Starting phenix.real_space_refine on Fri Dec 27 20:58:05 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8bms_16124/12_2024/8bms_16124.cif Found real_map, /net/cci-nas-00/data/ceres_data/8bms_16124/12_2024/8bms_16124.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8bms_16124/12_2024/8bms_16124.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8bms_16124/12_2024/8bms_16124.map" model { file = "/net/cci-nas-00/data/ceres_data/8bms_16124/12_2024/8bms_16124.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8bms_16124/12_2024/8bms_16124.cif" } resolution = 2.6 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= 0.096 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: 6 Type Number sf(0) Gaussians P 6 5.49 5 Mg 2 5.21 5 S 26 5.16 5 C 4173 2.51 5 N 1080 2.21 5 O 1283 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 6570 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 2133 Number of conformers: 1 Conformer: "" Number of residues, atoms: 278, 2133 Classifications: {'peptide': 278} Link IDs: {'PTRANS': 13, 'TRANS': 264} Chain breaks: 1 Chain: "B" Number of atoms: 2183 Number of conformers: 1 Conformer: "" Number of residues, atoms: 281, 2183 Classifications: {'peptide': 281} Link IDs: {'PTRANS': 14, 'TRANS': 266} Chain: "C" Number of atoms: 2118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 263, 2118 Classifications: {'peptide': 263} Link IDs: {'PTRANS': 9, 'TRANS': 253} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 35 Classifications: {'water': 35} Link IDs: {None: 34} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 28 Classifications: {'water': 28} Link IDs: {None: 27} Chain: "C" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Classifications: {'water': 9} Link IDs: {None: 8} Time building chain proxies: 4.50, per 1000 atoms: 0.68 Number of scatterers: 6570 At special positions: 0 Unit cell: (72.732, 75.24, 122.056, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 26 16.00 P 6 15.00 Mg 2 11.99 O 1283 8.00 N 1080 7.00 C 4173 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.71 Conformation dependent library (CDL) restraints added in 998.8 milliseconds 1628 Ramachandran restraints generated. 814 Oldfield, 0 Emsley, 814 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1528 Finding SS restraints... Secondary structure from input PDB file: 37 helices and 4 sheets defined 58.3% alpha, 11.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.77 Creating SS restraints... Processing helix chain 'A' and resid 45 through 54 Processing helix chain 'A' and resid 78 through 84 removed outlier: 3.555A pdb=" N GLU A 84 " --> pdb=" O TRP A 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 92 through 96 Processing helix chain 'A' and resid 101 through 113 removed outlier: 4.453A pdb=" N GLY A 109 " --> pdb=" O ASP A 105 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N LEU A 110 " --> pdb=" O VAL A 106 " (cutoff:3.500A) Processing helix chain 'A' and resid 116 through 131 removed outlier: 3.815A pdb=" N LYS A 122 " --> pdb=" O PRO A 118 " (cutoff:3.500A) Processing helix chain 'A' and resid 133 through 137 removed outlier: 3.937A pdb=" N ALA A 137 " --> pdb=" O ALA A 134 " (cutoff:3.500A) Processing helix chain 'A' and resid 145 through 159 removed outlier: 3.537A pdb=" N ILE A 157 " --> pdb=" O ALA A 153 " (cutoff:3.500A) Processing helix chain 'A' and resid 175 through 194 Processing helix chain 'A' and resid 203 through 209 removed outlier: 3.605A pdb=" N GLY A 209 " --> pdb=" O GLU A 205 " (cutoff:3.500A) Processing helix chain 'A' and resid 226 through 231 Processing helix chain 'A' and resid 233 through 240 Processing helix chain 'A' and resid 245 through 257 Processing helix chain 'A' and resid 267 through 281 removed outlier: 3.535A pdb=" N LYS A 281 " --> pdb=" O GLN A 277 " (cutoff:3.500A) Processing helix chain 'B' and resid 45 through 54 removed outlier: 3.742A pdb=" N ASN B 54 " --> pdb=" O MET B 50 " (cutoff:3.500A) Processing helix chain 'B' and resid 80 through 86 Processing helix chain 'B' and resid 93 through 97 Processing helix chain 'B' and resid 102 through 114 removed outlier: 4.464A pdb=" N GLY B 110 " --> pdb=" O ASP B 106 " (cutoff:3.500A) Proline residue: B 111 - end of helix Processing helix chain 'B' and resid 117 through 132 Processing helix chain 'B' and resid 135 through 141 removed outlier: 3.721A pdb=" N ILE B 139 " --> pdb=" O ASP B 136 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N GLU B 140 " --> pdb=" O ASP B 137 " (cutoff:3.500A) Processing helix chain 'B' and resid 147 through 161 Processing helix chain 'B' and resid 177 through 193 Processing helix chain 'B' and resid 204 through 212 removed outlier: 3.515A pdb=" N VAL B 208 " --> pdb=" O ASN B 204 " (cutoff:3.500A) Processing helix chain 'B' and resid 228 through 233 Processing helix chain 'B' and resid 235 through 242 Processing helix chain 'B' and resid 247 through 260 Processing helix chain 'B' and resid 269 through 282 Processing helix chain 'C' and resid 14 through 19 removed outlier: 3.884A pdb=" N ARG C 18 " --> pdb=" O THR C 14 " (cutoff:3.500A) Processing helix chain 'C' and resid 20 through 36 removed outlier: 3.675A pdb=" N PHE C 36 " --> pdb=" O ILE C 32 " (cutoff:3.500A) Processing helix chain 'C' and resid 40 through 57 Processing helix chain 'C' and resid 61 through 87 Proline residue: C 71 - end of helix Processing helix chain 'C' and resid 102 through 130 Processing helix chain 'C' and resid 131 through 143 Processing helix chain 'C' and resid 144 through 148 Processing helix chain 'C' and resid 152 through 184 removed outlier: 4.165A pdb=" N VAL C 167 " --> pdb=" O ALA C 163 " (cutoff:3.500A) Proline residue: C 168 - end of helix removed outlier: 3.608A pdb=" N ARG C 184 " --> pdb=" O ALA C 180 " (cutoff:3.500A) Processing helix chain 'C' and resid 192 through 201 Processing helix chain 'C' and resid 203 through 225 removed outlier: 3.558A pdb=" N SER C 219 " --> pdb=" O ALA C 215 " (cutoff:3.500A) Processing helix chain 'C' and resid 245 through 261 removed outlier: 3.887A pdb=" N VAL C 249 " --> pdb=" O ASP C 245 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU C 255 " --> pdb=" O TYR C 251 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N THR C 256 " --> pdb=" O CYS C 252 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 23 through 30 removed outlier: 5.636A pdb=" N SER A 24 " --> pdb=" O VAL A 11 " (cutoff:3.500A) removed outlier: 7.475A pdb=" N VAL A 11 " --> pdb=" O SER A 24 " (cutoff:3.500A) removed outlier: 7.390A pdb=" N PHE A 28 " --> pdb=" O SER A 7 " (cutoff:3.500A) removed outlier: 5.130A pdb=" N SER A 7 " --> pdb=" O PHE A 28 " (cutoff:3.500A) removed outlier: 7.616A pdb=" N ILE A 30 " --> pdb=" O ILE A 5 " (cutoff:3.500A) removed outlier: 5.945A pdb=" N ILE A 5 " --> pdb=" O ILE A 30 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 86 through 89 removed outlier: 6.668A pdb=" N THR A 36 " --> pdb=" O SER A 199 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N ASP A 217 " --> pdb=" O LEU A 221 " (cutoff:3.500A) removed outlier: 5.172A pdb=" N LEU A 221 " --> pdb=" O ASP A 217 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 20 through 30 removed outlier: 6.150A pdb=" N TYR B 10 " --> pdb=" O GLY B 22 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N ASP B 24 " --> pdb=" O VAL B 8 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N VAL B 8 " --> pdb=" O ASP B 24 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N LEU B 26 " --> pdb=" O GLU B 6 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N GLU B 6 " --> pdb=" O LEU B 26 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N PHE B 28 " --> pdb=" O LYS B 4 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N LYS B 4 " --> pdb=" O PHE B 28 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N VAL B 8 " --> pdb=" O SER B 61 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N SER B 61 " --> pdb=" O VAL B 8 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 87 through 90 removed outlier: 6.373A pdb=" N SER B 88 " --> pdb=" O CYS B 168 " (cutoff:3.500A) removed outlier: 7.763A pdb=" N ASP B 170 " --> pdb=" O SER B 88 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N ALA B 90 " --> pdb=" O ASP B 170 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N ILE B 167 " --> pdb=" O ILE B 199 " (cutoff:3.500A) removed outlier: 7.507A pdb=" N VAL B 201 " --> pdb=" O ILE B 167 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N LEU B 169 " --> pdb=" O VAL B 201 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N PHE B 35 " --> pdb=" O ASP B 214 " (cutoff:3.500A) removed outlier: 7.695A pdb=" N LEU B 216 " --> pdb=" O PHE B 35 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N ALA B 37 " --> pdb=" O LEU B 216 " (cutoff:3.500A) removed outlier: 7.454A pdb=" N LEU B 218 " --> pdb=" O ALA B 37 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N VAL B 39 " --> pdb=" O LEU B 218 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LYS B 225 " --> pdb=" O ALA B 217 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N GLU B 219 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 5.251A pdb=" N LEU B 223 " --> pdb=" O GLU B 219 " (cutoff:3.500A) 348 hydrogen bonds defined for protein. 1002 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.88 Time building geometry restraints manager: 1.96 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2078 1.34 - 1.46: 1013 1.46 - 1.57: 3479 1.57 - 1.69: 10 1.69 - 1.81: 50 Bond restraints: 6630 Sorted by residual: bond pdb=" CB ASN B 7 " pdb=" CG ASN B 7 " ideal model delta sigma weight residual 1.516 1.550 -0.034 2.50e-02 1.60e+03 1.83e+00 bond pdb=" CG1 ILE C 49 " pdb=" CD1 ILE C 49 " ideal model delta sigma weight residual 1.513 1.465 0.048 3.90e-02 6.57e+02 1.51e+00 bond pdb=" CA ASN B 7 " pdb=" CB ASN B 7 " ideal model delta sigma weight residual 1.529 1.542 -0.013 1.58e-02 4.01e+03 6.59e-01 bond pdb=" C VAL C 201 " pdb=" N PRO C 202 " ideal model delta sigma weight residual 1.337 1.344 -0.007 9.80e-03 1.04e+04 5.69e-01 bond pdb=" CG1 ILE A 88 " pdb=" CD1 ILE A 88 " ideal model delta sigma weight residual 1.513 1.484 0.029 3.90e-02 6.57e+02 5.60e-01 ... (remaining 6625 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.47: 8807 1.47 - 2.93: 144 2.93 - 4.40: 28 4.40 - 5.87: 12 5.87 - 7.33: 3 Bond angle restraints: 8994 Sorted by residual: angle pdb=" CA MET C 118 " pdb=" CB MET C 118 " pdb=" CG MET C 118 " ideal model delta sigma weight residual 114.10 108.83 5.27 2.00e+00 2.50e-01 6.95e+00 angle pdb=" CA ASN B 7 " pdb=" CB ASN B 7 " pdb=" CG ASN B 7 " ideal model delta sigma weight residual 112.60 114.79 -2.19 1.00e+00 1.00e+00 4.82e+00 angle pdb=" N VAL C 201 " pdb=" CA VAL C 201 " pdb=" C VAL C 201 " ideal model delta sigma weight residual 108.88 113.61 -4.73 2.16e+00 2.14e-01 4.79e+00 angle pdb=" CA VAL C 201 " pdb=" C VAL C 201 " pdb=" N PRO C 202 " ideal model delta sigma weight residual 118.88 122.22 -3.34 1.54e+00 4.22e-01 4.70e+00 angle pdb=" N PHE A 231 " pdb=" CA PHE A 231 " pdb=" C PHE A 231 " ideal model delta sigma weight residual 109.81 114.54 -4.73 2.21e+00 2.05e-01 4.58e+00 ... (remaining 8989 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.47: 3608 17.47 - 34.94: 311 34.94 - 52.41: 77 52.41 - 69.88: 13 69.88 - 87.35: 10 Dihedral angle restraints: 4019 sinusoidal: 1654 harmonic: 2365 Sorted by residual: dihedral pdb=" CA ARG B 84 " pdb=" C ARG B 84 " pdb=" N ARG B 85 " pdb=" CA ARG B 85 " ideal model delta harmonic sigma weight residual 180.00 162.84 17.16 0 5.00e+00 4.00e-02 1.18e+01 dihedral pdb=" CG ARG C 182 " pdb=" CD ARG C 182 " pdb=" NE ARG C 182 " pdb=" CZ ARG C 182 " ideal model delta sinusoidal sigma weight residual 180.00 137.23 42.77 2 1.50e+01 4.44e-03 9.84e+00 dihedral pdb=" CB GLU B 32 " pdb=" CG GLU B 32 " pdb=" CD GLU B 32 " pdb=" OE1 GLU B 32 " ideal model delta sinusoidal sigma weight residual 0.00 84.98 -84.98 1 3.00e+01 1.11e-03 9.73e+00 ... (remaining 4016 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 644 0.029 - 0.059: 225 0.059 - 0.088: 98 0.088 - 0.117: 55 0.117 - 0.147: 12 Chirality restraints: 1034 Sorted by residual: chirality pdb=" CA ILE B 167 " pdb=" N ILE B 167 " pdb=" C ILE B 167 " pdb=" CB ILE B 167 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.38e-01 chirality pdb=" CA ILE A 200 " pdb=" N ILE A 200 " pdb=" C ILE A 200 " pdb=" CB ILE A 200 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.12e-01 chirality pdb=" CA MET C 118 " pdb=" N MET C 118 " pdb=" C MET C 118 " pdb=" CB MET C 118 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 5.04e-01 ... (remaining 1031 not shown) Planarity restraints: 1127 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE A 231 " -0.038 5.00e-02 4.00e+02 5.72e-02 5.24e+00 pdb=" N PRO A 232 " 0.099 5.00e-02 4.00e+02 pdb=" CA PRO A 232 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO A 232 " -0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY B 110 " -0.028 5.00e-02 4.00e+02 4.22e-02 2.85e+00 pdb=" N PRO B 111 " 0.073 5.00e-02 4.00e+02 pdb=" CA PRO B 111 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO B 111 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR B 72 " 0.025 5.00e-02 4.00e+02 3.84e-02 2.36e+00 pdb=" N PRO B 73 " -0.066 5.00e-02 4.00e+02 pdb=" CA PRO B 73 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO B 73 " 0.022 5.00e-02 4.00e+02 ... (remaining 1124 not shown) Histogram of nonbonded interaction distances: 1.96 - 2.55: 54 2.55 - 3.13: 5081 3.13 - 3.72: 10515 3.72 - 4.31: 15344 4.31 - 4.90: 25482 Nonbonded interactions: 56476 Sorted by model distance: nonbonded pdb=" O2B ATP A 301 " pdb="MG MG A 302 " model vdw 1.956 2.170 nonbonded pdb=" OG SER B 47 " pdb="MG MG B 302 " model vdw 1.958 2.170 nonbonded pdb=" OE1 GLN A 91 " pdb="MG MG A 302 " model vdw 1.991 2.170 nonbonded pdb=" OE1 GLN B 92 " pdb="MG MG B 302 " model vdw 2.028 2.170 nonbonded pdb=" OG SER A 47 " pdb="MG MG A 302 " model vdw 2.043 2.170 ... (remaining 56471 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: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 9.140 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: 0.000 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 16.960 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.030 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:16.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 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 0.048 6630 Z= 0.168 Angle : 0.522 7.334 8994 Z= 0.270 Chirality : 0.041 0.147 1034 Planarity : 0.004 0.057 1127 Dihedral : 14.825 87.345 2491 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: 0.83 (0.29), residues: 814 helix: 1.57 (0.25), residues: 452 sheet: -0.80 (0.52), residues: 74 loop : -0.66 (0.35), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 128 HIS 0.002 0.000 HIS A 10 PHE 0.011 0.001 PHE C 50 TYR 0.008 0.001 TYR B 162 ARG 0.003 0.000 ARG B 181 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1628 Ramachandran restraints generated. 814 Oldfield, 0 Emsley, 814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1628 Ramachandran restraints generated. 814 Oldfield, 0 Emsley, 814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 114 time to evaluate : 0.754 Fit side-chains REVERT: A 180 GLU cc_start: 0.7829 (tt0) cc_final: 0.7373 (tt0) REVERT: A 184 ASP cc_start: 0.8172 (m-30) cc_final: 0.7873 (m-30) REVERT: C 106 LEU cc_start: 0.5436 (tt) cc_final: 0.4988 (tm) outliers start: 0 outliers final: 1 residues processed: 114 average time/residue: 1.2442 time to fit residues: 149.2594 Evaluate side-chains 91 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 90 time to evaluate : 0.822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 189 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 68 optimal weight: 1.9990 chunk 61 optimal weight: 0.7980 chunk 34 optimal weight: 0.8980 chunk 20 optimal weight: 3.9990 chunk 41 optimal weight: 0.4980 chunk 32 optimal weight: 4.9990 chunk 63 optimal weight: 5.9990 chunk 24 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 chunk 47 optimal weight: 1.9990 chunk 73 optimal weight: 1.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 10 HIS B 243 HIS C 181 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 moved from start: 0.1047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.074 6630 Z= 0.372 Angle : 0.627 8.226 8994 Z= 0.318 Chirality : 0.046 0.147 1034 Planarity : 0.005 0.063 1127 Dihedral : 10.382 86.138 941 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 2.57 % Allowed : 7.71 % Favored : 89.71 % 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: 0.84 (0.28), residues: 814 helix: 1.48 (0.24), residues: 448 sheet: -0.55 (0.54), residues: 73 loop : -0.52 (0.34), residues: 293 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 80 HIS 0.007 0.001 HIS A 10 PHE 0.015 0.002 PHE B 116 TYR 0.014 0.002 TYR C 251 ARG 0.003 0.001 ARG B 181 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1628 Ramachandran restraints generated. 814 Oldfield, 0 Emsley, 814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1628 Ramachandran restraints generated. 814 Oldfield, 0 Emsley, 814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 92 time to evaluate : 0.781 Fit side-chains REVERT: A 62 LEU cc_start: 0.7940 (OUTLIER) cc_final: 0.7686 (mm) REVERT: A 179 LYS cc_start: 0.8294 (OUTLIER) cc_final: 0.7833 (mtpt) REVERT: A 180 GLU cc_start: 0.7840 (tt0) cc_final: 0.7388 (tt0) REVERT: A 184 ASP cc_start: 0.8200 (m-30) cc_final: 0.7852 (m-30) REVERT: A 218 ASP cc_start: 0.8212 (OUTLIER) cc_final: 0.7958 (m-30) REVERT: A 264 GLU cc_start: 0.7359 (OUTLIER) cc_final: 0.7091 (mt-10) REVERT: B 82 ASP cc_start: 0.7447 (t0) cc_final: 0.7126 (m-30) REVERT: C 52 LEU cc_start: 0.7227 (OUTLIER) cc_final: 0.6905 (mt) REVERT: C 208 PHE cc_start: 0.6490 (OUTLIER) cc_final: 0.6016 (t80) REVERT: C 231 GLU cc_start: 0.7497 (OUTLIER) cc_final: 0.6957 (tm-30) outliers start: 18 outliers final: 6 residues processed: 99 average time/residue: 1.2790 time to fit residues: 133.4171 Evaluate side-chains 104 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 91 time to evaluate : 0.758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 ILE Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 179 LYS Chi-restraints excluded: chain A residue 218 ASP Chi-restraints excluded: chain A residue 264 GLU Chi-restraints excluded: chain B residue 6 GLU Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 136 ASP Chi-restraints excluded: chain B residue 167 ILE Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 193 LEU Chi-restraints excluded: chain C residue 208 PHE Chi-restraints excluded: chain C residue 231 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 40 optimal weight: 0.0770 chunk 22 optimal weight: 0.7980 chunk 61 optimal weight: 2.9990 chunk 50 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 73 optimal weight: 1.9990 chunk 79 optimal weight: 0.0050 chunk 65 optimal weight: 5.9990 chunk 25 optimal weight: 0.9980 chunk 59 optimal weight: 0.7980 chunk 72 optimal weight: 0.9980 overall best weight: 0.5352 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 10 HIS B 77 ASN B 226 HIS B 243 HIS C 189 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.1107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 6630 Z= 0.202 Angle : 0.522 7.552 8994 Z= 0.268 Chirality : 0.042 0.145 1034 Planarity : 0.005 0.058 1127 Dihedral : 9.775 84.927 939 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 2.57 % Allowed : 9.86 % Favored : 87.57 % 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: 1.11 (0.29), residues: 814 helix: 1.74 (0.24), residues: 447 sheet: -0.59 (0.54), residues: 73 loop : -0.43 (0.35), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 128 HIS 0.006 0.001 HIS A 10 PHE 0.011 0.001 PHE A 231 TYR 0.010 0.001 TYR C 251 ARG 0.003 0.000 ARG B 181 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1628 Ramachandran restraints generated. 814 Oldfield, 0 Emsley, 814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1628 Ramachandran restraints generated. 814 Oldfield, 0 Emsley, 814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 96 time to evaluate : 0.881 Fit side-chains REVERT: A 62 LEU cc_start: 0.7980 (OUTLIER) cc_final: 0.7704 (mm) REVERT: A 180 GLU cc_start: 0.7810 (tt0) cc_final: 0.7366 (tt0) REVERT: A 184 ASP cc_start: 0.8184 (m-30) cc_final: 0.7853 (m-30) REVERT: A 218 ASP cc_start: 0.8223 (OUTLIER) cc_final: 0.7998 (m-30) REVERT: A 264 GLU cc_start: 0.7370 (OUTLIER) cc_final: 0.7043 (mt-10) REVERT: B 4 LYS cc_start: 0.8228 (ttpt) cc_final: 0.8016 (ttpt) REVERT: B 82 ASP cc_start: 0.7375 (t0) cc_final: 0.7069 (m-30) REVERT: C 208 PHE cc_start: 0.6535 (OUTLIER) cc_final: 0.6085 (t80) outliers start: 18 outliers final: 6 residues processed: 102 average time/residue: 1.3293 time to fit residues: 143.0080 Evaluate side-chains 100 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 90 time to evaluate : 0.788 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 218 ASP Chi-restraints excluded: chain A residue 236 MET Chi-restraints excluded: chain A residue 264 GLU Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 136 ASP Chi-restraints excluded: chain B residue 167 ILE Chi-restraints excluded: chain C residue 193 LEU Chi-restraints excluded: chain C residue 208 PHE Chi-restraints excluded: chain C residue 259 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 55 optimal weight: 1.9990 chunk 38 optimal weight: 0.2980 chunk 8 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 73 optimal weight: 2.9990 chunk 78 optimal weight: 2.9990 chunk 70 optimal weight: 6.9990 chunk 21 optimal weight: 2.9990 chunk 65 optimal weight: 4.9990 chunk 44 optimal weight: 0.0070 overall best weight: 1.2604 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 10 HIS B 243 HIS C 189 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.1318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.074 6630 Z= 0.373 Angle : 0.612 7.877 8994 Z= 0.309 Chirality : 0.046 0.145 1034 Planarity : 0.005 0.064 1127 Dihedral : 10.287 85.461 939 Min Nonbonded Distance : 1.851 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 2.86 % Allowed : 12.29 % Favored : 84.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.86 (0.28), residues: 814 helix: 1.53 (0.24), residues: 447 sheet: -0.74 (0.54), residues: 74 loop : -0.48 (0.34), residues: 293 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 80 HIS 0.006 0.001 HIS A 10 PHE 0.015 0.002 PHE B 116 TYR 0.014 0.002 TYR B 162 ARG 0.003 0.001 ARG C 225 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1628 Ramachandran restraints generated. 814 Oldfield, 0 Emsley, 814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1628 Ramachandran restraints generated. 814 Oldfield, 0 Emsley, 814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 95 time to evaluate : 0.684 Fit side-chains REVERT: A 62 LEU cc_start: 0.8045 (OUTLIER) cc_final: 0.7732 (mm) REVERT: A 173 MET cc_start: 0.9010 (mtm) cc_final: 0.8778 (mtt) REVERT: A 180 GLU cc_start: 0.7835 (tt0) cc_final: 0.7419 (tt0) REVERT: A 184 ASP cc_start: 0.8227 (m-30) cc_final: 0.7863 (m-30) REVERT: A 218 ASP cc_start: 0.8251 (OUTLIER) cc_final: 0.7982 (m-30) REVERT: A 264 GLU cc_start: 0.7370 (OUTLIER) cc_final: 0.7095 (mt-10) REVERT: B 82 ASP cc_start: 0.7427 (t0) cc_final: 0.7104 (m-30) REVERT: C 52 LEU cc_start: 0.7220 (OUTLIER) cc_final: 0.6877 (mt) REVERT: C 87 MET cc_start: 0.4436 (mtt) cc_final: 0.4170 (pp-130) REVERT: C 208 PHE cc_start: 0.6576 (OUTLIER) cc_final: 0.6105 (t80) REVERT: C 231 GLU cc_start: 0.7510 (OUTLIER) cc_final: 0.6914 (tm-30) outliers start: 20 outliers final: 8 residues processed: 102 average time/residue: 1.2575 time to fit residues: 135.1075 Evaluate side-chains 103 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 89 time to evaluate : 0.792 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 ILE Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 66 SER Chi-restraints excluded: chain A residue 218 ASP Chi-restraints excluded: chain A residue 236 MET Chi-restraints excluded: chain A residue 264 GLU Chi-restraints excluded: chain B residue 6 GLU Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 136 ASP Chi-restraints excluded: chain B residue 167 ILE Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 193 LEU Chi-restraints excluded: chain C residue 208 PHE Chi-restraints excluded: chain C residue 231 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 1 optimal weight: 0.8980 chunk 58 optimal weight: 1.9990 chunk 32 optimal weight: 0.7980 chunk 66 optimal weight: 1.9990 chunk 54 optimal weight: 2.9990 chunk 0 optimal weight: 2.9990 chunk 39 optimal weight: 0.6980 chunk 70 optimal weight: 5.9990 chunk 19 optimal weight: 1.9990 chunk 26 optimal weight: 0.9990 chunk 15 optimal weight: 0.5980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 10 HIS B 243 HIS C 189 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.1336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 6630 Z= 0.259 Angle : 0.552 7.736 8994 Z= 0.280 Chirality : 0.043 0.149 1034 Planarity : 0.005 0.060 1127 Dihedral : 9.931 84.511 939 Min Nonbonded Distance : 1.859 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 2.86 % Allowed : 12.71 % Favored : 84.43 % 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: 0.95 (0.29), residues: 814 helix: 1.64 (0.24), residues: 454 sheet: -0.74 (0.53), residues: 73 loop : -0.57 (0.35), residues: 287 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 128 HIS 0.006 0.001 HIS A 10 PHE 0.013 0.001 PHE A 231 TYR 0.011 0.001 TYR C 251 ARG 0.004 0.000 ARG B 181 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1628 Ramachandran restraints generated. 814 Oldfield, 0 Emsley, 814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1628 Ramachandran restraints generated. 814 Oldfield, 0 Emsley, 814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 92 time to evaluate : 0.642 Fit side-chains REVERT: A 62 LEU cc_start: 0.8043 (OUTLIER) cc_final: 0.7737 (mm) REVERT: A 173 MET cc_start: 0.9009 (mtm) cc_final: 0.8756 (mtt) REVERT: A 180 GLU cc_start: 0.7826 (tt0) cc_final: 0.7391 (tt0) REVERT: A 184 ASP cc_start: 0.8189 (m-30) cc_final: 0.7838 (m-30) REVERT: A 218 ASP cc_start: 0.8240 (OUTLIER) cc_final: 0.7965 (m-30) REVERT: A 264 GLU cc_start: 0.7347 (OUTLIER) cc_final: 0.6987 (mt-10) REVERT: B 6 GLU cc_start: 0.7272 (OUTLIER) cc_final: 0.7048 (pp20) REVERT: B 82 ASP cc_start: 0.7402 (t0) cc_final: 0.7082 (m-30) REVERT: C 208 PHE cc_start: 0.6534 (OUTLIER) cc_final: 0.6073 (t80) outliers start: 20 outliers final: 8 residues processed: 101 average time/residue: 1.2702 time to fit residues: 134.9436 Evaluate side-chains 102 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 89 time to evaluate : 0.792 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 66 SER Chi-restraints excluded: chain A residue 218 ASP Chi-restraints excluded: chain A residue 236 MET Chi-restraints excluded: chain A residue 264 GLU Chi-restraints excluded: chain B residue 6 GLU Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 136 ASP Chi-restraints excluded: chain B residue 163 GLU Chi-restraints excluded: chain B residue 167 ILE Chi-restraints excluded: chain C residue 193 LEU Chi-restraints excluded: chain C residue 208 PHE Chi-restraints excluded: chain C residue 260 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 45 optimal weight: 3.9990 chunk 19 optimal weight: 1.9990 chunk 78 optimal weight: 2.9990 chunk 65 optimal weight: 4.9990 chunk 36 optimal weight: 0.6980 chunk 6 optimal weight: 0.6980 chunk 25 optimal weight: 2.9990 chunk 41 optimal weight: 0.4980 chunk 75 optimal weight: 0.4980 chunk 8 optimal weight: 0.9980 chunk 44 optimal weight: 0.5980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 10 HIS B 243 HIS C 189 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.1363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 6630 Z= 0.215 Angle : 0.527 7.418 8994 Z= 0.268 Chirality : 0.042 0.149 1034 Planarity : 0.005 0.061 1127 Dihedral : 9.774 84.855 939 Min Nonbonded Distance : 1.861 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 2.71 % Allowed : 13.43 % Favored : 83.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.09 (0.29), residues: 814 helix: 1.78 (0.24), residues: 454 sheet: -0.75 (0.53), residues: 73 loop : -0.54 (0.35), residues: 287 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 128 HIS 0.006 0.001 HIS A 10 PHE 0.010 0.001 PHE A 231 TYR 0.010 0.001 TYR C 251 ARG 0.008 0.000 ARG B 181 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1628 Ramachandran restraints generated. 814 Oldfield, 0 Emsley, 814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1628 Ramachandran restraints generated. 814 Oldfield, 0 Emsley, 814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 97 time to evaluate : 0.694 Fit side-chains REVERT: A 62 LEU cc_start: 0.8068 (OUTLIER) cc_final: 0.7731 (mm) REVERT: A 173 MET cc_start: 0.9001 (mtm) cc_final: 0.8728 (mtt) REVERT: A 180 GLU cc_start: 0.7815 (tt0) cc_final: 0.7395 (tt0) REVERT: A 184 ASP cc_start: 0.8188 (m-30) cc_final: 0.7855 (m-30) REVERT: A 218 ASP cc_start: 0.8254 (OUTLIER) cc_final: 0.7976 (m-30) REVERT: A 264 GLU cc_start: 0.7339 (OUTLIER) cc_final: 0.6988 (mt-10) REVERT: B 6 GLU cc_start: 0.7248 (OUTLIER) cc_final: 0.7039 (pp20) REVERT: B 82 ASP cc_start: 0.7362 (t0) cc_final: 0.7045 (m-30) REVERT: B 118 GLU cc_start: 0.7294 (mm-30) cc_final: 0.6973 (mp0) REVERT: B 214 ASP cc_start: 0.7812 (OUTLIER) cc_final: 0.7432 (t70) REVERT: C 208 PHE cc_start: 0.6525 (OUTLIER) cc_final: 0.6089 (t80) REVERT: C 231 GLU cc_start: 0.7500 (OUTLIER) cc_final: 0.6912 (tm-30) outliers start: 19 outliers final: 7 residues processed: 104 average time/residue: 1.2241 time to fit residues: 133.9994 Evaluate side-chains 106 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 92 time to evaluate : 0.789 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 ILE Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 66 SER Chi-restraints excluded: chain A residue 218 ASP Chi-restraints excluded: chain A residue 264 GLU Chi-restraints excluded: chain B residue 6 GLU Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 136 ASP Chi-restraints excluded: chain B residue 163 GLU Chi-restraints excluded: chain B residue 167 ILE Chi-restraints excluded: chain B residue 214 ASP Chi-restraints excluded: chain C residue 193 LEU Chi-restraints excluded: chain C residue 208 PHE Chi-restraints excluded: chain C residue 231 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 57 optimal weight: 0.6980 chunk 44 optimal weight: 0.6980 chunk 65 optimal weight: 4.9990 chunk 43 optimal weight: 0.5980 chunk 78 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 chunk 47 optimal weight: 0.9990 chunk 36 optimal weight: 0.0070 chunk 31 optimal weight: 0.7980 chunk 46 optimal weight: 0.5980 chunk 23 optimal weight: 0.7980 overall best weight: 0.5198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 10 HIS B 243 HIS C 181 GLN C 189 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 moved from start: 0.1404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 6630 Z= 0.201 Angle : 0.529 8.206 8994 Z= 0.268 Chirality : 0.042 0.153 1034 Planarity : 0.005 0.061 1127 Dihedral : 9.683 84.877 939 Min Nonbonded Distance : 1.861 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 2.86 % Allowed : 14.00 % Favored : 83.14 % 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: 1.16 (0.29), residues: 814 helix: 1.83 (0.24), residues: 455 sheet: -0.69 (0.53), residues: 73 loop : -0.51 (0.36), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 128 HIS 0.006 0.001 HIS A 10 PHE 0.012 0.001 PHE C 50 TYR 0.011 0.001 TYR C 251 ARG 0.009 0.000 ARG B 181 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1628 Ramachandran restraints generated. 814 Oldfield, 0 Emsley, 814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1628 Ramachandran restraints generated. 814 Oldfield, 0 Emsley, 814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 92 time to evaluate : 0.724 Fit side-chains REVERT: A 173 MET cc_start: 0.8998 (mtm) cc_final: 0.8726 (mtt) REVERT: A 180 GLU cc_start: 0.7807 (tt0) cc_final: 0.7389 (tt0) REVERT: A 184 ASP cc_start: 0.8199 (m-30) cc_final: 0.7869 (m-30) REVERT: A 218 ASP cc_start: 0.8248 (OUTLIER) cc_final: 0.7990 (m-30) REVERT: A 264 GLU cc_start: 0.7337 (OUTLIER) cc_final: 0.6986 (mt-10) REVERT: B 82 ASP cc_start: 0.7383 (t0) cc_final: 0.7043 (m-30) REVERT: B 120 GLU cc_start: 0.7775 (mt-10) cc_final: 0.7554 (mt-10) REVERT: B 214 ASP cc_start: 0.7777 (OUTLIER) cc_final: 0.7402 (t70) REVERT: C 208 PHE cc_start: 0.6530 (OUTLIER) cc_final: 0.6109 (t80) REVERT: C 231 GLU cc_start: 0.7479 (OUTLIER) cc_final: 0.6898 (tm-30) outliers start: 20 outliers final: 7 residues processed: 101 average time/residue: 1.1630 time to fit residues: 124.2075 Evaluate side-chains 105 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 93 time to evaluate : 0.762 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 ILE Chi-restraints excluded: chain A residue 66 SER Chi-restraints excluded: chain A residue 218 ASP Chi-restraints excluded: chain A residue 236 MET Chi-restraints excluded: chain A residue 264 GLU Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 136 ASP Chi-restraints excluded: chain B residue 163 GLU Chi-restraints excluded: chain B residue 167 ILE Chi-restraints excluded: chain B residue 214 ASP Chi-restraints excluded: chain C residue 208 PHE Chi-restraints excluded: chain C residue 231 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 15 optimal weight: 0.8980 chunk 49 optimal weight: 2.9990 chunk 53 optimal weight: 5.9990 chunk 38 optimal weight: 1.9990 chunk 7 optimal weight: 0.6980 chunk 61 optimal weight: 4.9990 chunk 71 optimal weight: 0.9980 chunk 74 optimal weight: 2.9990 chunk 68 optimal weight: 2.9990 chunk 72 optimal weight: 0.7980 chunk 43 optimal weight: 0.9980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 10 HIS B 243 HIS C 189 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.1425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 6630 Z= 0.280 Angle : 0.581 12.577 8994 Z= 0.289 Chirality : 0.044 0.194 1034 Planarity : 0.005 0.063 1127 Dihedral : 9.924 84.122 939 Min Nonbonded Distance : 1.852 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 2.57 % Allowed : 14.57 % Favored : 82.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.00 (0.29), residues: 814 helix: 1.68 (0.24), residues: 455 sheet: -0.80 (0.53), residues: 74 loop : -0.53 (0.35), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 128 HIS 0.006 0.001 HIS A 10 PHE 0.013 0.001 PHE B 116 TYR 0.013 0.001 TYR C 251 ARG 0.009 0.000 ARG B 181 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1628 Ramachandran restraints generated. 814 Oldfield, 0 Emsley, 814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1628 Ramachandran restraints generated. 814 Oldfield, 0 Emsley, 814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 94 time to evaluate : 0.705 Fit side-chains REVERT: A 84 GLU cc_start: 0.7685 (OUTLIER) cc_final: 0.7482 (pt0) REVERT: A 173 MET cc_start: 0.9009 (mtm) cc_final: 0.8764 (mtt) REVERT: A 180 GLU cc_start: 0.7825 (tt0) cc_final: 0.7398 (tt0) REVERT: A 184 ASP cc_start: 0.8217 (m-30) cc_final: 0.7868 (m-30) REVERT: A 218 ASP cc_start: 0.8241 (OUTLIER) cc_final: 0.7963 (m-30) REVERT: A 238 LYS cc_start: 0.8488 (mmmm) cc_final: 0.8284 (mmmm) REVERT: A 264 GLU cc_start: 0.7329 (OUTLIER) cc_final: 0.6966 (mt-10) REVERT: B 82 ASP cc_start: 0.7436 (t0) cc_final: 0.7098 (m-30) REVERT: B 118 GLU cc_start: 0.7318 (mm-30) cc_final: 0.7043 (mp0) REVERT: B 120 GLU cc_start: 0.7779 (mt-10) cc_final: 0.7468 (mt-10) REVERT: B 214 ASP cc_start: 0.7861 (OUTLIER) cc_final: 0.7487 (t70) REVERT: C 208 PHE cc_start: 0.6519 (OUTLIER) cc_final: 0.6099 (t80) REVERT: C 231 GLU cc_start: 0.7500 (OUTLIER) cc_final: 0.6906 (tm-30) outliers start: 18 outliers final: 9 residues processed: 103 average time/residue: 1.1893 time to fit residues: 129.2452 Evaluate side-chains 105 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 90 time to evaluate : 0.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 ILE Chi-restraints excluded: chain A residue 66 SER Chi-restraints excluded: chain A residue 84 GLU Chi-restraints excluded: chain A residue 218 ASP Chi-restraints excluded: chain A residue 236 MET Chi-restraints excluded: chain A residue 264 GLU Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 136 ASP Chi-restraints excluded: chain B residue 163 GLU Chi-restraints excluded: chain B residue 167 ILE Chi-restraints excluded: chain B residue 214 ASP Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 208 PHE Chi-restraints excluded: chain C residue 231 GLU Chi-restraints excluded: chain C residue 260 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 31 optimal weight: 1.9990 chunk 57 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 65 optimal weight: 0.8980 chunk 68 optimal weight: 0.6980 chunk 72 optimal weight: 1.9990 chunk 47 optimal weight: 0.0870 chunk 76 optimal weight: 3.9990 chunk 46 optimal weight: 0.8980 chunk 36 optimal weight: 0.8980 chunk 53 optimal weight: 5.9990 overall best weight: 0.6958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 10 HIS B 243 HIS C 189 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 moved from start: 0.1410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 6630 Z= 0.239 Angle : 0.537 7.455 8994 Z= 0.274 Chirality : 0.043 0.167 1034 Planarity : 0.005 0.060 1127 Dihedral : 9.814 84.103 939 Min Nonbonded Distance : 1.856 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 2.14 % Allowed : 15.14 % Favored : 82.71 % 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: 1.11 (0.29), residues: 814 helix: 1.78 (0.24), residues: 455 sheet: -0.69 (0.53), residues: 73 loop : -0.53 (0.35), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 128 HIS 0.007 0.001 HIS A 10 PHE 0.012 0.001 PHE B 116 TYR 0.013 0.001 TYR C 251 ARG 0.008 0.000 ARG B 181 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1628 Ramachandran restraints generated. 814 Oldfield, 0 Emsley, 814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1628 Ramachandran restraints generated. 814 Oldfield, 0 Emsley, 814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 93 time to evaluate : 0.791 Fit side-chains REVERT: A 62 LEU cc_start: 0.8031 (OUTLIER) cc_final: 0.7757 (mm) REVERT: A 173 MET cc_start: 0.9009 (mtm) cc_final: 0.8754 (mtt) REVERT: A 180 GLU cc_start: 0.7817 (tt0) cc_final: 0.7403 (tt0) REVERT: A 184 ASP cc_start: 0.8216 (m-30) cc_final: 0.7884 (m-30) REVERT: A 218 ASP cc_start: 0.8256 (OUTLIER) cc_final: 0.7979 (m-30) REVERT: A 264 GLU cc_start: 0.7327 (OUTLIER) cc_final: 0.6966 (mt-10) REVERT: B 82 ASP cc_start: 0.7405 (t0) cc_final: 0.7076 (m-30) REVERT: B 118 GLU cc_start: 0.7329 (mm-30) cc_final: 0.7034 (mp0) REVERT: B 120 GLU cc_start: 0.7759 (mt-10) cc_final: 0.7457 (mt-10) REVERT: B 214 ASP cc_start: 0.7839 (OUTLIER) cc_final: 0.7466 (t70) REVERT: C 208 PHE cc_start: 0.6531 (OUTLIER) cc_final: 0.6101 (t80) REVERT: C 231 GLU cc_start: 0.7505 (OUTLIER) cc_final: 0.6920 (tm-30) outliers start: 15 outliers final: 7 residues processed: 100 average time/residue: 1.2127 time to fit residues: 127.7645 Evaluate side-chains 104 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 91 time to evaluate : 0.757 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 ILE Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 66 SER Chi-restraints excluded: chain A residue 218 ASP Chi-restraints excluded: chain A residue 236 MET Chi-restraints excluded: chain A residue 264 GLU Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 136 ASP Chi-restraints excluded: chain B residue 163 GLU Chi-restraints excluded: chain B residue 167 ILE Chi-restraints excluded: chain B residue 214 ASP Chi-restraints excluded: chain C residue 208 PHE Chi-restraints excluded: chain C residue 231 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 80 optimal weight: 0.7980 chunk 74 optimal weight: 0.9990 chunk 64 optimal weight: 0.0570 chunk 6 optimal weight: 0.0370 chunk 49 optimal weight: 1.9990 chunk 39 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 68 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 59 optimal weight: 0.9990 chunk 9 optimal weight: 0.8980 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 10 HIS B 243 HIS C 189 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.1443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 6630 Z= 0.209 Angle : 0.539 10.391 8994 Z= 0.270 Chirality : 0.042 0.160 1034 Planarity : 0.005 0.061 1127 Dihedral : 9.702 84.062 939 Min Nonbonded Distance : 1.860 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 2.14 % Allowed : 15.57 % Favored : 82.29 % 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: 1.19 (0.29), residues: 814 helix: 1.85 (0.24), residues: 455 sheet: -0.68 (0.53), residues: 73 loop : -0.49 (0.36), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 128 HIS 0.007 0.001 HIS A 10 PHE 0.011 0.001 PHE A 231 TYR 0.011 0.001 TYR C 251 ARG 0.008 0.000 ARG B 181 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1628 Ramachandran restraints generated. 814 Oldfield, 0 Emsley, 814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1628 Ramachandran restraints generated. 814 Oldfield, 0 Emsley, 814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 91 time to evaluate : 0.754 Fit side-chains REVERT: A 62 LEU cc_start: 0.8016 (OUTLIER) cc_final: 0.7740 (mm) REVERT: A 173 MET cc_start: 0.9008 (mtm) cc_final: 0.8738 (mtt) REVERT: A 179 LYS cc_start: 0.8274 (mtmm) cc_final: 0.7808 (mtpp) REVERT: A 180 GLU cc_start: 0.7818 (tt0) cc_final: 0.7404 (tt0) REVERT: A 184 ASP cc_start: 0.8223 (m-30) cc_final: 0.7895 (m-30) REVERT: A 218 ASP cc_start: 0.8247 (OUTLIER) cc_final: 0.7991 (m-30) REVERT: A 264 GLU cc_start: 0.7318 (OUTLIER) cc_final: 0.6969 (mt-10) REVERT: B 82 ASP cc_start: 0.7397 (t0) cc_final: 0.7059 (m-30) REVERT: B 118 GLU cc_start: 0.7294 (mm-30) cc_final: 0.6998 (mp0) REVERT: B 120 GLU cc_start: 0.7661 (mt-10) cc_final: 0.7374 (mt-10) REVERT: B 214 ASP cc_start: 0.7774 (OUTLIER) cc_final: 0.7403 (t70) REVERT: C 208 PHE cc_start: 0.6524 (OUTLIER) cc_final: 0.6097 (t80) REVERT: C 231 GLU cc_start: 0.7475 (OUTLIER) cc_final: 0.6896 (tm-30) outliers start: 15 outliers final: 8 residues processed: 96 average time/residue: 1.1751 time to fit residues: 119.0999 Evaluate side-chains 103 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 89 time to evaluate : 0.813 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 ILE Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 66 SER Chi-restraints excluded: chain A residue 218 ASP Chi-restraints excluded: chain A residue 236 MET Chi-restraints excluded: chain A residue 264 GLU Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 136 ASP Chi-restraints excluded: chain B residue 163 GLU Chi-restraints excluded: chain B residue 167 ILE Chi-restraints excluded: chain B residue 214 ASP Chi-restraints excluded: chain C residue 193 LEU Chi-restraints excluded: chain C residue 208 PHE Chi-restraints excluded: chain C residue 231 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 17 optimal weight: 0.3980 chunk 64 optimal weight: 0.0980 chunk 26 optimal weight: 2.9990 chunk 66 optimal weight: 0.7980 chunk 8 optimal weight: 0.9980 chunk 11 optimal weight: 0.5980 chunk 56 optimal weight: 0.9980 chunk 3 optimal weight: 3.9990 chunk 46 optimal weight: 1.9990 chunk 73 optimal weight: 2.9990 chunk 43 optimal weight: 0.1980 overall best weight: 0.4180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 10 HIS B 243 HIS C 189 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.163078 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.125103 restraints weight = 6376.124| |-----------------------------------------------------------------------------| r_work (start): 0.3433 rms_B_bonded: 1.56 r_work: 0.3256 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3130 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.3130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.1495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6630 Z= 0.178 Angle : 0.529 14.818 8994 Z= 0.262 Chirality : 0.042 0.177 1034 Planarity : 0.005 0.060 1127 Dihedral : 9.515 84.452 939 Min Nonbonded Distance : 1.877 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 2.00 % Allowed : 15.86 % Favored : 82.14 % 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: 1.27 (0.29), residues: 814 helix: 1.93 (0.24), residues: 454 sheet: -0.73 (0.54), residues: 74 loop : -0.45 (0.36), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 128 HIS 0.006 0.001 HIS A 10 PHE 0.009 0.001 PHE C 50 TYR 0.010 0.001 TYR C 251 ARG 0.008 0.000 ARG B 181 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2756.75 seconds wall clock time: 50 minutes 42.32 seconds (3042.32 seconds total)