue 145 ASN Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 217 ILE Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain C residue 190 LEU Chi-restraints excluded: chain C residue 217 ILE Chi-restraints excluded: chain C residue 240 SER Chi-restraints excluded: chain C residue 241 GLU Chi-restraints excluded: chain C residue 250 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 21 optimal weight: 8.9990 chunk 31 optimal weight: 0.9980 chunk 37 optimal weight: 0.8980 chunk 23 optimal weight: 3.9990 chunk 22 optimal weight: 7.9990 chunk 17 optimal weight: 2.9990 chunk 15 optimal weight: 2.9990 chunk 11 optimal weight: 0.8980 chunk 7 optimal weight: 3.9990 chunk 25 optimal weight: 5.9990 chunk 18 optimal weight: 6.9990 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 138 GLN ** B 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8652 moved from start: 0.2545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3312 Z= 0.204 Angle : 0.593 6.620 4503 Z= 0.327 Chirality : 0.053 0.178 543 Planarity : 0.002 0.013 558 Dihedral : 6.226 18.358 447 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.02 % Favored : 90.98 % Rotamer: Outliers : 4.50 % Allowed : 18.25 % Favored : 77.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -4.18 (0.33), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.18 (0.25), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS C 239 PHE 0.006 0.001 PHE A 213 TYR 0.016 0.002 TYR A 143 ARG 0.001 0.000 ARG B 140 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 81 time to evaluate : 0.380 Fit side-chains REVERT: A 168 GLN cc_start: 0.8786 (mt0) cc_final: 0.8493 (mt0) REVERT: A 178 LYS cc_start: 0.8286 (OUTLIER) cc_final: 0.8014 (ttpt) REVERT: A 180 ARG cc_start: 0.7801 (ptp-170) cc_final: 0.7434 (mtm180) REVERT: A 217 ILE cc_start: 0.8696 (OUTLIER) cc_final: 0.8285 (mt) REVERT: B 168 GLN cc_start: 0.8819 (mt0) cc_final: 0.8591 (mt0) REVERT: B 180 ARG cc_start: 0.7906 (ptp-170) cc_final: 0.6026 (pmt-80) REVERT: B 190 LEU cc_start: 0.8902 (OUTLIER) cc_final: 0.8448 (tt) REVERT: C 180 ARG cc_start: 0.7898 (ptp90) cc_final: 0.5905 (mmp-170) REVERT: C 250 TYR cc_start: 0.7711 (OUTLIER) cc_final: 0.7313 (t80) outliers start: 17 outliers final: 8 residues processed: 85 average time/residue: 1.2269 time to fit residues: 107.1035 Evaluate side-chains 89 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 77 time to evaluate : 0.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 178 LYS Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain A residue 240 SER Chi-restraints excluded: chain B residue 134 SER Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain C residue 190 LEU Chi-restraints excluded: chain C residue 240 SER Chi-restraints excluded: chain C residue 241 GLU Chi-restraints excluded: chain C residue 250 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 3 optimal weight: 8.9990 chunk 29 optimal weight: 3.9990 chunk 34 optimal weight: 8.9990 chunk 36 optimal weight: 6.9990 chunk 32 optimal weight: 7.9990 chunk 35 optimal weight: 5.9990 chunk 21 optimal weight: 7.9990 chunk 15 optimal weight: 10.0000 chunk 27 optimal weight: 1.9990 chunk 10 optimal weight: 3.9990 chunk 31 optimal weight: 0.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 168 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8701 moved from start: 0.2470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 3312 Z= 0.353 Angle : 0.649 6.403 4503 Z= 0.362 Chirality : 0.055 0.210 543 Planarity : 0.002 0.015 558 Dihedral : 6.480 18.300 447 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.53 % Favored : 88.47 % Rotamer: Outliers : 4.76 % Allowed : 17.46 % Favored : 77.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -4.13 (0.33), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.14 (0.25), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS B 239 PHE 0.004 0.001 PHE B 213 TYR 0.021 0.002 TYR B 143 ARG 0.001 0.000 ARG B 180 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 75 time to evaluate : 0.396 Fit side-chains REVERT: A 168 GLN cc_start: 0.8814 (mt0) cc_final: 0.8563 (mt0) REVERT: A 178 LYS cc_start: 0.8470 (OUTLIER) cc_final: 0.8199 (ttpt) REVERT: A 180 ARG cc_start: 0.7864 (ptp-170) cc_final: 0.7406 (mtp85) REVERT: B 168 GLN cc_start: 0.8873 (mt0) cc_final: 0.8664 (mt0) REVERT: B 180 ARG cc_start: 0.7941 (ptp-170) cc_final: 0.5980 (pmt-80) REVERT: B 190 LEU cc_start: 0.8897 (OUTLIER) cc_final: 0.8463 (tt) REVERT: B 212 ASP cc_start: 0.9193 (m-30) cc_final: 0.8954 (m-30) REVERT: C 139 LYS cc_start: 0.9228 (mttt) cc_final: 0.8973 (mttp) REVERT: C 180 ARG cc_start: 0.8002 (ptp90) cc_final: 0.5983 (mmp-170) REVERT: C 250 TYR cc_start: 0.7999 (OUTLIER) cc_final: 0.7545 (t80) outliers start: 18 outliers final: 10 residues processed: 80 average time/residue: 1.3049 time to fit residues: 107.0164 Evaluate side-chains 84 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 71 time to evaluate : 0.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 178 LYS Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 192 MET Chi-restraints excluded: chain A residue 240 SER Chi-restraints excluded: chain B residue 134 SER Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 210 MET Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain C residue 190 LEU Chi-restraints excluded: chain C residue 240 SER Chi-restraints excluded: chain C residue 241 GLU Chi-restraints excluded: chain C residue 250 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 33 optimal weight: 5.9990 chunk 34 optimal weight: 8.9990 chunk 23 optimal weight: 0.9990 chunk 37 optimal weight: 3.9990 chunk 22 optimal weight: 6.9990 chunk 17 optimal weight: 0.9980 chunk 25 optimal weight: 4.9990 chunk 38 optimal weight: 4.9990 chunk 35 optimal weight: 9.9990 chunk 30 optimal weight: 8.9990 chunk 3 optimal weight: 6.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 168 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8693 moved from start: 0.2482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 3312 Z= 0.333 Angle : 0.651 6.668 4503 Z= 0.362 Chirality : 0.055 0.206 543 Planarity : 0.002 0.017 558 Dihedral : 6.481 17.999 447 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.53 % Favored : 89.47 % Rotamer: Outliers : 4.23 % Allowed : 17.99 % Favored : 77.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -4.11 (0.33), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.12 (0.25), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS B 239 PHE 0.004 0.001 PHE A 213 TYR 0.022 0.002 TYR B 143 ARG 0.001 0.000 ARG B 180 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 77 time to evaluate : 0.393 Fit side-chains REVERT: A 168 GLN cc_start: 0.8815 (mt0) cc_final: 0.8566 (mt0) REVERT: A 178 LYS cc_start: 0.8472 (OUTLIER) cc_final: 0.8177 (ttpt) REVERT: A 180 ARG cc_start: 0.7808 (ptp-170) cc_final: 0.7382 (mtp85) REVERT: B 168 GLN cc_start: 0.8872 (mt0) cc_final: 0.8662 (mt0) REVERT: B 180 ARG cc_start: 0.7953 (ptp-170) cc_final: 0.6033 (pmt-80) REVERT: B 190 LEU cc_start: 0.8891 (OUTLIER) cc_final: 0.8451 (tt) REVERT: C 139 LYS cc_start: 0.9201 (mttt) cc_final: 0.8939 (mttp) REVERT: C 180 ARG cc_start: 0.7996 (ptp90) cc_final: 0.5962 (mmp-170) REVERT: C 250 TYR cc_start: 0.7997 (OUTLIER) cc_final: 0.7556 (t80) outliers start: 16 outliers final: 9 residues processed: 82 average time/residue: 1.2180 time to fit residues: 102.4292 Evaluate side-chains 84 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 72 time to evaluate : 0.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 178 LYS Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 192 MET Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain A residue 240 SER Chi-restraints excluded: chain B residue 134 SER Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain C residue 190 LEU Chi-restraints excluded: chain C residue 240 SER Chi-restraints excluded: chain C residue 241 GLU Chi-restraints excluded: chain C residue 250 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 23 optimal weight: 3.9990 chunk 18 optimal weight: 9.9990 chunk 24 optimal weight: 3.9990 chunk 32 optimal weight: 0.3980 chunk 9 optimal weight: 9.9990 chunk 28 optimal weight: 1.9990 chunk 4 optimal weight: 10.0000 chunk 8 optimal weight: 9.9990 chunk 30 optimal weight: 1.9990 chunk 12 optimal weight: 3.9990 chunk 31 optimal weight: 2.9990 overall best weight: 2.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 168 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8668 moved from start: 0.2592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 3312 Z= 0.254 Angle : 0.630 7.732 4503 Z= 0.344 Chirality : 0.054 0.191 543 Planarity : 0.002 0.017 558 Dihedral : 6.303 17.813 447 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.78 % Favored : 89.22 % Rotamer: Outliers : 3.70 % Allowed : 18.78 % Favored : 77.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -4.07 (0.33), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.10 (0.25), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS C 239 PHE 0.004 0.001 PHE A 213 TYR 0.020 0.002 TYR B 143 ARG 0.001 0.000 ARG B 180 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 77 time to evaluate : 0.388 Fit side-chains REVERT: A 168 GLN cc_start: 0.8782 (mt0) cc_final: 0.8494 (mt0) REVERT: A 180 ARG cc_start: 0.7815 (ptp-170) cc_final: 0.7386 (mtp85) REVERT: B 168 GLN cc_start: 0.8834 (mt0) cc_final: 0.8613 (mt0) REVERT: B 180 ARG cc_start: 0.7901 (ptp-170) cc_final: 0.6013 (pmt-80) REVERT: B 190 LEU cc_start: 0.8885 (OUTLIER) cc_final: 0.8442 (tt) REVERT: C 180 ARG cc_start: 0.7976 (ptp90) cc_final: 0.5922 (mmp-170) REVERT: C 250 TYR cc_start: 0.7807 (OUTLIER) cc_final: 0.7429 (t80) outliers start: 14 outliers final: 10 residues processed: 83 average time/residue: 1.3272 time to fit residues: 112.9446 Evaluate side-chains 86 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 74 time to evaluate : 0.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 192 MET Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain A residue 240 SER Chi-restraints excluded: chain B residue 134 SER Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain C residue 190 LEU Chi-restraints excluded: chain C residue 240 SER Chi-restraints excluded: chain C residue 241 GLU Chi-restraints excluded: chain C residue 250 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 3 optimal weight: 8.9990 chunk 5 optimal weight: 9.9990 chunk 27 optimal weight: 5.9990 chunk 1 optimal weight: 6.9990 chunk 22 optimal weight: 1.9990 chunk 35 optimal weight: 6.9990 chunk 20 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 chunk 24 optimal weight: 5.9990 chunk 23 optimal weight: 3.9990 chunk 15 optimal weight: 0.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 168 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.122758 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.108948 restraints weight = 4047.831| |-----------------------------------------------------------------------------| r_work (start): 0.3584 rms_B_bonded: 1.81 r_work: 0.3488 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.3396 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.3396 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8822 moved from start: 0.2598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 3312 Z= 0.267 Angle : 0.641 8.740 4503 Z= 0.347 Chirality : 0.054 0.190 543 Planarity : 0.002 0.017 558 Dihedral : 6.292 17.392 447 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.53 % Favored : 89.47 % Rotamer: Outliers : 3.17 % Allowed : 19.31 % Favored : 77.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -4.08 (0.33), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.10 (0.25), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS C 239 PHE 0.004 0.001 PHE A 213 TYR 0.023 0.002 TYR A 143 ARG 0.001 0.000 ARG B 180 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2144.17 seconds wall clock time: 38 minutes 34.20 seconds (2314.20 seconds total)