Starting phenix.real_space_refine on Mon Feb 10 23:28:36 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8j7n_36043/02_2025/8j7n_36043_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8j7n_36043/02_2025/8j7n_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/cci-nas-00/data/ceres_data/8j7n_36043/02_2025/8j7n_36043.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8j7n_36043/02_2025/8j7n_36043.map" model { file = "/net/cci-nas-00/data/ceres_data/8j7n_36043/02_2025/8j7n_36043_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8j7n_36043/02_2025/8j7n_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. Time to flip 24 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 3258 Number of models: 1 Model: "" Number of chains: 1 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} Restraints were copied for chains: C, B Time building chain proxies: 2.49, per 1000 atoms: 0.76 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=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 214 " - pdb=" SG CYS A 253 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.72 Conformation dependent library (CDL) restraints added in 393.0 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: 0.52 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: 0.80 Time building geometry restraints manager: 0.85 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: 0.00 - 1.32: 4105 1.32 - 2.63: 340 2.63 - 3.95: 40 3.95 - 5.27: 12 5.27 - 6.58: 6 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: 233 23.01 - 34.52: 47 34.52 - 46.03: 27 46.03 - 57.53: 6 Dihedral angle restraints: 1989 sinusoidal: 771 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 1986 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: 2.03 - 2.60: 15 2.60 - 3.18: 2691 3.18 - 3.75: 4583 3.75 - 4.33: 6719 4.33 - 4.90: 12478 Nonbonded interactions: 26486 Sorted by model distance: nonbonded pdb=" SG CYS B 214 " pdb=" SG CYS B 253 " model vdw 2.025 3.760 nonbonded pdb=" SG CYS C 214 " pdb=" SG CYS C 253 " model vdw 2.026 3.760 nonbonded pdb=" NE2 GLN B 229 " pdb=" O GLU B 241 " model vdw 2.276 3.120 nonbonded pdb=" NE2 GLN C 229 " pdb=" O GLU C 241 " model vdw 2.276 3.120 nonbonded pdb=" NE2 GLN A 229 " pdb=" O GLU A 241 " model vdw 2.276 3.120 ... (remaining 26481 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' } 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: 1.560 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 12.120 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.960 ------------------------------------------------------------------------------- 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= 0.555 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 : 2.025 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 to be fit. rotamer outliers: 0 poor density : 92 time to evaluate : 0.422 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: 1.3389 time to fit residues: 126.1147 Evaluate side-chains 70 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 70 time to evaluate : 0.390 ------------------------------------------------------------------------------- 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: 0.9990 chunk 29 optimal weight: 2.9990 chunk 16 optimal weight: 6.9990 chunk 10 optimal weight: 3.9990 chunk 19 optimal weight: 4.9990 chunk 15 optimal weight: 6.9990 chunk 30 optimal weight: 6.9990 chunk 11 optimal weight: 0.6980 chunk 18 optimal weight: 2.9990 chunk 22 optimal weight: 0.5980 chunk 35 optimal weight: 4.9990 overall best weight: 1.6586 ------------------------------------------------------------------------------- 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** ** A 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 155 ASN B 156 ASN B 222 HIS B 229 GLN ** B 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 156 ASN C 222 HIS C 229 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.126906 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.113325 restraints weight = 4033.671| |-----------------------------------------------------------------------------| r_work (start): 0.3641 rms_B_bonded: 1.80 r_work: 0.3549 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.3456 rms_B_bonded: 3.31 restraints_weight: 0.2500 r_work (final): 0.3456 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8766 moved from start: 0.1967 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= 0.199 Angle : 0.603 6.446 4503 Z= 0.331 Chirality : 0.054 0.178 543 Planarity : 0.002 0.012 558 Dihedral : 6.329 20.048 447 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.03 % Favored : 89.97 % Rotamer: Outliers : 3.44 % Allowed : 11.64 % Favored : 84.92 % 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: -4.82 (0.31), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.67 (0.24), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.002 HIS B 239 PHE 0.005 0.001 PHE A 213 TYR 0.014 0.002 TYR C 143 ARG 0.001 0.000 ARG C 140 *********************** 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 to be fit. rotamer outliers: 13 poor density : 83 time to evaluate : 0.403 Fit side-chains REVERT: A 168 GLN cc_start: 0.8990 (mt0) cc_final: 0.8706 (mt0) REVERT: A 178 LYS cc_start: 0.8362 (OUTLIER) cc_final: 0.8110 (ttpt) REVERT: A 208 SER cc_start: 0.8690 (m) cc_final: 0.8327 (t) REVERT: B 129 LYS cc_start: 0.9129 (ptpp) cc_final: 0.8879 (ptmt) REVERT: B 180 ARG cc_start: 0.8198 (ptp-170) cc_final: 0.6049 (pmt-80) REVERT: B 190 LEU cc_start: 0.9002 (OUTLIER) cc_final: 0.8502 (tt) REVERT: C 180 ARG cc_start: 0.8050 (ptp-170) cc_final: 0.5744 (mmp-170) REVERT: C 250 TYR cc_start: 0.7667 (t80) cc_final: 0.7426 (t80) outliers start: 13 outliers final: 2 residues processed: 85 average time/residue: 1.3236 time to fit residues: 115.3074 Evaluate side-chains 79 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 75 time to evaluate : 0.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 178 LYS Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 217 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 25 optimal weight: 3.9990 chunk 14 optimal weight: 7.9990 chunk 3 optimal weight: 8.9990 chunk 19 optimal weight: 0.0370 chunk 13 optimal weight: 6.9990 chunk 34 optimal weight: 7.9990 chunk 7 optimal weight: 6.9990 chunk 8 optimal weight: 6.9990 chunk 23 optimal weight: 2.9990 chunk 17 optimal weight: 0.6980 chunk 11 optimal weight: 9.9990 overall best weight: 2.9464 ------------------------------------------------------------------------------- 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** ** A 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 223 ASN ** B 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.120910 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.107146 restraints weight = 4092.070| |-----------------------------------------------------------------------------| r_work (start): 0.3552 rms_B_bonded: 1.79 r_work: 0.3464 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.3373 rms_B_bonded: 3.24 restraints_weight: 0.2500 r_work (final): 0.3373 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8811 moved from start: 0.2069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.030 3312 Z= 0.303 Angle : 0.627 6.734 4503 Z= 0.349 Chirality : 0.054 0.195 543 Planarity : 0.002 0.013 558 Dihedral : 6.493 19.981 447 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.78 % Favored : 88.22 % Rotamer: Outliers : 3.44 % Allowed : 15.08 % Favored : 81.48 % 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: -4.61 (0.31), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.51 (0.24), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS B 239 PHE 0.006 0.001 PHE A 213 TYR 0.017 0.002 TYR A 143 ARG 0.001 0.000 ARG A 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 93 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 80 time to evaluate : 0.394 Fit side-chains REVERT: A 168 GLN cc_start: 0.8989 (mt0) cc_final: 0.8695 (mt0) REVERT: A 178 LYS cc_start: 0.8386 (OUTLIER) cc_final: 0.8139 (ttpt) REVERT: A 208 SER cc_start: 0.8569 (m) cc_final: 0.8309 (t) REVERT: B 180 ARG cc_start: 0.8199 (ptp-170) cc_final: 0.6011 (pmt-80) REVERT: B 190 LEU cc_start: 0.8955 (OUTLIER) cc_final: 0.8463 (tt) REVERT: C 180 ARG cc_start: 0.8076 (ptp-170) cc_final: 0.7781 (ptp90) outliers start: 13 outliers final: 4 residues processed: 82 average time/residue: 1.2664 time to fit residues: 106.5918 Evaluate side-chains 78 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 72 time to evaluate : 0.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 178 LYS Chi-restraints excluded: chain A residue 190 LEU 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 6 optimal weight: 9.9990 chunk 37 optimal weight: 1.9990 chunk 36 optimal weight: 0.8980 chunk 33 optimal weight: 7.9990 chunk 19 optimal weight: 0.7980 chunk 38 optimal weight: 7.9990 chunk 2 optimal weight: 6.9990 chunk 25 optimal weight: 1.9990 chunk 1 optimal weight: 7.9990 chunk 13 optimal weight: 7.9990 chunk 21 optimal weight: 10.0000 overall best weight: 2.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 229 GLN ** A 239 HIS ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.122212 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.108502 restraints weight = 4104.608| |-----------------------------------------------------------------------------| r_work (start): 0.3568 rms_B_bonded: 1.79 r_work: 0.3484 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.3393 rms_B_bonded: 3.24 restraints_weight: 0.2500 r_work (final): 0.3393 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8801 moved from start: 0.2295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 3312 Z= 0.265 Angle : 0.604 6.717 4503 Z= 0.335 Chirality : 0.054 0.186 543 Planarity : 0.002 0.012 558 Dihedral : 6.354 20.338 447 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.78 % Favored : 89.22 % 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: -4.44 (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 0.005 0.002 HIS C 239 PHE 0.013 0.001 PHE A 213 TYR 0.017 0.002 TYR C 250 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 97 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 79 time to evaluate : 0.393 Fit side-chains REVERT: A 168 GLN cc_start: 0.8994 (mt0) cc_final: 0.8702 (mt0) REVERT: A 178 LYS cc_start: 0.8353 (OUTLIER) cc_final: 0.8103 (ttpt) REVERT: A 208 SER cc_start: 0.8590 (m) cc_final: 0.8328 (t) REVERT: B 180 ARG cc_start: 0.8206 (ptp-170) cc_final: 0.6039 (pmt-80) REVERT: B 190 LEU cc_start: 0.8994 (OUTLIER) cc_final: 0.8526 (tt) REVERT: C 180 ARG cc_start: 0.8008 (ptp-170) cc_final: 0.7590 (ptp90) REVERT: C 246 GLU cc_start: 0.8657 (mt-10) cc_final: 0.8068 (mm-30) outliers start: 18 outliers final: 8 residues processed: 83 average time/residue: 1.2701 time to fit residues: 108.2570 Evaluate side-chains 85 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 75 time to evaluate : 0.394 ------------------------------------------------------------------------------- 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 228 MET Chi-restraints excluded: chain B residue 134 SER Chi-restraints excluded: chain B residue 138 GLN 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 2 optimal weight: 6.9990 chunk 36 optimal weight: 4.9990 chunk 3 optimal weight: 3.9990 chunk 7 optimal weight: 8.9990 chunk 5 optimal weight: 10.0000 chunk 9 optimal weight: 9.9990 chunk 26 optimal weight: 10.0000 chunk 12 optimal weight: 3.9990 chunk 27 optimal weight: 0.9990 chunk 24 optimal weight: 0.0470 chunk 19 optimal weight: 1.9990 overall best weight: 2.2086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 239 HIS ** 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 = 0.3732 r_free = 0.3732 target = 0.123255 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.109612 restraints weight = 4070.467| |-----------------------------------------------------------------------------| r_work (start): 0.3580 rms_B_bonded: 1.78 r_work: 0.3494 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.3403 rms_B_bonded: 3.26 restraints_weight: 0.2500 r_work (final): 0.3403 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8795 moved from start: 0.2474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 3312 Z= 0.236 Angle : 0.591 6.666 4503 Z= 0.328 Chirality : 0.053 0.184 543 Planarity : 0.002 0.012 558 Dihedral : 6.243 20.326 447 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.28 % Favored : 88.72 % Rotamer: Outliers : 5.03 % Allowed : 15.61 % Favored : 79.37 % 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: -4.33 (0.32), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.29 (0.25), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS C 239 PHE 0.011 0.001 PHE A 213 TYR 0.016 0.002 TYR C 250 ARG 0.001 0.000 ARG B 180 *********************** 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 97 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 78 time to evaluate : 0.396 Fit side-chains REVERT: A 168 GLN cc_start: 0.8954 (mt0) cc_final: 0.8639 (mt0) REVERT: A 178 LYS cc_start: 0.8339 (OUTLIER) cc_final: 0.8096 (ttpt) REVERT: A 208 SER cc_start: 0.8587 (m) cc_final: 0.8310 (t) REVERT: B 180 ARG cc_start: 0.8200 (ptp-170) cc_final: 0.6039 (pmt-80) REVERT: B 190 LEU cc_start: 0.8911 (OUTLIER) cc_final: 0.8451 (tt) REVERT: C 180 ARG cc_start: 0.8010 (ptp-170) cc_final: 0.7591 (ptp90) outliers start: 19 outliers final: 6 residues processed: 82 average time/residue: 1.1732 time to fit residues: 98.8903 Evaluate side-chains 83 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 75 time to evaluate : 0.431 ------------------------------------------------------------------------------- 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 B residue 134 SER Chi-restraints excluded: chain B residue 138 GLN Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 217 ILE Chi-restraints excluded: chain C residue 190 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 26 optimal weight: 5.9990 chunk 21 optimal weight: 10.0000 chunk 15 optimal weight: 10.0000 chunk 24 optimal weight: 4.9990 chunk 27 optimal weight: 3.9990 chunk 10 optimal weight: 8.9990 chunk 12 optimal weight: 5.9990 chunk 25 optimal weight: 3.9990 chunk 22 optimal weight: 0.8980 chunk 34 optimal weight: 10.0000 chunk 33 optimal weight: 6.9990 overall best weight: 3.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 168 GLN ** B 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 168 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.119064 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.105374 restraints weight = 4203.204| |-----------------------------------------------------------------------------| r_work (start): 0.3524 rms_B_bonded: 1.80 r_work: 0.3435 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.3345 rms_B_bonded: 3.20 restraints_weight: 0.2500 r_work (final): 0.3345 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8839 moved from start: 0.2336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.038 3312 Z= 0.397 Angle : 0.669 6.396 4503 Z= 0.372 Chirality : 0.055 0.201 543 Planarity : 0.002 0.014 558 Dihedral : 6.612 21.887 447 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.28 % Favored : 88.72 % Rotamer: Outliers : 5.03 % Allowed : 17.20 % 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: -4.30 (0.33), 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 0.012 0.001 PHE A 213 TYR 0.024 0.002 TYR C 158 ARG 0.001 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 91 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 72 time to evaluate : 0.379 Fit side-chains REVERT: A 168 GLN cc_start: 0.8979 (mt0) cc_final: 0.8679 (mt0) REVERT: A 178 LYS cc_start: 0.8540 (OUTLIER) cc_final: 0.8310 (ttpt) REVERT: A 208 SER cc_start: 0.8575 (m) cc_final: 0.8314 (t) REVERT: B 180 ARG cc_start: 0.8217 (ptp-170) cc_final: 0.6016 (pmt-80) REVERT: B 190 LEU cc_start: 0.8917 (OUTLIER) cc_final: 0.8465 (tt) REVERT: C 180 ARG cc_start: 0.8103 (ptp-170) cc_final: 0.7792 (ptp90) outliers start: 19 outliers final: 8 residues processed: 81 average time/residue: 1.2072 time to fit residues: 100.4569 Evaluate side-chains 80 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 70 time to evaluate : 0.391 ------------------------------------------------------------------------------- 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 228 MET Chi-restraints excluded: chain A residue 240 SER Chi-restraints excluded: chain B residue 134 SER Chi-restraints excluded: chain B residue 138 GLN Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 217 ILE Chi-restraints excluded: chain C residue 190 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 22 optimal weight: 4.9990 chunk 19 optimal weight: 0.9980 chunk 17 optimal weight: 2.9990 chunk 9 optimal weight: 9.9990 chunk 24 optimal weight: 0.0370 chunk 4 optimal weight: 0.9990 chunk 7 optimal weight: 2.9990 chunk 25 optimal weight: 5.9990 chunk 31 optimal weight: 5.9990 chunk 35 optimal weight: 0.9980 chunk 18 optimal weight: 3.9990 overall best weight: 1.2062 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 239 HIS B 239 HIS C 138 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.128085 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.114585 restraints weight = 4028.180| |-----------------------------------------------------------------------------| r_work (start): 0.3658 rms_B_bonded: 1.78 r_work: 0.3574 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.3484 rms_B_bonded: 3.31 restraints_weight: 0.2500 r_work (final): 0.3484 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8744 moved from start: 0.2809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 3312 Z= 0.159 Angle : 0.577 6.579 4503 Z= 0.315 Chirality : 0.053 0.166 543 Planarity : 0.002 0.013 558 Dihedral : 5.986 19.969 447 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.02 % Favored : 90.98 % Rotamer: Outliers : 3.70 % Allowed : 18.52 % 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: -4.17 (0.33), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.17 (0.25), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS C 239 PHE 0.008 0.001 PHE A 213 TYR 0.020 0.001 TYR C 250 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 103 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 89 time to evaluate : 0.359 Fit side-chains REVERT: A 168 GLN cc_start: 0.8938 (mt0) cc_final: 0.8633 (mt0) REVERT: A 208 SER cc_start: 0.8544 (m) cc_final: 0.8316 (t) REVERT: A 250 TYR cc_start: 0.7391 (t80) cc_final: 0.7033 (t80) REVERT: B 178 LYS cc_start: 0.8208 (OUTLIER) cc_final: 0.7719 (ttmt) REVERT: B 180 ARG cc_start: 0.8141 (ptp-170) cc_final: 0.6024 (pmt-80) REVERT: B 190 LEU cc_start: 0.8960 (OUTLIER) cc_final: 0.8497 (tt) REVERT: B 250 TYR cc_start: 0.5940 (t80) cc_final: 0.5370 (t80) REVERT: C 180 ARG cc_start: 0.7926 (ptp-170) cc_final: 0.5609 (mmp-170) REVERT: C 246 GLU cc_start: 0.8591 (mt-10) cc_final: 0.7963 (mm-30) REVERT: C 250 TYR cc_start: 0.7810 (t80) cc_final: 0.7422 (t80) outliers start: 14 outliers final: 5 residues processed: 91 average time/residue: 1.1803 time to fit residues: 110.3944 Evaluate side-chains 86 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 79 time to evaluate : 0.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain B residue 134 SER Chi-restraints excluded: chain B residue 178 LYS 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 26 optimal weight: 10.0000 chunk 9 optimal weight: 8.9990 chunk 15 optimal weight: 7.9990 chunk 28 optimal weight: 4.9990 chunk 6 optimal weight: 10.0000 chunk 38 optimal weight: 0.5980 chunk 10 optimal weight: 2.9990 chunk 34 optimal weight: 7.9990 chunk 37 optimal weight: 2.9990 chunk 20 optimal weight: 0.2980 chunk 29 optimal weight: 5.9990 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 168 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.123904 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.110112 restraints weight = 4029.723| |-----------------------------------------------------------------------------| r_work (start): 0.3590 rms_B_bonded: 1.78 r_work: 0.3505 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.3413 rms_B_bonded: 3.24 restraints_weight: 0.2500 r_work (final): 0.3413 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8799 moved from start: 0.2654 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= 0.259 Angle : 0.609 6.542 4503 Z= 0.338 Chirality : 0.053 0.184 543 Planarity : 0.002 0.014 558 Dihedral : 6.127 21.217 447 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.53 % Favored : 88.47 % Rotamer: Outliers : 3.44 % Allowed : 19.58 % Favored : 76.98 % 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: -4.16 (0.33), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.16 (0.25), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS C 239 PHE 0.010 0.001 PHE A 213 TYR 0.020 0.002 TYR B 143 ARG 0.001 0.000 ARG A 140 *********************** 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 to be fit. rotamer outliers: 13 poor density : 80 time to evaluate : 0.555 Fit side-chains REVERT: A 168 GLN cc_start: 0.8940 (mt0) cc_final: 0.8643 (mt0) REVERT: A 208 SER cc_start: 0.8550 (m) cc_final: 0.8341 (t) REVERT: A 217 ILE cc_start: 0.8705 (OUTLIER) cc_final: 0.8225 (mt) REVERT: A 250 TYR cc_start: 0.7599 (t80) cc_final: 0.7105 (t80) REVERT: B 178 LYS cc_start: 0.8325 (OUTLIER) cc_final: 0.7834 (ttmt) REVERT: B 180 ARG cc_start: 0.8214 (ptp-170) cc_final: 0.6093 (pmt-80) REVERT: B 190 LEU cc_start: 0.8881 (OUTLIER) cc_final: 0.8427 (tt) REVERT: B 250 TYR cc_start: 0.5795 (t80) cc_final: 0.5278 (t80) REVERT: C 250 TYR cc_start: 0.7996 (t80) cc_final: 0.7605 (t80) outliers start: 13 outliers final: 6 residues processed: 85 average time/residue: 1.3314 time to fit residues: 116.2421 Evaluate side-chains 85 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 76 time to evaluate : 0.388 ------------------------------------------------------------------------------- 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 B residue 134 SER Chi-restraints excluded: chain B residue 178 LYS 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 17 optimal weight: 1.9990 chunk 16 optimal weight: 7.9990 chunk 5 optimal weight: 7.9990 chunk 13 optimal weight: 0.7980 chunk 38 optimal weight: 6.9990 chunk 1 optimal weight: 5.9990 chunk 29 optimal weight: 3.9990 chunk 26 optimal weight: 9.9990 chunk 32 optimal weight: 5.9990 chunk 18 optimal weight: 2.9990 chunk 11 optimal weight: 0.7980 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 168 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.124701 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.110756 restraints weight = 4075.123| |-----------------------------------------------------------------------------| r_work (start): 0.3609 rms_B_bonded: 1.82 r_work: 0.3524 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.3433 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.3433 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8787 moved from start: 0.2809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 3312 Z= 0.237 Angle : 0.627 8.163 4503 Z= 0.341 Chirality : 0.055 0.185 543 Planarity : 0.002 0.015 558 Dihedral : 6.092 21.033 447 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.53 % Favored : 89.47 % Rotamer: Outliers : 3.17 % Allowed : 19.84 % Favored : 76.98 % 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 0.001 HIS C 239 PHE 0.007 0.001 PHE A 213 TYR 0.019 0.002 TYR B 143 ARG 0.001 0.000 ARG A 140 *********************** 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 88 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 76 time to evaluate : 0.365 Fit side-chains REVERT: A 168 GLN cc_start: 0.8924 (mt0) cc_final: 0.8605 (mt0) REVERT: A 208 SER cc_start: 0.8549 (m) cc_final: 0.8329 (t) REVERT: B 178 LYS cc_start: 0.8310 (OUTLIER) cc_final: 0.7823 (ttmt) REVERT: B 190 LEU cc_start: 0.8882 (OUTLIER) cc_final: 0.8408 (tt) REVERT: B 212 ASP cc_start: 0.9181 (m-30) cc_final: 0.8933 (m-30) REVERT: C 178 LYS cc_start: 0.8468 (OUTLIER) cc_final: 0.7982 (ttmt) REVERT: C 180 ARG cc_start: 0.8139 (ptp-170) cc_final: 0.5624 (mmp-170) REVERT: C 246 GLU cc_start: 0.8678 (mt-10) cc_final: 0.8082 (mm-30) REVERT: C 250 TYR cc_start: 0.7928 (t80) cc_final: 0.7402 (t80) outliers start: 12 outliers final: 7 residues processed: 81 average time/residue: 1.4278 time to fit residues: 118.3302 Evaluate side-chains 83 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 73 time to evaluate : 0.352 ------------------------------------------------------------------------------- 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 B residue 134 SER Chi-restraints excluded: chain B residue 178 LYS 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 178 LYS Chi-restraints excluded: chain C residue 190 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 21 optimal weight: 0.5980 chunk 20 optimal weight: 4.9990 chunk 33 optimal weight: 6.9990 chunk 1 optimal weight: 6.9990 chunk 3 optimal weight: 8.9990 chunk 26 optimal weight: 0.0770 chunk 27 optimal weight: 4.9990 chunk 11 optimal weight: 5.9990 chunk 36 optimal weight: 2.9990 chunk 24 optimal weight: 0.9990 chunk 15 optimal weight: 4.9990 overall best weight: 1.9344 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 168 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.126015 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.112166 restraints weight = 3994.640| |-----------------------------------------------------------------------------| r_work (start): 0.3619 rms_B_bonded: 1.80 r_work: 0.3533 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.3443 rms_B_bonded: 3.29 restraints_weight: 0.2500 r_work (final): 0.3443 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8777 moved from start: 0.2864 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= 0.226 Angle : 0.631 8.470 4503 Z= 0.340 Chirality : 0.054 0.185 543 Planarity : 0.002 0.015 558 Dihedral : 6.020 20.755 447 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.53 % Favored : 88.47 % Rotamer: Outliers : 3.17 % Allowed : 20.63 % Favored : 76.19 % 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: -4.14 (0.33), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.15 (0.25), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS C 239 PHE 0.008 0.001 PHE A 213 TYR 0.022 0.002 TYR A 143 ARG 0.001 0.000 ARG B 140 ********************** 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 87 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 75 time to evaluate : 0.363 Fit side-chains REVERT: A 168 GLN cc_start: 0.8925 (mt0) cc_final: 0.8604 (mt0) REVERT: A 180 ARG cc_start: 0.8007 (OUTLIER) cc_final: 0.7408 (mtm180) REVERT: B 178 LYS cc_start: 0.8287 (OUTLIER) cc_final: 0.7796 (ttmt) REVERT: B 190 LEU cc_start: 0.8875 (OUTLIER) cc_final: 0.8404 (tt) REVERT: C 178 LYS cc_start: 0.8437 (OUTLIER) cc_final: 0.7931 (ttmt) REVERT: C 180 ARG cc_start: 0.8111 (ptp-170) cc_final: 0.5636 (mmp-170) REVERT: C 246 GLU cc_start: 0.8681 (mt-10) cc_final: 0.8081 (mm-30) REVERT: C 250 TYR cc_start: 0.7926 (t80) cc_final: 0.7403 (t80) outliers start: 12 outliers final: 7 residues processed: 79 average time/residue: 1.3490 time to fit residues: 109.2440 Evaluate side-chains 80 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 69 time to evaluate : 0.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 180 ARG 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 B residue 134 SER Chi-restraints excluded: chain B residue 178 LYS 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 178 LYS Chi-restraints excluded: chain C residue 190 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 4 optimal weight: 9.9990 chunk 36 optimal weight: 4.9990 chunk 3 optimal weight: 4.9990 chunk 13 optimal weight: 8.9990 chunk 0 optimal weight: 6.9990 chunk 30 optimal weight: 3.9990 chunk 38 optimal weight: 2.9990 chunk 7 optimal weight: 3.9990 chunk 35 optimal weight: 6.9990 chunk 23 optimal weight: 2.9990 chunk 19 optimal weight: 7.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 138 GLN C 168 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.120295 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.106445 restraints weight = 4133.731| |-----------------------------------------------------------------------------| r_work (start): 0.3546 rms_B_bonded: 1.81 r_work: 0.3457 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.3366 rms_B_bonded: 3.26 restraints_weight: 0.2500 r_work (final): 0.3366 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8834 moved from start: 0.2695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.042 3312 Z= 0.388 Angle : 0.703 8.920 4503 Z= 0.380 Chirality : 0.056 0.207 543 Planarity : 0.002 0.016 558 Dihedral : 6.484 23.577 447 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.28 % Favored : 88.72 % Rotamer: Outliers : 2.91 % Allowed : 21.16 % Favored : 75.93 % 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: -4.17 (0.33), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.17 (0.25), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS C 239 PHE 0.010 0.001 PHE A 213 TYR 0.024 0.002 TYR B 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: 2934.66 seconds wall clock time: 52 minutes 25.99 seconds (3145.99 seconds total)