Starting phenix.real_space_refine on Thu Nov 14 05:22:07 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9jsw_61785/11_2024/9jsw_61785.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9jsw_61785/11_2024/9jsw_61785.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=1.94 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9jsw_61785/11_2024/9jsw_61785.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9jsw_61785/11_2024/9jsw_61785.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9jsw_61785/11_2024/9jsw_61785.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9jsw_61785/11_2024/9jsw_61785.cif" } resolution = 1.94 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= 0.003 sd= 0.020 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: 5 Type Number sf(0) Gaussians S 8 5.16 5 C 1440 2.51 5 N 368 2.21 5 O 360 1.98 5 H 2128 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 4304 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 538 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 538 Classifications: {'peptide': 35} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 1, 'TRANS': 33} Chain: "B" Number of atoms: 538 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 538 Classifications: {'peptide': 35} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 1, 'TRANS': 33} Chain: "C" Number of atoms: 538 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 538 Classifications: {'peptide': 35} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 1, 'TRANS': 33} Chain: "D" Number of atoms: 538 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 538 Classifications: {'peptide': 35} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 1, 'TRANS': 33} Chain: "E" Number of atoms: 538 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 538 Classifications: {'peptide': 35} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 1, 'TRANS': 33} Chain: "F" Number of atoms: 538 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 538 Classifications: {'peptide': 35} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 1, 'TRANS': 33} Chain: "G" Number of atoms: 538 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 538 Classifications: {'peptide': 35} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 1, 'TRANS': 33} Chain: "H" Number of atoms: 538 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 538 Classifications: {'peptide': 35} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 1, 'TRANS': 33} Time building chain proxies: 2.61, per 1000 atoms: 0.61 Number of scatterers: 4304 At special positions: 0 Unit cell: (79.9344, 65.0016, 49.1904, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 8 16.00 O 360 8.00 N 368 7.00 C 1440 6.00 H 2128 1.00 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: 1.18 Conformation dependent library (CDL) restraints added in 386.2 milliseconds 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 448 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 4 sheets defined 0.0% alpha, 77.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.33 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 149 through 164 Processing sheet with id=AA2, first strand: chain 'A' and resid 167 through 179 removed outlier: 6.791A pdb=" N LEU B 170 " --> pdb=" O GLY A 169 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N SER A 171 " --> pdb=" O LEU B 170 " (cutoff:3.500A) removed outlier: 7.212A pdb=" N ILE B 172 " --> pdb=" O SER A 171 " (cutoff:3.500A) removed outlier: 7.298A pdb=" N GLY A 173 " --> pdb=" O ILE B 172 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N THR B 174 " --> pdb=" O GLY A 173 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N LEU C 170 " --> pdb=" O GLY B 169 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N SER B 171 " --> pdb=" O LEU C 170 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N ILE C 172 " --> pdb=" O SER B 171 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N GLY B 173 " --> pdb=" O ILE C 172 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N LEU D 170 " --> pdb=" O GLY C 169 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N SER C 171 " --> pdb=" O LEU D 170 " (cutoff:3.500A) removed outlier: 7.074A pdb=" N ILE D 172 " --> pdb=" O SER C 171 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N GLY C 173 " --> pdb=" O ILE D 172 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 149 through 164 Processing sheet with id=AA4, first strand: chain 'E' and resid 167 through 179 removed outlier: 6.839A pdb=" N LEU F 170 " --> pdb=" O GLY E 169 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N SER E 171 " --> pdb=" O LEU F 170 " (cutoff:3.500A) removed outlier: 7.215A pdb=" N ILE F 172 " --> pdb=" O SER E 171 " (cutoff:3.500A) removed outlier: 7.263A pdb=" N GLY E 173 " --> pdb=" O ILE F 172 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N THR F 174 " --> pdb=" O GLY E 173 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLY E 175 " --> pdb=" O THR F 174 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N LEU G 170 " --> pdb=" O GLY F 169 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N SER F 171 " --> pdb=" O LEU G 170 " (cutoff:3.500A) removed outlier: 7.144A pdb=" N ILE G 172 " --> pdb=" O SER F 171 " (cutoff:3.500A) removed outlier: 7.109A pdb=" N GLY F 173 " --> pdb=" O ILE G 172 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ARG G 176 " --> pdb=" O GLY F 175 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N LEU H 170 " --> pdb=" O GLY G 169 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N SER G 171 " --> pdb=" O LEU H 170 " (cutoff:3.500A) removed outlier: 7.051A pdb=" N ILE H 172 " --> pdb=" O SER G 171 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N GLY G 173 " --> pdb=" O ILE H 172 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ARG H 176 " --> pdb=" O GLY G 175 " (cutoff:3.500A) 133 hydrogen bonds defined for protein. 399 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: 1.45 Time building geometry restraints manager: 1.39 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.93 - 1.10: 2128 1.10 - 1.28: 296 1.28 - 1.46: 902 1.46 - 1.64: 1042 1.64 - 1.82: 16 Bond restraints: 4384 Sorted by residual: bond pdb=" CD1 TRP E 153 " pdb=" HD1 TRP E 153 " ideal model delta sigma weight residual 0.930 1.081 -0.151 2.00e-02 2.50e+03 5.68e+01 bond pdb=" N VAL B 152 " pdb=" H VAL B 152 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.66e+01 bond pdb=" CD1 TRP G 156 " pdb=" HD1 TRP G 156 " ideal model delta sigma weight residual 0.930 1.080 -0.150 2.00e-02 2.50e+03 5.66e+01 bond pdb=" CE1 TYR E 159 " pdb=" HE1 TYR E 159 " ideal model delta sigma weight residual 0.930 1.080 -0.150 2.00e-02 2.50e+03 5.66e+01 bond pdb=" CH2 TRP B 160 " pdb=" HH2 TRP B 160 " ideal model delta sigma weight residual 0.930 1.080 -0.150 2.00e-02 2.50e+03 5.66e+01 ... (remaining 4379 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.79: 5804 1.79 - 3.58: 1471 3.58 - 5.37: 364 5.37 - 7.16: 186 7.16 - 8.95: 15 Bond angle restraints: 7840 Sorted by residual: angle pdb=" N GLY B 164 " pdb=" CA GLY B 164 " pdb=" C GLY B 164 " ideal model delta sigma weight residual 111.19 120.14 -8.95 1.45e+00 4.76e-01 3.81e+01 angle pdb=" N GLY G 164 " pdb=" CA GLY G 164 " pdb=" C GLY G 164 " ideal model delta sigma weight residual 111.19 119.89 -8.70 1.45e+00 4.76e-01 3.60e+01 angle pdb=" N GLY E 164 " pdb=" CA GLY E 164 " pdb=" C GLY E 164 " ideal model delta sigma weight residual 110.74 117.89 -7.15 1.37e+00 5.33e-01 2.72e+01 angle pdb=" N GLY F 164 " pdb=" CA GLY F 164 " pdb=" C GLY F 164 " ideal model delta sigma weight residual 110.42 118.17 -7.75 1.49e+00 4.50e-01 2.71e+01 angle pdb=" N GLY C 164 " pdb=" CA GLY C 164 " pdb=" C GLY C 164 " ideal model delta sigma weight residual 111.08 119.08 -8.00 1.62e+00 3.81e-01 2.44e+01 ... (remaining 7835 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.45: 1757 13.45 - 26.90: 117 26.90 - 40.35: 33 40.35 - 53.79: 55 53.79 - 67.24: 78 Dihedral angle restraints: 2040 sinusoidal: 1032 harmonic: 1008 Sorted by residual: dihedral pdb=" CA LEU B 163 " pdb=" C LEU B 163 " pdb=" N GLY B 164 " pdb=" CA GLY B 164 " ideal model delta harmonic sigma weight residual 180.00 -153.50 -26.50 0 5.00e+00 4.00e-02 2.81e+01 dihedral pdb=" CA LEU G 163 " pdb=" C LEU G 163 " pdb=" N GLY G 164 " pdb=" CA GLY G 164 " ideal model delta harmonic sigma weight residual -180.00 -153.73 -26.27 0 5.00e+00 4.00e-02 2.76e+01 dihedral pdb=" CA TRP G 160 " pdb=" C TRP G 160 " pdb=" N GLN G 161 " pdb=" CA GLN G 161 " ideal model delta harmonic sigma weight residual 180.00 156.25 23.75 0 5.00e+00 4.00e-02 2.26e+01 ... (remaining 2037 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 185 0.060 - 0.119: 97 0.119 - 0.179: 19 0.179 - 0.239: 3 0.239 - 0.299: 8 Chirality restraints: 312 Sorted by residual: chirality pdb=" CA SER G 148 " pdb=" N SER G 148 " pdb=" C SER G 148 " pdb=" CB SER G 148 " both_signs ideal model delta sigma weight residual False 2.57 2.27 0.30 2.00e-01 2.50e+01 2.23e+00 chirality pdb=" CA SER C 148 " pdb=" N SER C 148 " pdb=" C SER C 148 " pdb=" CB SER C 148 " both_signs ideal model delta sigma weight residual False 2.57 2.27 0.30 2.00e-01 2.50e+01 2.18e+00 chirality pdb=" CA SER D 148 " pdb=" N SER D 148 " pdb=" C SER D 148 " pdb=" CB SER D 148 " both_signs ideal model delta sigma weight residual False 2.57 2.28 0.28 2.00e-01 2.50e+01 2.02e+00 ... (remaining 309 not shown) Planarity restraints: 624 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP H 160 " 0.059 2.00e-02 2.50e+03 4.39e-02 7.70e+01 pdb=" CG TRP H 160 " 0.027 2.00e-02 2.50e+03 pdb=" CD1 TRP H 160 " 0.004 2.00e-02 2.50e+03 pdb=" CD2 TRP H 160 " 0.016 2.00e-02 2.50e+03 pdb=" NE1 TRP H 160 " -0.035 2.00e-02 2.50e+03 pdb=" CE2 TRP H 160 " 0.017 2.00e-02 2.50e+03 pdb=" CE3 TRP H 160 " -0.015 2.00e-02 2.50e+03 pdb=" CZ2 TRP H 160 " 0.046 2.00e-02 2.50e+03 pdb=" CZ3 TRP H 160 " -0.027 2.00e-02 2.50e+03 pdb=" CH2 TRP H 160 " 0.009 2.00e-02 2.50e+03 pdb=" HD1 TRP H 160 " -0.001 2.00e-02 2.50e+03 pdb=" HE1 TRP H 160 " -0.112 2.00e-02 2.50e+03 pdb=" HE3 TRP H 160 " -0.027 2.00e-02 2.50e+03 pdb=" HZ2 TRP H 160 " 0.072 2.00e-02 2.50e+03 pdb=" HZ3 TRP H 160 " -0.053 2.00e-02 2.50e+03 pdb=" HH2 TRP H 160 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP H 153 " -0.100 2.00e-02 2.50e+03 4.14e-02 6.85e+01 pdb=" CG TRP H 153 " -0.025 2.00e-02 2.50e+03 pdb=" CD1 TRP H 153 " 0.000 2.00e-02 2.50e+03 pdb=" CD2 TRP H 153 " 0.029 2.00e-02 2.50e+03 pdb=" NE1 TRP H 153 " 0.025 2.00e-02 2.50e+03 pdb=" CE2 TRP H 153 " 0.012 2.00e-02 2.50e+03 pdb=" CE3 TRP H 153 " 0.049 2.00e-02 2.50e+03 pdb=" CZ2 TRP H 153 " -0.019 2.00e-02 2.50e+03 pdb=" CZ3 TRP H 153 " 0.019 2.00e-02 2.50e+03 pdb=" CH2 TRP H 153 " -0.026 2.00e-02 2.50e+03 pdb=" HD1 TRP H 153 " -0.002 2.00e-02 2.50e+03 pdb=" HE1 TRP H 153 " 0.064 2.00e-02 2.50e+03 pdb=" HE3 TRP H 153 " 0.052 2.00e-02 2.50e+03 pdb=" HZ2 TRP H 153 " -0.034 2.00e-02 2.50e+03 pdb=" HZ3 TRP H 153 " 0.012 2.00e-02 2.50e+03 pdb=" HH2 TRP H 153 " -0.056 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP C 160 " -0.047 2.00e-02 2.50e+03 3.79e-02 5.73e+01 pdb=" CG TRP C 160 " -0.032 2.00e-02 2.50e+03 pdb=" CD1 TRP C 160 " -0.015 2.00e-02 2.50e+03 pdb=" CD2 TRP C 160 " -0.007 2.00e-02 2.50e+03 pdb=" NE1 TRP C 160 " 0.024 2.00e-02 2.50e+03 pdb=" CE2 TRP C 160 " -0.009 2.00e-02 2.50e+03 pdb=" CE3 TRP C 160 " 0.022 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 160 " -0.032 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 160 " 0.018 2.00e-02 2.50e+03 pdb=" CH2 TRP C 160 " -0.007 2.00e-02 2.50e+03 pdb=" HD1 TRP C 160 " -0.003 2.00e-02 2.50e+03 pdb=" HE1 TRP C 160 " 0.103 2.00e-02 2.50e+03 pdb=" HE3 TRP C 160 " 0.033 2.00e-02 2.50e+03 pdb=" HZ2 TRP C 160 " -0.061 2.00e-02 2.50e+03 pdb=" HZ3 TRP C 160 " 0.032 2.00e-02 2.50e+03 pdb=" HH2 TRP C 160 " -0.020 2.00e-02 2.50e+03 ... (remaining 621 not shown) Histogram of nonbonded interaction distances: 1.76 - 2.33: 689 2.33 - 2.90: 8816 2.90 - 3.47: 11510 3.47 - 4.03: 16237 4.03 - 4.60: 21776 Nonbonded interactions: 59028 Sorted by model distance: nonbonded pdb="HE21 GLN B 161 " pdb=" OE1 GLN C 161 " model vdw 1.764 2.450 nonbonded pdb="HE21 GLN F 161 " pdb=" OE1 GLN G 161 " model vdw 1.770 2.450 nonbonded pdb="HE21 GLN A 161 " pdb=" OE1 GLN B 161 " model vdw 1.775 2.450 nonbonded pdb="HE21 GLN E 161 " pdb=" OE1 GLN F 161 " model vdw 1.782 2.450 nonbonded pdb="HE21 GLN G 161 " pdb=" OE1 GLN H 161 " model vdw 1.817 2.450 ... (remaining 59023 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 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } 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: 0.030 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: 0.080 Extract box with map and model: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 14.890 Find NCS groups from input model: 0.110 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:12.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8673 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 : 0.012 0.039 2256 Z= 0.793 Angle : 1.762 8.945 3072 Z= 1.166 Chirality : 0.081 0.299 312 Planarity : 0.011 0.037 360 Dihedral : 11.152 49.321 712 Min Nonbonded Distance : 2.664 Molprobity Statistics. All-atom Clashscore : 2.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % 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: -2.00 (0.42), residues: 264 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.52 (0.32), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.073 0.015 TRP B 153 HIS 0.008 0.002 HIS F 182 PHE 0.025 0.008 PHE G 149 TYR 0.039 0.012 TYR F 151 ARG 0.002 0.001 ARG C 176 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 45 time to evaluate : 0.297 Fit side-chains revert: symmetry clash REVERT: D 176 ARG cc_start: 0.6311 (ttm170) cc_final: 0.6010 (mtp180) outliers start: 0 outliers final: 0 residues processed: 45 average time/residue: 2.6358 time to fit residues: 120.9377 Evaluate side-chains 43 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 43 time to evaluate : 0.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 20 optimal weight: 10.0000 chunk 18 optimal weight: 6.9990 chunk 10 optimal weight: 5.9990 chunk 6 optimal weight: 6.9990 chunk 12 optimal weight: 6.9990 chunk 9 optimal weight: 6.9990 chunk 7 optimal weight: 5.9990 chunk 11 optimal weight: 7.9990 chunk 14 optimal weight: 7.9990 chunk 21 optimal weight: 5.9990 chunk 23 optimal weight: 9.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8771 moved from start: 0.3066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.023 2256 Z= 0.240 Angle : 0.667 4.393 3072 Z= 0.362 Chirality : 0.051 0.127 312 Planarity : 0.004 0.038 360 Dihedral : 7.368 22.296 296 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 1.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 1.39 % Allowed : 10.65 % Favored : 87.96 % 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: -1.92 (0.44), residues: 264 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.45 (0.34), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP E 153 HIS 0.002 0.001 HIS E 182 PHE 0.007 0.002 PHE C 149 TYR 0.009 0.002 TYR F 159 ARG 0.003 0.001 ARG G 176 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 44 time to evaluate : 0.352 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 176 ARG cc_start: 0.6097 (mmp-170) cc_final: 0.5674 (tpt90) outliers start: 3 outliers final: 2 residues processed: 44 average time/residue: 2.6185 time to fit residues: 117.5297 Evaluate side-chains 46 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 44 time to evaluate : 0.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 172 ILE Chi-restraints excluded: chain F residue 176 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 19 optimal weight: 10.0000 chunk 21 optimal weight: 0.7980 chunk 7 optimal weight: 10.0000 chunk 17 optimal weight: 7.9990 chunk 16 optimal weight: 1.9990 chunk 11 optimal weight: 8.9990 chunk 2 optimal weight: 20.0000 chunk 10 optimal weight: 1.9990 chunk 14 optimal weight: 5.9990 chunk 23 optimal weight: 8.9990 chunk 20 optimal weight: 7.9990 overall best weight: 3.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8740 moved from start: 0.3619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 2256 Z= 0.170 Angle : 0.566 4.628 3072 Z= 0.306 Chirality : 0.051 0.136 312 Planarity : 0.004 0.034 360 Dihedral : 6.968 20.545 296 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 0.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 0.00 % Allowed : 12.04 % Favored : 87.96 % 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: -1.69 (0.47), residues: 264 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.28 (0.36), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 153 HIS 0.001 0.000 HIS H 182 PHE 0.006 0.001 PHE C 149 TYR 0.006 0.001 TYR C 159 ARG 0.002 0.000 ARG G 176 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 44 time to evaluate : 0.344 Fit side-chains revert: symmetry clash REVERT: A 176 ARG cc_start: 0.5842 (pmt-80) cc_final: 0.4952 (ptt-90) REVERT: H 176 ARG cc_start: 0.5903 (mmp-170) cc_final: 0.5648 (tpt90) outliers start: 0 outliers final: 0 residues processed: 44 average time/residue: 2.6468 time to fit residues: 118.8402 Evaluate side-chains 44 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 44 time to evaluate : 0.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 6 optimal weight: 9.9990 chunk 19 optimal weight: 10.0000 chunk 13 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 17 optimal weight: 20.0000 chunk 9 optimal weight: 4.9990 chunk 16 optimal weight: 0.9980 chunk 11 optimal weight: 20.0000 chunk 20 optimal weight: 5.9990 chunk 5 optimal weight: 20.0000 chunk 7 optimal weight: 7.9990 overall best weight: 5.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8767 moved from start: 0.3771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 2256 Z= 0.219 Angle : 0.594 4.695 3072 Z= 0.317 Chirality : 0.050 0.138 312 Planarity : 0.004 0.031 360 Dihedral : 7.229 23.694 296 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 0.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 0.93 % Allowed : 12.50 % Favored : 86.57 % 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: -1.67 (0.47), residues: 264 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.26 (0.36), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP C 153 HIS 0.002 0.000 HIS C 182 PHE 0.008 0.002 PHE D 149 TYR 0.007 0.001 TYR B 159 ARG 0.003 0.000 ARG G 176 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 44 time to evaluate : 0.393 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 176 ARG cc_start: 0.6140 (mmp-170) cc_final: 0.5826 (tpt90) outliers start: 2 outliers final: 1 residues processed: 44 average time/residue: 2.8551 time to fit residues: 128.1464 Evaluate side-chains 45 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 44 time to evaluate : 0.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 176 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 20 optimal weight: 30.0000 chunk 4 optimal weight: 10.0000 chunk 13 optimal weight: 9.9990 chunk 5 optimal weight: 20.0000 chunk 23 optimal weight: 0.7980 chunk 19 optimal weight: 8.9990 chunk 10 optimal weight: 8.9990 chunk 1 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 chunk 12 optimal weight: 6.9990 chunk 22 optimal weight: 0.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8726 moved from start: 0.3921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 2256 Z= 0.148 Angle : 0.530 4.780 3072 Z= 0.283 Chirality : 0.050 0.136 312 Planarity : 0.003 0.029 360 Dihedral : 6.752 20.734 296 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 0.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 0.46 % Allowed : 12.50 % Favored : 87.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.71 (0.47), residues: 264 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.29 (0.36), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 153 HIS 0.001 0.000 HIS C 182 PHE 0.004 0.001 PHE C 149 TYR 0.005 0.001 TYR C 159 ARG 0.001 0.000 ARG G 176 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 43 time to evaluate : 0.284 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 178 MET cc_start: 0.7848 (mtp) cc_final: 0.7568 (mtm) REVERT: H 176 ARG cc_start: 0.6084 (mmp-170) cc_final: 0.5787 (tpt90) outliers start: 1 outliers final: 1 residues processed: 43 average time/residue: 2.2968 time to fit residues: 100.5127 Evaluate side-chains 44 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 43 time to evaluate : 0.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 176 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 2 optimal weight: 1.9990 chunk 13 optimal weight: 10.0000 chunk 16 optimal weight: 1.9990 chunk 19 optimal weight: 5.9990 chunk 12 optimal weight: 1.9990 chunk 23 optimal weight: 10.0000 chunk 14 optimal weight: 20.0000 chunk 10 optimal weight: 1.9990 chunk 9 optimal weight: 3.9990 chunk 6 optimal weight: 5.9990 chunk 4 optimal weight: 8.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8708 moved from start: 0.4048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 2256 Z= 0.152 Angle : 0.536 4.946 3072 Z= 0.282 Chirality : 0.050 0.134 312 Planarity : 0.004 0.054 360 Dihedral : 6.546 20.159 296 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 0.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 0.46 % Allowed : 12.96 % Favored : 86.57 % 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: -1.72 (0.47), residues: 264 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.30 (0.35), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 153 HIS 0.001 0.000 HIS C 182 PHE 0.004 0.001 PHE C 149 TYR 0.005 0.001 TYR C 159 ARG 0.009 0.001 ARG E 176 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 41 time to evaluate : 0.375 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 178 MET cc_start: 0.7848 (mtp) cc_final: 0.7592 (mtm) outliers start: 1 outliers final: 1 residues processed: 41 average time/residue: 2.7630 time to fit residues: 115.5443 Evaluate side-chains 42 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 41 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 176 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 4 optimal weight: 10.0000 chunk 14 optimal weight: 20.0000 chunk 15 optimal weight: 20.0000 chunk 11 optimal weight: 20.0000 chunk 2 optimal weight: 0.2980 chunk 18 optimal weight: 3.9990 chunk 21 optimal weight: 9.9990 chunk 22 optimal weight: 10.0000 chunk 20 optimal weight: 30.0000 chunk 12 optimal weight: 1.9990 chunk 9 optimal weight: 9.9990 overall best weight: 5.2588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8753 moved from start: 0.3973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 2256 Z= 0.192 Angle : 0.558 4.740 3072 Z= 0.298 Chirality : 0.050 0.139 312 Planarity : 0.004 0.044 360 Dihedral : 7.008 22.883 296 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 0.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 0.46 % Allowed : 12.50 % Favored : 87.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.72 (0.47), residues: 264 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.30 (0.36), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP F 153 HIS 0.002 0.000 HIS C 182 PHE 0.007 0.001 PHE D 149 TYR 0.006 0.001 TYR C 159 ARG 0.006 0.001 ARG E 176 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 43 time to evaluate : 0.378 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 178 MET cc_start: 0.7842 (mtp) cc_final: 0.7606 (mtm) outliers start: 1 outliers final: 1 residues processed: 43 average time/residue: 2.8310 time to fit residues: 124.0579 Evaluate side-chains 44 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 43 time to evaluate : 0.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 176 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 16 optimal weight: 9.9990 chunk 6 optimal weight: 9.9990 chunk 19 optimal weight: 5.9990 chunk 20 optimal weight: 5.9990 chunk 21 optimal weight: 10.0000 chunk 14 optimal weight: 6.9990 chunk 22 optimal weight: 1.9990 chunk 13 optimal weight: 0.9990 chunk 10 optimal weight: 9.9990 chunk 15 optimal weight: 9.9990 chunk 23 optimal weight: 10.0000 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8739 moved from start: 0.4054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 2256 Z= 0.179 Angle : 0.555 5.286 3072 Z= 0.294 Chirality : 0.050 0.136 312 Planarity : 0.004 0.053 360 Dihedral : 6.847 21.954 296 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 0.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 0.46 % Allowed : 13.43 % Favored : 86.11 % 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: -1.78 (0.46), residues: 264 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.35 (0.35), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP E 153 HIS 0.001 0.000 HIS C 182 PHE 0.007 0.001 PHE D 149 TYR 0.005 0.001 TYR B 159 ARG 0.007 0.001 ARG E 176 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 42 time to evaluate : 0.383 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 178 MET cc_start: 0.7827 (mtp) cc_final: 0.7595 (mtm) REVERT: H 176 ARG cc_start: 0.5993 (mmp-170) cc_final: 0.5409 (tpt90) outliers start: 1 outliers final: 1 residues processed: 42 average time/residue: 2.7151 time to fit residues: 116.3458 Evaluate side-chains 43 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 42 time to evaluate : 0.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 176 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 22 optimal weight: 10.0000 chunk 19 optimal weight: 4.9990 chunk 1 optimal weight: 10.0000 chunk 14 optimal weight: 30.0000 chunk 11 optimal weight: 0.7980 chunk 15 optimal weight: 10.0000 chunk 20 optimal weight: 20.0000 chunk 5 optimal weight: 20.0000 chunk 17 optimal weight: 5.9990 chunk 2 optimal weight: 6.9990 chunk 7 optimal weight: 9.9990 overall best weight: 5.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8759 moved from start: 0.4030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 2256 Z= 0.206 Angle : 0.564 5.082 3072 Z= 0.302 Chirality : 0.050 0.140 312 Planarity : 0.004 0.054 360 Dihedral : 7.109 23.951 296 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 0.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 0.46 % Allowed : 12.50 % Favored : 87.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.78 (0.47), residues: 264 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.35 (0.36), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP F 153 HIS 0.002 0.000 HIS C 182 PHE 0.008 0.001 PHE D 149 TYR 0.006 0.001 TYR B 159 ARG 0.007 0.001 ARG E 176 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 43 time to evaluate : 0.388 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 178 MET cc_start: 0.7839 (mtp) cc_final: 0.7610 (mtm) REVERT: H 176 ARG cc_start: 0.6063 (mmp-170) cc_final: 0.5479 (tpt90) outliers start: 1 outliers final: 1 residues processed: 43 average time/residue: 2.8310 time to fit residues: 123.9975 Evaluate side-chains 44 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 43 time to evaluate : 0.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 176 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 19 optimal weight: 9.9990 chunk 2 optimal weight: 8.9990 chunk 3 optimal weight: 10.0000 chunk 16 optimal weight: 4.9990 chunk 1 optimal weight: 8.9990 chunk 13 optimal weight: 0.9980 chunk 21 optimal weight: 10.0000 chunk 12 optimal weight: 9.9990 chunk 0 optimal weight: 0.9990 chunk 15 optimal weight: 3.9990 chunk 14 optimal weight: 8.9990 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8737 moved from start: 0.4093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 2256 Z= 0.168 Angle : 0.540 4.949 3072 Z= 0.287 Chirality : 0.050 0.137 312 Planarity : 0.004 0.055 360 Dihedral : 6.811 21.894 296 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 0.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 0.46 % Allowed : 13.43 % Favored : 86.11 % 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: -1.85 (0.46), residues: 264 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.40 (0.35), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 153 HIS 0.002 0.000 HIS C 182 PHE 0.006 0.001 PHE D 149 TYR 0.005 0.001 TYR B 159 ARG 0.008 0.001 ARG E 176 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 42 time to evaluate : 0.330 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 176 ARG cc_start: 0.5972 (mmp-170) cc_final: 0.5421 (tpt90) outliers start: 1 outliers final: 1 residues processed: 42 average time/residue: 2.7008 time to fit residues: 115.7578 Evaluate side-chains 43 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 42 time to evaluate : 0.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 176 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 13 optimal weight: 10.0000 chunk 9 optimal weight: 10.0000 chunk 8 optimal weight: 30.0000 chunk 23 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 4 optimal weight: 10.0000 chunk 2 optimal weight: 20.0000 chunk 5 optimal weight: 6.9990 chunk 19 optimal weight: 9.9990 chunk 22 optimal weight: 3.9990 chunk 10 optimal weight: 0.9980 overall best weight: 5.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.161435 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.125912 restraints weight = 4682.314| |-----------------------------------------------------------------------------| r_work (start): 0.3659 rms_B_bonded: 1.39 r_work: 0.3588 rms_B_bonded: 1.28 restraints_weight: 0.5000 r_work: 0.3511 rms_B_bonded: 2.02 restraints_weight: 0.2500 r_work: 0.3358 rms_B_bonded: 4.94 restraints_weight: 0.1250 r_work (final): 0.3358 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9031 moved from start: 0.4080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 2256 Z= 0.211 Angle : 0.575 5.403 3072 Z= 0.305 Chirality : 0.050 0.141 312 Planarity : 0.005 0.056 360 Dihedral : 7.085 23.669 296 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 0.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 0.46 % Allowed : 13.89 % Favored : 85.65 % 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: -1.86 (0.46), residues: 264 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.41 (0.35), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP F 153 HIS 0.002 0.000 HIS C 182 PHE 0.008 0.001 PHE D 149 TYR 0.006 0.001 TYR B 159 ARG 0.007 0.001 ARG E 176 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3032.09 seconds wall clock time: 55 minutes 40.67 seconds (3340.67 seconds total)