Starting phenix.real_space_refine on Thu Nov 14 04:22:44 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9jsu_61783/11_2024/9jsu_61783.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9jsu_61783/11_2024/9jsu_61783.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=1.79 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9jsu_61783/11_2024/9jsu_61783.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9jsu_61783/11_2024/9jsu_61783.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9jsu_61783/11_2024/9jsu_61783.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9jsu_61783/11_2024/9jsu_61783.cif" } resolution = 1.79 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.006 sd= 0.050 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 1336 2.51 5 N 352 2.21 5 O 344 1.98 5 H 2000 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 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: 4040 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 505 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 505 Classifications: {'peptide': 33} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'TRANS': 31} Chain: "B" Number of atoms: 505 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 505 Classifications: {'peptide': 33} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'TRANS': 31} Chain: "C" Number of atoms: 505 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 505 Classifications: {'peptide': 33} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'TRANS': 31} Chain: "D" Number of atoms: 505 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 505 Classifications: {'peptide': 33} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'TRANS': 31} Chain: "E" Number of atoms: 505 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 505 Classifications: {'peptide': 33} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'TRANS': 31} Chain: "F" Number of atoms: 505 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 505 Classifications: {'peptide': 33} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'TRANS': 31} Chain: "G" Number of atoms: 505 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 505 Classifications: {'peptide': 33} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'TRANS': 31} Chain: "H" Number of atoms: 505 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 505 Classifications: {'peptide': 33} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'TRANS': 31} Time building chain proxies: 2.54, per 1000 atoms: 0.63 Number of scatterers: 4040 At special positions: 0 Unit cell: (71.1504, 76.4208, 38.6496, 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 344 8.00 N 352 7.00 C 1336 6.00 H 2000 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: 1.05 Conformation dependent library (CDL) restraints added in 280.5 milliseconds 496 Ramachandran restraints generated. 248 Oldfield, 0 Emsley, 248 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 416 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 4 sheets defined 0.0% alpha, 66.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.29 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 152 through 162 removed outlier: 6.366A pdb=" N TRP A 153 " --> pdb=" O LYS B 154 " (cutoff:3.500A) removed outlier: 7.895A pdb=" N TRP B 156 " --> pdb=" O TRP A 153 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N THR A 155 " --> pdb=" O TRP B 156 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N GLN B 158 " --> pdb=" O THR A 155 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N GLY A 157 " --> pdb=" O GLN B 158 " (cutoff:3.500A) removed outlier: 7.929A pdb=" N TRP B 160 " --> pdb=" O GLY A 157 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N TYR A 159 " --> pdb=" O TRP B 160 " (cutoff:3.500A) removed outlier: 7.554A pdb=" N VAL B 162 " --> pdb=" O TYR A 159 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N GLN A 161 " --> pdb=" O VAL B 162 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 167 through 179 removed outlier: 8.759A pdb=" N SER A 168 " --> pdb=" O GLY B 169 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N SER B 171 " --> pdb=" O SER A 168 " (cutoff:3.500A) removed outlier: 8.878A pdb=" N LEU A 170 " --> pdb=" O SER B 171 " (cutoff:3.500A) removed outlier: 10.384A pdb=" N GLY B 173 " --> pdb=" O LEU A 170 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N ILE A 172 " --> pdb=" O GLY B 173 " (cutoff:3.500A) removed outlier: 7.721A pdb=" N GLY B 175 " --> pdb=" O ILE A 172 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N THR A 174 " --> pdb=" O GLY B 175 " (cutoff:3.500A) removed outlier: 7.979A pdb=" N ALA B 177 " --> pdb=" O THR A 174 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N ARG A 176 " --> pdb=" O ALA B 177 " (cutoff:3.500A) removed outlier: 7.864A pdb=" N LEU B 179 " --> pdb=" O ARG A 176 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N MET A 178 " --> pdb=" O LEU B 179 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N LEU B 170 " --> pdb=" O GLY C 169 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N SER C 171 " --> pdb=" O LEU B 170 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N ILE B 172 " --> pdb=" O SER C 171 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N GLY C 173 " --> pdb=" O ILE B 172 " (cutoff:3.500A) removed outlier: 8.756A pdb=" N SER C 168 " --> pdb=" O GLY D 169 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N SER D 171 " --> pdb=" O SER C 168 " (cutoff:3.500A) removed outlier: 8.969A pdb=" N LEU C 170 " --> pdb=" O SER D 171 " (cutoff:3.500A) removed outlier: 10.410A pdb=" N GLY D 173 " --> pdb=" O LEU C 170 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N ILE C 172 " --> pdb=" O GLY D 173 " (cutoff:3.500A) removed outlier: 7.812A pdb=" N GLY D 175 " --> pdb=" O ILE C 172 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N THR C 174 " --> pdb=" O GLY D 175 " (cutoff:3.500A) removed outlier: 7.908A pdb=" N ALA D 177 " --> pdb=" O THR C 174 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N ARG C 176 " --> pdb=" O ALA D 177 " (cutoff:3.500A) removed outlier: 7.862A pdb=" N LEU D 179 " --> pdb=" O ARG C 176 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N MET C 178 " --> pdb=" O LEU D 179 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 152 through 162 removed outlier: 6.345A pdb=" N TRP E 153 " --> pdb=" O LYS F 154 " (cutoff:3.500A) removed outlier: 7.900A pdb=" N TRP F 156 " --> pdb=" O TRP E 153 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N THR E 155 " --> pdb=" O TRP F 156 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N GLN F 158 " --> pdb=" O THR E 155 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N GLY E 157 " --> pdb=" O GLN F 158 " (cutoff:3.500A) removed outlier: 7.910A pdb=" N TRP F 160 " --> pdb=" O GLY E 157 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N TYR E 159 " --> pdb=" O TRP F 160 " (cutoff:3.500A) removed outlier: 7.545A pdb=" N VAL F 162 " --> pdb=" O TYR E 159 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N GLN E 161 " --> pdb=" O VAL F 162 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 167 through 179 removed outlier: 8.749A pdb=" N SER E 168 " --> pdb=" O GLY F 169 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N SER F 171 " --> pdb=" O SER E 168 " (cutoff:3.500A) removed outlier: 8.888A pdb=" N LEU E 170 " --> pdb=" O SER F 171 " (cutoff:3.500A) removed outlier: 10.352A pdb=" N GLY F 173 " --> pdb=" O LEU E 170 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N ILE E 172 " --> pdb=" O GLY F 173 " (cutoff:3.500A) removed outlier: 7.695A pdb=" N GLY F 175 " --> pdb=" O ILE E 172 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N THR E 174 " --> pdb=" O GLY F 175 " (cutoff:3.500A) removed outlier: 7.892A pdb=" N ALA F 177 " --> pdb=" O THR E 174 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N ARG E 176 " --> pdb=" O ALA F 177 " (cutoff:3.500A) removed outlier: 7.871A pdb=" N LEU F 179 " --> pdb=" O ARG E 176 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N MET E 178 " --> pdb=" O LEU F 179 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N LEU F 170 " --> pdb=" O GLY G 169 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N SER G 171 " --> pdb=" O LEU F 170 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N ILE F 172 " --> pdb=" O SER G 171 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N GLY G 173 " --> pdb=" O ILE F 172 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N LEU G 170 " --> pdb=" O GLY H 169 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N SER H 171 " --> pdb=" O LEU G 170 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N ILE G 172 " --> pdb=" O SER H 171 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N GLY H 173 " --> pdb=" O ILE G 172 " (cutoff:3.500A) 64 hydrogen bonds defined for protein. 192 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: 1.64 Time building geometry restraints manager: 1.27 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.95 - 1.12: 2000 1.12 - 1.30: 289 1.30 - 1.47: 919 1.47 - 1.64: 888 1.64 - 1.81: 16 Bond restraints: 4112 Sorted by residual: bond pdb=" CZ3 TRP C 153 " pdb=" HZ3 TRP C 153 " ideal model delta sigma weight residual 0.930 1.081 -0.151 2.00e-02 2.50e+03 5.67e+01 bond pdb=" N MET D 178 " pdb=" H MET D 178 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.66e+01 bond pdb=" N TRP F 153 " pdb=" H TRP F 153 " ideal model delta sigma weight residual 0.860 1.010 -0.150 2.00e-02 2.50e+03 5.66e+01 bond pdb=" N LYS F 154 " pdb=" H LYS F 154 " ideal model delta sigma weight residual 0.860 1.010 -0.150 2.00e-02 2.50e+03 5.66e+01 bond pdb=" CD1 TRP F 153 " pdb=" HD1 TRP F 153 " ideal model delta sigma weight residual 0.930 1.080 -0.150 2.00e-02 2.50e+03 5.66e+01 ... (remaining 4107 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.55: 5068 1.55 - 3.09: 1588 3.09 - 4.64: 383 4.64 - 6.18: 261 6.18 - 7.73: 60 Bond angle restraints: 7360 Sorted by residual: angle pdb=" N GLY G 175 " pdb=" CA GLY G 175 " pdb=" C GLY G 175 " ideal model delta sigma weight residual 110.58 118.31 -7.73 1.35e+00 5.49e-01 3.27e+01 angle pdb=" N GLY C 175 " pdb=" CA GLY C 175 " pdb=" C GLY C 175 " ideal model delta sigma weight residual 110.58 117.98 -7.40 1.35e+00 5.49e-01 3.01e+01 angle pdb=" N GLY B 175 " pdb=" CA GLY B 175 " pdb=" C GLY B 175 " ideal model delta sigma weight residual 110.45 117.52 -7.07 1.30e+00 5.92e-01 2.96e+01 angle pdb=" N GLY F 175 " pdb=" CA GLY F 175 " pdb=" C GLY F 175 " ideal model delta sigma weight residual 110.45 117.43 -6.98 1.30e+00 5.92e-01 2.88e+01 angle pdb=" OE1 GLN H 158 " pdb=" CD GLN H 158 " pdb=" NE2 GLN H 158 " ideal model delta sigma weight residual 122.60 118.28 4.32 1.00e+00 1.00e+00 1.86e+01 ... (remaining 7355 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.02: 1663 14.02 - 28.04: 105 28.04 - 42.06: 41 42.06 - 56.08: 43 56.08 - 70.10: 52 Dihedral angle restraints: 1904 sinusoidal: 984 harmonic: 920 Sorted by residual: dihedral pdb=" CA TRP H 160 " pdb=" C TRP H 160 " pdb=" N GLN H 161 " pdb=" CA GLN H 161 " ideal model delta harmonic sigma weight residual 180.00 156.43 23.57 0 5.00e+00 4.00e-02 2.22e+01 dihedral pdb=" CA TRP E 160 " pdb=" C TRP E 160 " pdb=" N GLN E 161 " pdb=" CA GLN E 161 " ideal model delta harmonic sigma weight residual 180.00 156.78 23.22 0 5.00e+00 4.00e-02 2.16e+01 dihedral pdb=" CA TRP D 160 " pdb=" C TRP D 160 " pdb=" N GLN D 161 " pdb=" CA GLN D 161 " ideal model delta harmonic sigma weight residual 180.00 156.79 23.21 0 5.00e+00 4.00e-02 2.15e+01 ... (remaining 1901 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 103 0.039 - 0.077: 93 0.077 - 0.116: 72 0.116 - 0.155: 24 0.155 - 0.193: 4 Chirality restraints: 296 Sorted by residual: chirality pdb=" CA THR G 183 " pdb=" N THR G 183 " pdb=" C THR G 183 " pdb=" CB THR G 183 " both_signs ideal model delta sigma weight residual False 2.53 2.33 0.19 2.00e-01 2.50e+01 9.34e-01 chirality pdb=" CA THR C 183 " pdb=" N THR C 183 " pdb=" C THR C 183 " pdb=" CB THR C 183 " both_signs ideal model delta sigma weight residual False 2.53 2.34 0.19 2.00e-01 2.50e+01 8.86e-01 chirality pdb=" CA THR B 183 " pdb=" N THR B 183 " pdb=" C THR B 183 " pdb=" CB THR B 183 " both_signs ideal model delta sigma weight residual False 2.53 2.34 0.19 2.00e-01 2.50e+01 8.63e-01 ... (remaining 293 not shown) Planarity restraints: 584 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 153 " 0.076 2.00e-02 2.50e+03 3.26e-02 4.24e+01 pdb=" CG TRP A 153 " 0.001 2.00e-02 2.50e+03 pdb=" CD1 TRP A 153 " -0.003 2.00e-02 2.50e+03 pdb=" CD2 TRP A 153 " -0.041 2.00e-02 2.50e+03 pdb=" NE1 TRP A 153 " -0.030 2.00e-02 2.50e+03 pdb=" CE2 TRP A 153 " -0.026 2.00e-02 2.50e+03 pdb=" CE3 TRP A 153 " -0.046 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 153 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 153 " -0.015 2.00e-02 2.50e+03 pdb=" CH2 TRP A 153 " 0.014 2.00e-02 2.50e+03 pdb=" HD1 TRP A 153 " 0.028 2.00e-02 2.50e+03 pdb=" HE1 TRP A 153 " -0.021 2.00e-02 2.50e+03 pdb=" HE3 TRP A 153 " -0.027 2.00e-02 2.50e+03 pdb=" HZ2 TRP A 153 " 0.024 2.00e-02 2.50e+03 pdb=" HZ3 TRP A 153 " 0.015 2.00e-02 2.50e+03 pdb=" HH2 TRP A 153 " 0.052 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 160 " -0.035 2.00e-02 2.50e+03 3.14e-02 3.94e+01 pdb=" CG TRP A 160 " -0.027 2.00e-02 2.50e+03 pdb=" CD1 TRP A 160 " 0.000 2.00e-02 2.50e+03 pdb=" CD2 TRP A 160 " -0.033 2.00e-02 2.50e+03 pdb=" NE1 TRP A 160 " 0.012 2.00e-02 2.50e+03 pdb=" CE2 TRP A 160 " -0.027 2.00e-02 2.50e+03 pdb=" CE3 TRP A 160 " 0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 160 " -0.032 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 160 " 0.025 2.00e-02 2.50e+03 pdb=" CH2 TRP A 160 " -0.006 2.00e-02 2.50e+03 pdb=" HD1 TRP A 160 " 0.029 2.00e-02 2.50e+03 pdb=" HE1 TRP A 160 " 0.071 2.00e-02 2.50e+03 pdb=" HE3 TRP A 160 " 0.020 2.00e-02 2.50e+03 pdb=" HZ2 TRP A 160 " -0.037 2.00e-02 2.50e+03 pdb=" HZ3 TRP A 160 " 0.049 2.00e-02 2.50e+03 pdb=" HH2 TRP A 160 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP E 160 " -0.034 2.00e-02 2.50e+03 3.02e-02 3.65e+01 pdb=" CG TRP E 160 " -0.032 2.00e-02 2.50e+03 pdb=" CD1 TRP E 160 " 0.002 2.00e-02 2.50e+03 pdb=" CD2 TRP E 160 " -0.033 2.00e-02 2.50e+03 pdb=" NE1 TRP E 160 " 0.011 2.00e-02 2.50e+03 pdb=" CE2 TRP E 160 " -0.029 2.00e-02 2.50e+03 pdb=" CE3 TRP E 160 " 0.008 2.00e-02 2.50e+03 pdb=" CZ2 TRP E 160 " -0.027 2.00e-02 2.50e+03 pdb=" CZ3 TRP E 160 " 0.021 2.00e-02 2.50e+03 pdb=" CH2 TRP E 160 " -0.006 2.00e-02 2.50e+03 pdb=" HD1 TRP E 160 " 0.026 2.00e-02 2.50e+03 pdb=" HE1 TRP E 160 " 0.070 2.00e-02 2.50e+03 pdb=" HE3 TRP E 160 " 0.028 2.00e-02 2.50e+03 pdb=" HZ2 TRP E 160 " -0.033 2.00e-02 2.50e+03 pdb=" HZ3 TRP E 160 " 0.040 2.00e-02 2.50e+03 pdb=" HH2 TRP E 160 " -0.010 2.00e-02 2.50e+03 ... (remaining 581 not shown) Histogram of nonbonded interaction distances: 1.81 - 2.36: 852 2.36 - 2.92: 8389 2.92 - 3.48: 10759 3.48 - 4.04: 15237 4.04 - 4.60: 20099 Nonbonded interactions: 55336 Sorted by model distance: nonbonded pdb=" HE3 MET B 178 " pdb=" HE ARG C 176 " model vdw 1.806 2.270 nonbonded pdb=" O THR C 183 " pdb=" HG1 THR D 183 " model vdw 1.816 2.450 nonbonded pdb=" O THR F 183 " pdb=" HG1 THR G 183 " model vdw 1.817 2.450 nonbonded pdb=" O THR B 183 " pdb=" HG1 THR C 183 " model vdw 1.819 2.450 nonbonded pdb=" H LEU F 163 " pdb=" O VAL G 162 " model vdw 1.820 2.450 ... (remaining 55331 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: 0.040 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: 0.090 Extract box with map and model: 0.180 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 14.380 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6900 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 0.041 2112 Z= 0.782 Angle : 1.698 7.725 2880 Z= 1.106 Chirality : 0.073 0.193 296 Planarity : 0.010 0.052 336 Dihedral : 11.861 65.051 672 Min Nonbonded Distance : 2.673 Molprobity Statistics. All-atom Clashscore : 0.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 100.00 % 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: -2.92 (0.33), residues: 248 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.22 (0.25), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.054 0.013 TRP A 153 HIS 0.006 0.002 HIS D 182 TYR 0.035 0.007 TYR E 159 ARG 0.002 0.000 ARG H 176 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 496 Ramachandran restraints generated. 248 Oldfield, 0 Emsley, 248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 496 Ramachandran restraints generated. 248 Oldfield, 0 Emsley, 248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 51 time to evaluate : 0.354 Fit side-chains revert: symmetry clash REVERT: A 154 LYS cc_start: 0.7602 (mttt) cc_final: 0.7300 (mttt) REVERT: A 178 MET cc_start: 0.7652 (mtm) cc_final: 0.7252 (mtp) REVERT: B 152 VAL cc_start: 0.7749 (t) cc_final: 0.7504 (p) REVERT: B 154 LYS cc_start: 0.7397 (mttt) cc_final: 0.7063 (mttt) REVERT: B 163 LEU cc_start: 0.7973 (mt) cc_final: 0.7677 (mm) REVERT: B 176 ARG cc_start: 0.7080 (mtp85) cc_final: 0.6726 (mtm180) REVERT: C 154 LYS cc_start: 0.7334 (mttt) cc_final: 0.6999 (mtpt) REVERT: C 176 ARG cc_start: 0.7075 (mtp180) cc_final: 0.6833 (mtm180) REVERT: D 152 VAL cc_start: 0.7528 (t) cc_final: 0.7167 (p) REVERT: D 176 ARG cc_start: 0.7319 (mtp85) cc_final: 0.7080 (ttm170) REVERT: D 178 MET cc_start: 0.7814 (mtm) cc_final: 0.7433 (mtp) REVERT: E 154 LYS cc_start: 0.7572 (mttt) cc_final: 0.7290 (mttt) REVERT: E 178 MET cc_start: 0.7633 (mtm) cc_final: 0.7205 (mtp) REVERT: F 154 LYS cc_start: 0.7448 (mttt) cc_final: 0.7200 (mttt) REVERT: F 163 LEU cc_start: 0.8005 (mt) cc_final: 0.7701 (mm) REVERT: F 176 ARG cc_start: 0.7109 (mtp85) cc_final: 0.6685 (mtm180) REVERT: G 154 LYS cc_start: 0.7406 (mttt) cc_final: 0.7090 (mtpt) REVERT: G 176 ARG cc_start: 0.7209 (mtp85) cc_final: 0.6967 (ttm170) REVERT: H 152 VAL cc_start: 0.7601 (t) cc_final: 0.7228 (p) REVERT: H 178 MET cc_start: 0.7840 (mtm) cc_final: 0.7399 (mtp) outliers start: 0 outliers final: 0 residues processed: 51 average time/residue: 1.8674 time to fit residues: 97.1568 Evaluate side-chains 47 residues out of total 200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 47 time to evaluate : 0.330 ------------------------------------------------------------------------------- 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: 7.9990 chunk 18 optimal weight: 6.9990 chunk 10 optimal weight: 5.9990 chunk 6 optimal weight: 5.9990 chunk 12 optimal weight: 5.9990 chunk 9 optimal weight: 6.9990 chunk 7 optimal weight: 5.9990 chunk 11 optimal weight: 10.0000 chunk 14 optimal weight: 6.9990 chunk 21 optimal weight: 5.9990 chunk 23 optimal weight: 5.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- 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: 0.6977 moved from start: 0.2268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 2112 Z= 0.188 Angle : 0.597 4.814 2880 Z= 0.308 Chirality : 0.047 0.148 296 Planarity : 0.004 0.022 336 Dihedral : 6.924 19.357 280 Min Nonbonded Distance : 2.693 Molprobity Statistics. All-atom Clashscore : 2.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 100.00 % 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: -3.00 (0.33), residues: 248 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.28 (0.25), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP G 160 HIS 0.003 0.001 HIS A 182 TYR 0.005 0.001 TYR A 151 ARG 0.001 0.000 ARG E 176 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 496 Ramachandran restraints generated. 248 Oldfield, 0 Emsley, 248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 496 Ramachandran restraints generated. 248 Oldfield, 0 Emsley, 248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 47 time to evaluate : 0.322 Fit side-chains REVERT: A 154 LYS cc_start: 0.7676 (mttt) cc_final: 0.7363 (mttt) REVERT: A 178 MET cc_start: 0.7707 (mtm) cc_final: 0.7289 (mtp) REVERT: B 154 LYS cc_start: 0.7345 (mttt) cc_final: 0.7062 (mttt) REVERT: B 176 ARG cc_start: 0.7005 (mtp85) cc_final: 0.6696 (mtm180) REVERT: C 154 LYS cc_start: 0.7177 (mttt) cc_final: 0.6855 (mtpt) REVERT: C 176 ARG cc_start: 0.7115 (mtp180) cc_final: 0.6827 (mtm180) REVERT: D 152 VAL cc_start: 0.7434 (t) cc_final: 0.7065 (p) REVERT: D 178 MET cc_start: 0.7781 (mtm) cc_final: 0.7402 (mtp) REVERT: E 154 LYS cc_start: 0.7662 (mttt) cc_final: 0.7381 (mttt) REVERT: E 176 ARG cc_start: 0.7058 (mtp85) cc_final: 0.6828 (mtm180) REVERT: E 178 MET cc_start: 0.7747 (mtm) cc_final: 0.7334 (mtp) REVERT: F 154 LYS cc_start: 0.7377 (mttt) cc_final: 0.7165 (mttt) REVERT: F 176 ARG cc_start: 0.6952 (mtp85) cc_final: 0.6565 (mtm180) REVERT: G 154 LYS cc_start: 0.7180 (mttt) cc_final: 0.6883 (mtpt) REVERT: G 176 ARG cc_start: 0.7069 (mtp85) cc_final: 0.6700 (ttm170) REVERT: H 178 MET cc_start: 0.7781 (mtm) cc_final: 0.7377 (mtp) outliers start: 0 outliers final: 0 residues processed: 47 average time/residue: 2.7307 time to fit residues: 130.5260 Evaluate side-chains 46 residues out of total 200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 46 time to evaluate : 0.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 19 optimal weight: 5.9990 chunk 21 optimal weight: 10.0000 chunk 7 optimal weight: 9.9990 chunk 17 optimal weight: 9.9990 chunk 16 optimal weight: 5.9990 chunk 11 optimal weight: 9.9990 chunk 2 optimal weight: 10.0000 chunk 10 optimal weight: 4.9990 chunk 14 optimal weight: 2.9990 chunk 23 optimal weight: 8.9990 chunk 20 optimal weight: 0.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- 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: 0.6974 moved from start: 0.2907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 2112 Z= 0.151 Angle : 0.527 3.817 2880 Z= 0.276 Chirality : 0.046 0.137 296 Planarity : 0.004 0.022 336 Dihedral : 6.517 18.231 280 Min Nonbonded Distance : 2.696 Molprobity Statistics. All-atom Clashscore : 1.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 0.00 % Allowed : 6.50 % Favored : 93.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 100.00 % 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: -3.06 (0.33), residues: 248 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.33 (0.26), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 153 HIS 0.001 0.000 HIS A 182 TYR 0.005 0.001 TYR G 151 ARG 0.001 0.000 ARG H 176 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 496 Ramachandran restraints generated. 248 Oldfield, 0 Emsley, 248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 496 Ramachandran restraints generated. 248 Oldfield, 0 Emsley, 248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 47 time to evaluate : 0.344 Fit side-chains REVERT: A 154 LYS cc_start: 0.7737 (mttt) cc_final: 0.7445 (mttt) REVERT: A 178 MET cc_start: 0.7779 (mtm) cc_final: 0.7290 (mtp) REVERT: B 154 LYS cc_start: 0.7347 (mttt) cc_final: 0.7059 (mttt) REVERT: B 176 ARG cc_start: 0.6970 (mtp85) cc_final: 0.6711 (mtm180) REVERT: C 154 LYS cc_start: 0.7191 (mttt) cc_final: 0.6890 (mtpt) REVERT: D 152 VAL cc_start: 0.7384 (t) cc_final: 0.7001 (p) REVERT: D 178 MET cc_start: 0.7702 (mtm) cc_final: 0.7367 (mtp) REVERT: E 154 LYS cc_start: 0.7689 (mttt) cc_final: 0.7401 (mttt) REVERT: E 176 ARG cc_start: 0.7118 (mtp85) cc_final: 0.6890 (mtm180) REVERT: E 178 MET cc_start: 0.7774 (mtm) cc_final: 0.7569 (mtp) REVERT: F 154 LYS cc_start: 0.7383 (mttt) cc_final: 0.7172 (mttt) REVERT: F 176 ARG cc_start: 0.6884 (mtp85) cc_final: 0.6672 (ttm170) REVERT: G 154 LYS cc_start: 0.7171 (mttt) cc_final: 0.6860 (mtpt) REVERT: G 176 ARG cc_start: 0.7040 (mtp85) cc_final: 0.6703 (ttm170) REVERT: H 178 MET cc_start: 0.7756 (mtm) cc_final: 0.7375 (mtp) outliers start: 0 outliers final: 0 residues processed: 47 average time/residue: 2.8356 time to fit residues: 135.5451 Evaluate side-chains 46 residues out of total 200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 46 time to evaluate : 0.358 ------------------------------------------------------------------------------- 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: 20.0000 chunk 19 optimal weight: 9.9990 chunk 13 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 17 optimal weight: 7.9990 chunk 9 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 11 optimal weight: 10.0000 chunk 20 optimal weight: 1.9990 chunk 5 optimal weight: 5.9990 chunk 7 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: 0.6982 moved from start: 0.3102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 2112 Z= 0.155 Angle : 0.524 3.531 2880 Z= 0.274 Chirality : 0.046 0.137 296 Planarity : 0.004 0.023 336 Dihedral : 6.395 17.827 280 Min Nonbonded Distance : 2.691 Molprobity Statistics. All-atom Clashscore : 1.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 1.00 % Allowed : 7.50 % Favored : 91.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 100.00 % 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: -2.99 (0.35), residues: 248 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.27 (0.27), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 153 HIS 0.001 0.000 HIS A 182 TYR 0.005 0.001 TYR C 151 ARG 0.001 0.000 ARG A 176 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 496 Ramachandran restraints generated. 248 Oldfield, 0 Emsley, 248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 496 Ramachandran restraints generated. 248 Oldfield, 0 Emsley, 248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 48 time to evaluate : 0.398 Fit side-chains REVERT: A 154 LYS cc_start: 0.7735 (mttt) cc_final: 0.7423 (mttt) REVERT: A 178 MET cc_start: 0.7750 (mtm) cc_final: 0.7294 (mtp) REVERT: B 154 LYS cc_start: 0.7372 (mttt) cc_final: 0.7096 (mttt) REVERT: B 176 ARG cc_start: 0.6962 (mtp85) cc_final: 0.6723 (mtm180) REVERT: C 154 LYS cc_start: 0.7189 (mttt) cc_final: 0.6869 (mtpt) REVERT: D 178 MET cc_start: 0.7757 (mtm) cc_final: 0.7394 (mtp) REVERT: E 154 LYS cc_start: 0.7720 (mttt) cc_final: 0.7444 (mttt) REVERT: E 176 ARG cc_start: 0.7097 (mtp85) cc_final: 0.6871 (mtm180) REVERT: E 178 MET cc_start: 0.7755 (mtm) cc_final: 0.7527 (mtp) REVERT: F 154 LYS cc_start: 0.7386 (mttt) cc_final: 0.7174 (mttt) REVERT: F 176 ARG cc_start: 0.6907 (mtp85) cc_final: 0.6695 (ttm170) REVERT: G 154 LYS cc_start: 0.7232 (mttt) cc_final: 0.6936 (mtpt) REVERT: G 176 ARG cc_start: 0.7006 (mtp85) cc_final: 0.6684 (ttm170) REVERT: H 178 MET cc_start: 0.7748 (mtm) cc_final: 0.7370 (mtp) outliers start: 2 outliers final: 0 residues processed: 49 average time/residue: 2.6800 time to fit residues: 133.6519 Evaluate side-chains 46 residues out of total 200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 46 time to evaluate : 0.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 20 optimal weight: 20.0000 chunk 4 optimal weight: 7.9990 chunk 13 optimal weight: 9.9990 chunk 5 optimal weight: 9.9990 chunk 23 optimal weight: 3.9990 chunk 19 optimal weight: 9.9990 chunk 10 optimal weight: 7.9990 chunk 1 optimal weight: 2.9990 chunk 7 optimal weight: 0.8980 chunk 12 optimal weight: 10.0000 chunk 22 optimal weight: 2.9990 overall best weight: 3.7788 ------------------------------------------------------------------------------- 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: 0.6981 moved from start: 0.3344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 2112 Z= 0.143 Angle : 0.491 3.353 2880 Z= 0.262 Chirality : 0.046 0.133 296 Planarity : 0.004 0.023 336 Dihedral : 6.256 17.452 280 Min Nonbonded Distance : 2.694 Molprobity Statistics. All-atom Clashscore : 1.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 1.00 % Allowed : 6.50 % Favored : 92.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 100.00 % 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: -3.02 (0.35), residues: 248 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.29 (0.27), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 160 HIS 0.001 0.000 HIS E 182 TYR 0.004 0.001 TYR G 151 ARG 0.001 0.000 ARG G 176 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 496 Ramachandran restraints generated. 248 Oldfield, 0 Emsley, 248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 496 Ramachandran restraints generated. 248 Oldfield, 0 Emsley, 248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 46 time to evaluate : 0.330 Fit side-chains REVERT: A 154 LYS cc_start: 0.7732 (mttt) cc_final: 0.7426 (mttt) REVERT: A 178 MET cc_start: 0.7760 (mtm) cc_final: 0.7300 (mtp) REVERT: B 154 LYS cc_start: 0.7369 (mttt) cc_final: 0.7098 (mttt) REVERT: B 176 ARG cc_start: 0.6940 (mtp85) cc_final: 0.6685 (mtm180) REVERT: C 154 LYS cc_start: 0.7179 (mttt) cc_final: 0.6876 (mtpt) REVERT: D 178 MET cc_start: 0.7749 (mtm) cc_final: 0.7371 (mtp) REVERT: E 154 LYS cc_start: 0.7723 (mttt) cc_final: 0.7424 (mttt) REVERT: E 176 ARG cc_start: 0.7098 (mtp85) cc_final: 0.6874 (mtm180) REVERT: E 178 MET cc_start: 0.7758 (mtm) cc_final: 0.7552 (mtp) REVERT: F 154 LYS cc_start: 0.7415 (mttt) cc_final: 0.7202 (mttt) REVERT: G 154 LYS cc_start: 0.7227 (mttt) cc_final: 0.6919 (mtpt) REVERT: G 176 ARG cc_start: 0.6980 (mtp85) cc_final: 0.6706 (ttm170) REVERT: H 178 MET cc_start: 0.7745 (mtm) cc_final: 0.7362 (mtp) outliers start: 2 outliers final: 0 residues processed: 47 average time/residue: 2.2915 time to fit residues: 109.5592 Evaluate side-chains 46 residues out of total 200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 46 time to evaluate : 0.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 2 optimal weight: 8.9990 chunk 13 optimal weight: 9.9990 chunk 16 optimal weight: 6.9990 chunk 19 optimal weight: 7.9990 chunk 12 optimal weight: 10.0000 chunk 23 optimal weight: 10.0000 chunk 14 optimal weight: 0.9980 chunk 10 optimal weight: 8.9990 chunk 9 optimal weight: 9.9990 chunk 6 optimal weight: 9.9990 chunk 4 optimal weight: 9.9990 overall best weight: 6.7988 ------------------------------------------------------------------------------- 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: 0.6989 moved from start: 0.3443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 2112 Z= 0.205 Angle : 0.558 3.936 2880 Z= 0.293 Chirality : 0.047 0.145 296 Planarity : 0.004 0.022 336 Dihedral : 6.481 18.072 280 Min Nonbonded Distance : 2.697 Molprobity Statistics. All-atom Clashscore : 1.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 0.50 % Allowed : 6.50 % Favored : 93.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 100.00 % 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: -2.98 (0.35), residues: 248 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.26 (0.27), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 160 HIS 0.001 0.001 HIS E 182 TYR 0.005 0.001 TYR E 159 ARG 0.001 0.000 ARG F 176 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 496 Ramachandran restraints generated. 248 Oldfield, 0 Emsley, 248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 496 Ramachandran restraints generated. 248 Oldfield, 0 Emsley, 248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 46 time to evaluate : 0.360 Fit side-chains revert: symmetry clash REVERT: A 154 LYS cc_start: 0.7736 (mttt) cc_final: 0.7423 (mttt) REVERT: A 178 MET cc_start: 0.7739 (mtm) cc_final: 0.7289 (mtp) REVERT: B 154 LYS cc_start: 0.7335 (mttt) cc_final: 0.7050 (mttt) REVERT: B 176 ARG cc_start: 0.6978 (mtp85) cc_final: 0.6728 (mtm180) REVERT: C 154 LYS cc_start: 0.7185 (mttt) cc_final: 0.6883 (mtpt) REVERT: D 178 MET cc_start: 0.7784 (mtm) cc_final: 0.7398 (mtp) REVERT: E 154 LYS cc_start: 0.7699 (mttt) cc_final: 0.7399 (mttt) REVERT: E 176 ARG cc_start: 0.7102 (mtp85) cc_final: 0.6896 (mtm180) REVERT: F 154 LYS cc_start: 0.7378 (mttt) cc_final: 0.7168 (mttt) REVERT: G 154 LYS cc_start: 0.7240 (mttt) cc_final: 0.6949 (mttt) REVERT: G 176 ARG cc_start: 0.7000 (mtp85) cc_final: 0.6722 (ttm170) REVERT: H 178 MET cc_start: 0.7753 (mtm) cc_final: 0.7374 (mtp) outliers start: 1 outliers final: 0 residues processed: 46 average time/residue: 2.8187 time to fit residues: 131.8089 Evaluate side-chains 45 residues out of total 200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 45 time to evaluate : 0.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 4 optimal weight: 7.9990 chunk 14 optimal weight: 8.9990 chunk 15 optimal weight: 9.9990 chunk 11 optimal weight: 9.9990 chunk 2 optimal weight: 9.9990 chunk 18 optimal weight: 5.9990 chunk 21 optimal weight: 0.9990 chunk 22 optimal weight: 8.9990 chunk 20 optimal weight: 10.0000 chunk 12 optimal weight: 0.9990 chunk 9 optimal weight: 10.0000 overall best weight: 4.9990 ------------------------------------------------------------------------------- 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: 0.6992 moved from start: 0.3451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 2112 Z= 0.169 Angle : 0.514 3.419 2880 Z= 0.271 Chirality : 0.046 0.137 296 Planarity : 0.004 0.023 336 Dihedral : 6.366 17.703 280 Min Nonbonded Distance : 2.697 Molprobity Statistics. All-atom Clashscore : 1.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 0.00 % Allowed : 7.50 % Favored : 92.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 100.00 % 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: -3.03 (0.35), residues: 248 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.30 (0.27), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 160 HIS 0.001 0.000 HIS A 182 TYR 0.005 0.001 TYR G 151 ARG 0.001 0.000 ARG F 176 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 496 Ramachandran restraints generated. 248 Oldfield, 0 Emsley, 248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 496 Ramachandran restraints generated. 248 Oldfield, 0 Emsley, 248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 47 time to evaluate : 0.345 Fit side-chains revert: symmetry clash REVERT: A 154 LYS cc_start: 0.7723 (mttt) cc_final: 0.7409 (mttt) REVERT: A 178 MET cc_start: 0.7744 (mtm) cc_final: 0.7319 (mtp) REVERT: B 154 LYS cc_start: 0.7370 (mttt) cc_final: 0.7101 (mttt) REVERT: B 176 ARG cc_start: 0.6968 (mtp85) cc_final: 0.6716 (mtm180) REVERT: C 154 LYS cc_start: 0.7242 (mttt) cc_final: 0.6934 (mtpt) REVERT: D 178 MET cc_start: 0.7769 (mtm) cc_final: 0.7373 (mtp) REVERT: E 154 LYS cc_start: 0.7707 (mttt) cc_final: 0.7400 (mttt) REVERT: E 176 ARG cc_start: 0.7078 (mtp85) cc_final: 0.6873 (mtm180) REVERT: F 154 LYS cc_start: 0.7414 (mttt) cc_final: 0.7207 (mttt) REVERT: G 154 LYS cc_start: 0.7229 (mttt) cc_final: 0.6930 (mtpt) REVERT: G 176 ARG cc_start: 0.6941 (mtp85) cc_final: 0.6696 (ttm170) REVERT: H 178 MET cc_start: 0.7740 (mtm) cc_final: 0.7357 (mtp) outliers start: 0 outliers final: 0 residues processed: 47 average time/residue: 2.7565 time to fit residues: 131.8170 Evaluate side-chains 46 residues out of total 200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 46 time to evaluate : 0.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 16 optimal weight: 10.0000 chunk 6 optimal weight: 10.0000 chunk 19 optimal weight: 2.9990 chunk 20 optimal weight: 9.9990 chunk 21 optimal weight: 10.0000 chunk 14 optimal weight: 5.9990 chunk 22 optimal weight: 0.8980 chunk 13 optimal weight: 3.9990 chunk 10 optimal weight: 8.9990 chunk 15 optimal weight: 7.9990 chunk 23 optimal weight: 4.9990 overall best weight: 3.7788 ------------------------------------------------------------------------------- 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: 0.6989 moved from start: 0.3441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 2112 Z= 0.143 Angle : 0.491 3.291 2880 Z= 0.261 Chirality : 0.046 0.134 296 Planarity : 0.004 0.023 336 Dihedral : 6.257 17.386 280 Min Nonbonded Distance : 2.695 Molprobity Statistics. All-atom Clashscore : 1.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 0.00 % Allowed : 7.50 % Favored : 92.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 100.00 % 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: -3.05 (0.35), residues: 248 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.31 (0.27), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 160 HIS 0.001 0.000 HIS E 182 TYR 0.004 0.001 TYR C 151 ARG 0.001 0.000 ARG G 176 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 496 Ramachandran restraints generated. 248 Oldfield, 0 Emsley, 248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 496 Ramachandran restraints generated. 248 Oldfield, 0 Emsley, 248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 46 time to evaluate : 0.389 Fit side-chains REVERT: A 154 LYS cc_start: 0.7765 (mttt) cc_final: 0.7442 (mttt) REVERT: A 178 MET cc_start: 0.7751 (mtm) cc_final: 0.7322 (mtp) REVERT: B 154 LYS cc_start: 0.7372 (mttt) cc_final: 0.7093 (mttt) REVERT: B 176 ARG cc_start: 0.6951 (mtp85) cc_final: 0.6691 (mtm180) REVERT: C 154 LYS cc_start: 0.7243 (mttt) cc_final: 0.6941 (mtpt) REVERT: D 178 MET cc_start: 0.7773 (mtm) cc_final: 0.7371 (mtp) REVERT: E 154 LYS cc_start: 0.7756 (mttt) cc_final: 0.7437 (mttt) REVERT: F 154 LYS cc_start: 0.7417 (mttt) cc_final: 0.7212 (mttt) REVERT: G 154 LYS cc_start: 0.7224 (mttt) cc_final: 0.6923 (mtpt) REVERT: G 176 ARG cc_start: 0.6939 (mtp85) cc_final: 0.6738 (ttm170) REVERT: H 178 MET cc_start: 0.7748 (mtm) cc_final: 0.7359 (mtp) outliers start: 0 outliers final: 0 residues processed: 46 average time/residue: 2.8327 time to fit residues: 132.4763 Evaluate side-chains 46 residues out of total 200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 46 time to evaluate : 0.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 22 optimal weight: 0.0270 chunk 19 optimal weight: 3.9990 chunk 1 optimal weight: 1.9990 chunk 14 optimal weight: 5.9990 chunk 11 optimal weight: 0.4980 chunk 15 optimal weight: 10.0000 chunk 20 optimal weight: 9.9990 chunk 5 optimal weight: 9.9990 chunk 17 optimal weight: 3.9990 chunk 2 optimal weight: 6.9990 chunk 7 optimal weight: 10.0000 overall best weight: 2.1044 ------------------------------------------------------------------------------- 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: 0.6986 moved from start: 0.3548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 2112 Z= 0.119 Angle : 0.460 2.828 2880 Z= 0.248 Chirality : 0.046 0.128 296 Planarity : 0.003 0.025 336 Dihedral : 6.077 16.686 280 Min Nonbonded Distance : 2.693 Molprobity Statistics. All-atom Clashscore : 1.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 0.00 % Allowed : 8.00 % Favored : 92.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 100.00 % 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: -3.05 (0.36), residues: 248 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.31 (0.27), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 153 HIS 0.001 0.000 HIS A 182 TYR 0.003 0.001 TYR G 151 ARG 0.001 0.000 ARG G 176 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 496 Ramachandran restraints generated. 248 Oldfield, 0 Emsley, 248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 496 Ramachandran restraints generated. 248 Oldfield, 0 Emsley, 248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 48 time to evaluate : 0.273 Fit side-chains REVERT: A 154 LYS cc_start: 0.7763 (mttt) cc_final: 0.7442 (mttt) REVERT: A 178 MET cc_start: 0.7748 (mtm) cc_final: 0.7327 (mtp) REVERT: B 154 LYS cc_start: 0.7369 (mttt) cc_final: 0.7099 (mttt) REVERT: B 176 ARG cc_start: 0.6887 (mtp85) cc_final: 0.6619 (mtm180) REVERT: C 154 LYS cc_start: 0.7234 (mttt) cc_final: 0.6923 (mtpt) REVERT: E 154 LYS cc_start: 0.7741 (mttt) cc_final: 0.7435 (mttt) REVERT: F 154 LYS cc_start: 0.7421 (mttt) cc_final: 0.7210 (mttt) REVERT: F 176 ARG cc_start: 0.7018 (ttm170) cc_final: 0.6578 (ttm170) REVERT: G 154 LYS cc_start: 0.7224 (mttt) cc_final: 0.6924 (mtpt) REVERT: H 178 MET cc_start: 0.7736 (mtm) cc_final: 0.7343 (mtp) outliers start: 0 outliers final: 0 residues processed: 48 average time/residue: 2.6890 time to fit residues: 131.3645 Evaluate side-chains 48 residues out of total 200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 48 time to evaluate : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 19 optimal weight: 10.0000 chunk 2 optimal weight: 8.9990 chunk 3 optimal weight: 20.0000 chunk 16 optimal weight: 4.9990 chunk 1 optimal weight: 1.9990 chunk 13 optimal weight: 3.9990 chunk 21 optimal weight: 0.0870 chunk 12 optimal weight: 10.0000 chunk 0 optimal weight: 0.9990 chunk 15 optimal weight: 9.9990 chunk 14 optimal weight: 6.9990 overall best weight: 2.4166 ------------------------------------------------------------------------------- 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: 0.6990 moved from start: 0.3708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 2112 Z= 0.121 Angle : 0.464 2.919 2880 Z= 0.249 Chirality : 0.046 0.129 296 Planarity : 0.003 0.024 336 Dihedral : 6.064 16.842 280 Min Nonbonded Distance : 2.695 Molprobity Statistics. All-atom Clashscore : 1.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 0.00 % Allowed : 8.00 % Favored : 92.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 100.00 % 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: -3.06 (0.36), residues: 248 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.32 (0.27), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 160 HIS 0.001 0.000 HIS A 182 TYR 0.003 0.001 TYR D 159 ARG 0.003 0.000 ARG F 176 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 496 Ramachandran restraints generated. 248 Oldfield, 0 Emsley, 248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 496 Ramachandran restraints generated. 248 Oldfield, 0 Emsley, 248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 48 time to evaluate : 0.331 Fit side-chains REVERT: A 154 LYS cc_start: 0.7743 (mttt) cc_final: 0.7425 (mttt) REVERT: A 178 MET cc_start: 0.7760 (mtm) cc_final: 0.7331 (mtp) REVERT: B 154 LYS cc_start: 0.7354 (mttt) cc_final: 0.7086 (mttt) REVERT: B 176 ARG cc_start: 0.6893 (mtp85) cc_final: 0.6620 (mtm180) REVERT: C 154 LYS cc_start: 0.7260 (mttt) cc_final: 0.6955 (mtpt) REVERT: D 178 MET cc_start: 0.7676 (mtm) cc_final: 0.7325 (mtp) REVERT: E 154 LYS cc_start: 0.7755 (mttt) cc_final: 0.7454 (mttt) REVERT: F 154 LYS cc_start: 0.7461 (mttt) cc_final: 0.7253 (mttt) REVERT: G 154 LYS cc_start: 0.7248 (mttt) cc_final: 0.6940 (mtpt) REVERT: H 178 MET cc_start: 0.7735 (mtm) cc_final: 0.7332 (mtp) outliers start: 0 outliers final: 0 residues processed: 48 average time/residue: 2.7004 time to fit residues: 131.8550 Evaluate side-chains 48 residues out of total 200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 48 time to evaluate : 0.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 13 optimal weight: 9.9990 chunk 9 optimal weight: 10.0000 chunk 8 optimal weight: 9.9990 chunk 23 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 4 optimal weight: 5.9990 chunk 2 optimal weight: 6.9990 chunk 5 optimal weight: 0.9990 chunk 19 optimal weight: 9.9990 chunk 22 optimal weight: 8.9990 chunk 10 optimal weight: 6.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- 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 = 0.3982 r_free = 0.3982 target = 0.142705 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.111583 restraints weight = 4478.715| |-----------------------------------------------------------------------------| r_work (start): 0.3588 rms_B_bonded: 1.59 r_work: 0.3453 rms_B_bonded: 1.59 restraints_weight: 0.5000 r_work: 0.3371 rms_B_bonded: 2.43 restraints_weight: 0.2500 r_work (final): 0.3371 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9210 moved from start: 0.3658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 2112 Z= 0.186 Angle : 0.544 3.740 2880 Z= 0.284 Chirality : 0.047 0.142 296 Planarity : 0.004 0.022 336 Dihedral : 6.400 19.188 280 Min Nonbonded Distance : 2.696 Molprobity Statistics. All-atom Clashscore : 1.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 0.00 % Allowed : 8.50 % Favored : 91.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 100.00 % 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: -3.08 (0.35), residues: 248 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.34 (0.27), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP C 160 HIS 0.001 0.000 HIS A 182 TYR 0.005 0.001 TYR A 159 ARG 0.002 0.000 ARG E 176 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2996.94 seconds wall clock time: 58 minutes 36.77 seconds (3516.77 seconds total)