Starting phenix.real_space_refine on Thu Oct 22 17:12:43 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9pei_71563/10_2026/9pei_71563.cif Found real_map, /net/cci-nas-00/data/ceres_data/9pei_71563/10_2026/9pei_71563.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9pei_71563/10_2026/9pei_71563.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9pei_71563/10_2026/9pei_71563.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9pei_71563/10_2026/9pei_71563.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9pei_71563/10_2026/9pei_71563.map" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.001 sd= 0.016 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: 3 Type Number sf(0) Gaussians C 1026 2.51 5 N 198 2.21 5 O 198 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 23 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 1422 Number of models: 1 Model: "" Number of chains: 36 Chain: "M" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 78 Unusual residues: {'ACE': 1} Classifications: {'peptide': 8, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 7} Chain: "M" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "N" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 78 Unusual residues: {'ACE': 1} Classifications: {'peptide': 8, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 7} Chain: "N" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 78 Unusual residues: {'ACE': 1} Classifications: {'peptide': 8, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 7} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 78 Unusual residues: {'ACE': 1} Classifications: {'peptide': 8, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 7} Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "O" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 78 Unusual residues: {'ACE': 1} Classifications: {'peptide': 8, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 7} Chain: "O" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "P" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 78 Unusual residues: {'ACE': 1} Classifications: {'peptide': 8, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 7} Chain: "P" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "Q" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 78 Unusual residues: {'ACE': 1} Classifications: {'peptide': 8, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 7} Chain: "Q" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "R" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 78 Unusual residues: {'ACE': 1} Classifications: {'peptide': 8, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 7} Chain: "R" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "S" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 78 Unusual residues: {'ACE': 1} Classifications: {'peptide': 8, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 7} Chain: "S" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "T" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 78 Unusual residues: {'ACE': 1} Classifications: {'peptide': 8, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 7} Chain: "T" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "U" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 78 Unusual residues: {'ACE': 1} Classifications: {'peptide': 8, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 7} Chain: "U" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "V" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 78 Unusual residues: {'ACE': 1} Classifications: {'peptide': 8, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 7} Chain: "V" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 78 Unusual residues: {'ACE': 1} Classifications: {'peptide': 8, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 7} Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "X" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 78 Unusual residues: {'ACE': 1} Classifications: {'peptide': 8, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 7} Chain: "X" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 78 Unusual residues: {'ACE': 1} Classifications: {'peptide': 8, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 7} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "W" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 78 Unusual residues: {'ACE': 1} Classifications: {'peptide': 8, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 7} Chain: "W" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 78 Unusual residues: {'ACE': 1} Classifications: {'peptide': 8, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 7} Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "Y" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 78 Unusual residues: {'ACE': 1} Classifications: {'peptide': 8, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 7} Chain: "Y" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Time building chain proxies: 0.29, per 1000 atoms: 0.20 Number of scatterers: 1422 At special positions: 0 Unit cell: (73.04, 98.77, 78.02, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 3 Type Number sf(0) O 198 8.00 N 198 7.00 C 1026 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=18, symmetry=0 Number of additional bonds: simple=18, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.09 Conformation dependent library (CDL) restraints added in 21.8 milliseconds 216 Ramachandran restraints generated. 108 Oldfield, 0 Emsley, 108 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 252 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 8 sheets defined 0.0% alpha, 38.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.02 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'M' and resid 2 through 6 Processing sheet with id=AA2, first strand: chain 'D' and resid 3 through 6 Processing sheet with id=AA3, first strand: chain 'O' and resid 2 through 6 removed outlier: 3.537A pdb=" N GLU P 4 " --> pdb=" O GLU O 4 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'Q' and resid 2 through 6 Processing sheet with id=AA5, first strand: chain 'U' and resid 2 through 6 Processing sheet with id=AA6, first strand: chain 'F' and resid 3 through 6 Processing sheet with id=AA7, first strand: chain 'E' and resid 3 through 6 Processing sheet with id=AA8, first strand: chain 'G' and resid 3 through 6 removed outlier: 6.826A pdb=" N PHE G 3 " --> pdb=" O GLU Y 4 " (cutoff:3.500A) removed outlier: 8.234A pdb=" N LYS Y 6 " --> pdb=" O PHE G 3 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N PHE G 5 " --> pdb=" O LYS Y 6 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 32 hydrogen bonds defined for protein. 72 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.07 Time building geometry restraints manager: 0.09 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.26: 184 1.26 - 1.33: 121 1.33 - 1.41: 433 1.41 - 1.48: 181 1.48 - 1.56: 539 Bond restraints: 1458 Sorted by residual: bond pdb=" C PHE W 7 " pdb=" N GLY W 8 " ideal model delta sigma weight residual 1.329 1.431 -0.102 1.40e-02 5.10e+03 5.30e+01 bond pdb=" C PHE R 7 " pdb=" N GLY R 8 " ideal model delta sigma weight residual 1.329 1.430 -0.101 1.40e-02 5.10e+03 5.25e+01 bond pdb=" C PHE S 7 " pdb=" N GLY S 8 " ideal model delta sigma weight residual 1.329 1.430 -0.101 1.40e-02 5.10e+03 5.24e+01 bond pdb=" C PHE O 7 " pdb=" N GLY O 8 " ideal model delta sigma weight residual 1.329 1.430 -0.101 1.40e-02 5.10e+03 5.24e+01 bond pdb=" C PHE Q 7 " pdb=" N GLY Q 8 " ideal model delta sigma weight residual 1.329 1.430 -0.101 1.40e-02 5.10e+03 5.22e+01 ... (remaining 1453 not shown) Histogram of bond angle deviations from ideal: 0.00 - 9.02: 1836 9.02 - 18.05: 14 18.05 - 27.07: 11 27.07 - 36.09: 6 36.09 - 45.12: 5 Bond angle restraints: 1872 Sorted by residual: angle pdb=" O PHE U 7 " pdb=" C PHE U 7 " pdb=" N GLY U 8 " ideal model delta sigma weight residual 122.43 77.51 44.92 1.34e+00 5.57e-01 1.12e+03 angle pdb=" O PHE O 7 " pdb=" C PHE O 7 " pdb=" N GLY O 8 " ideal model delta sigma weight residual 122.43 79.09 43.34 1.34e+00 5.57e-01 1.05e+03 angle pdb=" O PHE M 7 " pdb=" C PHE M 7 " pdb=" N GLY M 8 " ideal model delta sigma weight residual 122.61 86.24 36.37 1.32e+00 5.74e-01 7.59e+02 angle pdb=" CA PHE U 7 " pdb=" C PHE U 7 " pdb=" N GLY U 8 " ideal model delta sigma weight residual 118.14 153.44 -35.30 1.31e+00 5.83e-01 7.26e+02 angle pdb=" C PHE U 7 " pdb=" N GLY U 8 " pdb=" CA GLY U 8 " ideal model delta sigma weight residual 121.70 166.82 -45.12 1.80e+00 3.09e-01 6.28e+02 ... (remaining 1867 not shown) Histogram of dihedral angle deviations from ideal: 0.01 - 36.00: 722 36.00 - 72.00: 16 72.00 - 108.00: 0 108.00 - 144.00: 0 144.00 - 180.00: 18 Dihedral angle restraints: 756 sinusoidal: 378 harmonic: 378 Sorted by residual: dihedral pdb=" CH3 ACE Y 0 " pdb=" C ACE Y 0 " pdb=" N PHE Y 1 " pdb=" CA PHE Y 1 " ideal model delta sinusoidal sigma weight residual -180.00 -0.00 -180.00 1 5.00e+00 4.00e-02 7.68e+02 dihedral pdb=" CH3 ACE R 0 " pdb=" C ACE R 0 " pdb=" N PHE R 1 " pdb=" CA PHE R 1 " ideal model delta sinusoidal sigma weight residual -180.00 -0.01 -179.99 1 5.00e+00 4.00e-02 7.68e+02 dihedral pdb=" CH3 ACE D 0 " pdb=" C ACE D 0 " pdb=" N PHE D 1 " pdb=" CA PHE D 1 " ideal model delta sinusoidal sigma weight residual -180.00 -0.01 -179.99 1 5.00e+00 4.00e-02 7.68e+02 ... (remaining 753 not shown) Histogram of chiral volume deviations from ideal: 0.001 - 0.018: 55 0.018 - 0.035: 51 0.035 - 0.052: 15 0.052 - 0.070: 4 0.070 - 0.087: 1 Chirality restraints: 126 Sorted by residual: chirality pdb=" CA GLU R 4 " pdb=" N GLU R 4 " pdb=" C GLU R 4 " pdb=" CB GLU R 4 " both_signs ideal model delta sigma weight residual False 2.51 2.60 -0.09 2.00e-01 2.50e+01 1.89e-01 chirality pdb=" CA LYS E 2 " pdb=" N LYS E 2 " pdb=" C LYS E 2 " pdb=" CB LYS E 2 " both_signs ideal model delta sigma weight residual False 2.51 2.57 -0.06 2.00e-01 2.50e+01 1.01e-01 chirality pdb=" CA PHE T 5 " pdb=" N PHE T 5 " pdb=" C PHE T 5 " pdb=" CB PHE T 5 " both_signs ideal model delta sigma weight residual False 2.51 2.45 0.06 2.00e-01 2.50e+01 8.25e-02 ... (remaining 123 not shown) Planarity restraints: 234 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE Q 7 " 0.097 2.00e-02 2.50e+03 1.70e-01 2.88e+02 pdb=" C PHE Q 7 " -0.293 2.00e-02 2.50e+03 pdb=" O PHE Q 7 " 0.113 2.00e-02 2.50e+03 pdb=" N GLY Q 8 " 0.083 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE M 7 " 0.068 2.00e-02 2.50e+03 9.96e-02 9.93e+01 pdb=" C PHE M 7 " -0.172 2.00e-02 2.50e+03 pdb=" O PHE M 7 " 0.044 2.00e-02 2.50e+03 pdb=" N GLY M 8 " 0.060 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE O 7 " -0.069 2.00e-02 2.50e+03 9.68e-02 9.37e+01 pdb=" C PHE O 7 " 0.166 2.00e-02 2.50e+03 pdb=" O PHE O 7 " -0.035 2.00e-02 2.50e+03 pdb=" N GLY O 8 " -0.062 2.00e-02 2.50e+03 ... (remaining 231 not shown) Histogram of nonbonded interaction distances: 2.38 - 2.89: 525 2.89 - 3.39: 908 3.39 - 3.89: 1910 3.89 - 4.40: 2034 4.40 - 4.90: 3402 Nonbonded interactions: 8779 Sorted by model distance: nonbonded pdb=" N PHE G 7 " pdb=" N GLY G 8 " model vdw 2.382 2.560 nonbonded pdb=" N PHE F 7 " pdb=" N GLY F 8 " model vdw 2.384 2.560 nonbonded pdb=" N GLU O 4 " pdb=" OE1 GLU O 4 " model vdw 2.389 3.120 nonbonded pdb=" N GLU U 4 " pdb=" OE1 GLU U 4 " model vdw 2.399 3.120 nonbonded pdb=" N PHE E 7 " pdb=" N GLY E 8 " model vdw 2.411 2.560 ... (remaining 8774 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 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.600 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.020 Check model and map are aligned: 0.000 Set scattering table: 0.020 Process input model: 1.800 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.000 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:0.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 4.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7715 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 : 0.021 0.135 1476 Z= 1.190 Angle : 3.907 45.116 1872 Z= 2.553 Chirality : 0.026 0.087 126 Planarity : 0.019 0.170 234 Dihedral : 36.651 179.999 504 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 1.59 % Allowed : 10.32 % Favored : 88.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.79 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.88 (0.45), residues: 108 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.95 (0.34), residues: 108 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.017 0.001 PHE M 5 Details of bonding type rmsd/Z covalent geometry : bond 0.02062 / 1.17 ( 1458) covalent geometry : angle 3.90685 / 2.55 ( 1872) hydrogen bonds : bond 0.28183 / 14.51 ( 32) hydrogen bonds : angle 18.10561 / 11.38 ( 72) Misc. bond : bond 0.02192 / 1.18 ( 18) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 216 Ramachandran restraints generated. 108 Oldfield, 0 Emsley, 108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 216 Ramachandran restraints generated. 108 Oldfield, 0 Emsley, 108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 56 time to evaluate : 0.031 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 2 LYS cc_start: 0.8101 (mttt) cc_final: 0.7880 (tptt) REVERT: D 2 LYS cc_start: 0.7470 (mttt) cc_final: 0.7146 (pttm) REVERT: Q 2 LYS cc_start: 0.8174 (mttt) cc_final: 0.7382 (tppt) REVERT: R 6 LYS cc_start: 0.8315 (mmmt) cc_final: 0.8020 (mmmm) REVERT: S 2 LYS cc_start: 0.8697 (mttt) cc_final: 0.8354 (mmmt) REVERT: T 2 LYS cc_start: 0.8586 (OUTLIER) cc_final: 0.7775 (mptt) REVERT: W 2 LYS cc_start: 0.8615 (mttt) cc_final: 0.8358 (tppt) REVERT: G 6 LYS cc_start: 0.8598 (mttt) cc_final: 0.8335 (pttm) outliers start: 2 outliers final: 1 residues processed: 57 average time/residue: 0.0898 time to fit residues: 5.3468 Evaluate side-chains 44 residues out of total 126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 42 time to evaluate : 0.031 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 1 PHE Chi-restraints excluded: chain T residue 2 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: [0] chunk 0 optimal weight: 0.8980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.083776 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.078467 restraints weight = 6257.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.080069 restraints weight = 2919.782| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.081091 restraints weight = 1659.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.081742 restraints weight = 1049.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.082069 restraints weight = 707.921| |-----------------------------------------------------------------------------| r_work (final): 0.3716 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7457 moved from start: 0.5275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 1476 Z= 0.167 Angle : 1.412 12.000 1872 Z= 0.526 Chirality : 0.039 0.103 126 Planarity : 0.003 0.009 234 Dihedral : 58.817 179.860 168 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 3.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.93 % Favored : 99.07 % Rotamer: Outliers : 1.59 % Allowed : 15.08 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.97 (0.45), residues: 108 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.02 (0.34), residues: 108 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.013 0.001 PHE Q 3 Details of bonding type rmsd/Z covalent geometry : bond 0.00389 / 0.17 ( 1458) covalent geometry : angle 1.41176 / 0.53 ( 1872) hydrogen bonds : bond 0.02390 / 1.25 ( 32) hydrogen bonds : angle 9.82114 / 5.94 ( 72) Misc. bond : bond 0.00038 / 0.02 ( 18) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 216 Ramachandran restraints generated. 108 Oldfield, 0 Emsley, 108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 216 Ramachandran restraints generated. 108 Oldfield, 0 Emsley, 108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 47 time to evaluate : 0.032 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 2 LYS cc_start: 0.8174 (mttt) cc_final: 0.7827 (tptt) REVERT: D 2 LYS cc_start: 0.8253 (mttt) cc_final: 0.7774 (pttm) REVERT: Q 2 LYS cc_start: 0.8095 (mttt) cc_final: 0.7189 (tppt) REVERT: S 2 LYS cc_start: 0.8768 (mttt) cc_final: 0.8288 (mmmt) REVERT: S 6 LYS cc_start: 0.8480 (mmtm) cc_final: 0.8271 (mmtm) REVERT: T 6 LYS cc_start: 0.8697 (mmtt) cc_final: 0.8347 (mmmt) REVERT: W 2 LYS cc_start: 0.8496 (mttt) cc_final: 0.8205 (tppt) REVERT: G 6 LYS cc_start: 0.8856 (mttt) cc_final: 0.8483 (pttm) REVERT: Y 4 GLU cc_start: 0.7895 (mp0) cc_final: 0.7682 (mp0) outliers start: 2 outliers final: 2 residues processed: 48 average time/residue: 0.1001 time to fit residues: 5.0250 Evaluate side-chains 41 residues out of total 126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 39 time to evaluate : 0.059 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 1 PHE Chi-restraints excluded: chain T residue 7 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: [0] chunk 0 optimal weight: 8.9990 overall best weight: 8.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.077955 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.072765 restraints weight = 6875.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.074129 restraints weight = 3053.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.074997 restraints weight = 1731.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.075507 restraints weight = 1120.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.075877 restraints weight = 802.261| |-----------------------------------------------------------------------------| r_work (final): 0.3568 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7676 moved from start: 0.8372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.054 1476 Z= 0.528 Angle : 1.595 14.314 1872 Z= 0.672 Chirality : 0.064 0.200 126 Planarity : 0.006 0.053 234 Dihedral : 58.513 179.605 164 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 15.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.48 % Favored : 93.52 % Rotamer: Outliers : 3.17 % Allowed : 19.05 % Favored : 77.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.97 (0.48), residues: 108 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.02 (0.37), residues: 108 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.025 0.003 PHE W 5 Details of bonding type rmsd/Z covalent geometry : bond 0.01255 / 0.53 ( 1458) covalent geometry : angle 1.59452 / 0.67 ( 1872) hydrogen bonds : bond 0.03981 / 2.03 ( 32) hydrogen bonds : angle 11.28421 / 7.20 ( 72) Misc. bond : bond 0.00049 / 0.03 ( 18) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 216 Ramachandran restraints generated. 108 Oldfield, 0 Emsley, 108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 216 Ramachandran restraints generated. 108 Oldfield, 0 Emsley, 108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 37 time to evaluate : 0.031 Fit side-chains REVERT: M 2 LYS cc_start: 0.8684 (mttt) cc_final: 0.8133 (tptt) REVERT: D 2 LYS cc_start: 0.9067 (mttt) cc_final: 0.8330 (pptt) REVERT: O 4 GLU cc_start: 0.8727 (mp0) cc_final: 0.8521 (mp0) REVERT: Q 6 LYS cc_start: 0.8504 (mmtp) cc_final: 0.8189 (mmtm) REVERT: R 2 LYS cc_start: 0.8720 (mptt) cc_final: 0.8348 (mptt) REVERT: R 6 LYS cc_start: 0.8338 (mmmt) cc_final: 0.7891 (mmtm) REVERT: S 2 LYS cc_start: 0.8849 (mttt) cc_final: 0.7893 (mmmt) REVERT: T 6 LYS cc_start: 0.8294 (mmtt) cc_final: 0.7880 (mmmm) REVERT: T 7 PHE cc_start: 0.8601 (OUTLIER) cc_final: 0.7858 (m-80) REVERT: W 2 LYS cc_start: 0.8578 (mttt) cc_final: 0.7942 (tppt) REVERT: W 4 GLU cc_start: 0.7738 (mp0) cc_final: 0.7304 (mp0) outliers start: 4 outliers final: 1 residues processed: 41 average time/residue: 0.0959 time to fit residues: 4.1154 Evaluate side-chains 33 residues out of total 126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 31 time to evaluate : 0.031 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 1 PHE Chi-restraints excluded: chain T residue 7 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: [0] chunk 0 optimal weight: 4.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.080579 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.074930 restraints weight = 7181.759| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.076450 restraints weight = 3139.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.077370 restraints weight = 1758.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.078007 restraints weight = 1159.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.078406 restraints weight = 817.945| |-----------------------------------------------------------------------------| r_work (final): 0.3601 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7575 moved from start: 0.9179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.035 1476 Z= 0.306 Angle : 1.509 13.069 1872 Z= 0.601 Chirality : 0.054 0.160 126 Planarity : 0.004 0.030 234 Dihedral : 59.334 179.825 162 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 12.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 3.97 % Allowed : 22.22 % Favored : 73.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.97 (0.50), residues: 108 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.02 (0.38), residues: 108 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.017 0.002 PHE W 5 Details of bonding type rmsd/Z covalent geometry : bond 0.00747 / 0.31 ( 1458) covalent geometry : angle 1.50885 / 0.60 ( 1872) hydrogen bonds : bond 0.03403 / 1.92 ( 32) hydrogen bonds : angle 9.57873 / 6.10 ( 72) Misc. bond : bond 0.00034 / 0.02 ( 18) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 216 Ramachandran restraints generated. 108 Oldfield, 0 Emsley, 108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 216 Ramachandran restraints generated. 108 Oldfield, 0 Emsley, 108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 32 time to evaluate : 0.041 Fit side-chains REVERT: D 2 LYS cc_start: 0.9107 (mttt) cc_final: 0.8426 (pptt) REVERT: O 4 GLU cc_start: 0.8575 (mp0) cc_final: 0.8278 (mp0) REVERT: P 4 GLU cc_start: 0.2409 (tp30) cc_final: 0.2193 (tp30) REVERT: Q 6 LYS cc_start: 0.8561 (mmtp) cc_final: 0.8065 (mmtm) REVERT: R 6 LYS cc_start: 0.8345 (mmmt) cc_final: 0.7912 (mmtm) REVERT: S 2 LYS cc_start: 0.8955 (mttt) cc_final: 0.8439 (mmmt) REVERT: T 6 LYS cc_start: 0.8447 (mmtt) cc_final: 0.8061 (mmmt) REVERT: W 2 LYS cc_start: 0.8538 (mttt) cc_final: 0.7225 (mmmt) REVERT: W 4 GLU cc_start: 0.7871 (mp0) cc_final: 0.7108 (mp0) REVERT: Y 2 LYS cc_start: 0.3801 (mmmt) cc_final: 0.3600 (mmmt) outliers start: 5 outliers final: 3 residues processed: 37 average time/residue: 0.1112 time to fit residues: 4.3275 Evaluate side-chains 30 residues out of total 126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 27 time to evaluate : 0.033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain T residue 5 PHE Chi-restraints excluded: chain T residue 7 PHE Chi-restraints excluded: chain F residue 2 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: [0] chunk 0 optimal weight: 7.9990 overall best weight: 7.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.079412 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.073558 restraints weight = 7496.680| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.075020 restraints weight = 3189.210| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.075964 restraints weight = 1781.345| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.076535 restraints weight = 1145.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.076991 restraints weight = 833.758| |-----------------------------------------------------------------------------| r_work (final): 0.3577 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7603 moved from start: 1.0201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.048 1476 Z= 0.470 Angle : 1.632 13.350 1872 Z= 0.686 Chirality : 0.066 0.201 126 Planarity : 0.005 0.041 234 Dihedral : 58.836 179.457 162 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 17.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 7.94 % Allowed : 20.63 % Favored : 71.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.79 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.93 (0.56), residues: 108 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.99 (0.43), residues: 108 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.023 0.003 PHE W 5 Details of bonding type rmsd/Z covalent geometry : bond 0.01137 / 0.47 ( 1458) covalent geometry : angle 1.63223 / 0.69 ( 1872) hydrogen bonds : bond 0.05025 / 3.14 ( 32) hydrogen bonds : angle 10.50173 / 6.56 ( 72) Misc. bond : bond 0.00050 / 0.03 ( 18) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 216 Ramachandran restraints generated. 108 Oldfield, 0 Emsley, 108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 216 Ramachandran restraints generated. 108 Oldfield, 0 Emsley, 108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 28 time to evaluate : 0.057 Fit side-chains REVERT: M 2 LYS cc_start: 0.5562 (mmmt) cc_final: 0.5215 (tppt) REVERT: D 2 LYS cc_start: 0.9066 (mttt) cc_final: 0.8434 (pptt) REVERT: Q 6 LYS cc_start: 0.8520 (mmtp) cc_final: 0.8187 (mmtm) REVERT: R 6 LYS cc_start: 0.8352 (mmmt) cc_final: 0.8057 (mmtm) REVERT: S 2 LYS cc_start: 0.8931 (mttt) cc_final: 0.8513 (mmmt) REVERT: T 6 LYS cc_start: 0.8164 (mmtt) cc_final: 0.7943 (mmmt) REVERT: U 2 LYS cc_start: 0.3898 (OUTLIER) cc_final: 0.2480 (tptt) REVERT: F 2 LYS cc_start: 0.6073 (OUTLIER) cc_final: 0.5295 (pttm) REVERT: W 2 LYS cc_start: 0.8696 (mttt) cc_final: 0.8070 (tppt) outliers start: 10 outliers final: 5 residues processed: 37 average time/residue: 0.1350 time to fit residues: 5.2512 Evaluate side-chains 32 residues out of total 126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 25 time to evaluate : 0.033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 3 PHE Chi-restraints excluded: chain L residue 5 PHE Chi-restraints excluded: chain T residue 5 PHE Chi-restraints excluded: chain T residue 7 PHE Chi-restraints excluded: chain U residue 2 LYS Chi-restraints excluded: chain F residue 2 LYS Chi-restraints excluded: chain X residue 5 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: [0] chunk 0 optimal weight: 5.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.081083 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.075471 restraints weight = 7333.137| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.076869 restraints weight = 3174.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.077778 restraints weight = 1781.578| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.078393 restraints weight = 1165.953| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.078654 restraints weight = 833.000| |-----------------------------------------------------------------------------| r_work (final): 0.3593 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7576 moved from start: 1.0489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.035 1476 Z= 0.351 Angle : 1.566 13.557 1872 Z= 0.636 Chirality : 0.058 0.161 126 Planarity : 0.004 0.034 234 Dihedral : 59.058 179.073 162 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 16.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 7.94 % Allowed : 23.02 % Favored : 69.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.05 (0.56), residues: 108 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.08 (0.43), residues: 108 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.014 0.002 PHE W 5 Details of bonding type rmsd/Z covalent geometry : bond 0.00858 / 0.35 ( 1458) covalent geometry : angle 1.56615 / 0.64 ( 1872) hydrogen bonds : bond 0.04084 / 2.49 ( 32) hydrogen bonds : angle 10.07211 / 6.21 ( 72) Misc. bond : bond 0.00029 / 0.01 ( 18) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 216 Ramachandran restraints generated. 108 Oldfield, 0 Emsley, 108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 216 Ramachandran restraints generated. 108 Oldfield, 0 Emsley, 108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 24 time to evaluate : 0.052 Fit side-chains REVERT: M 2 LYS cc_start: 0.6087 (mmmt) cc_final: 0.5718 (tppt) REVERT: D 2 LYS cc_start: 0.9085 (mttt) cc_final: 0.8480 (pptt) REVERT: Q 6 LYS cc_start: 0.8545 (mmtp) cc_final: 0.8215 (mmtm) REVERT: R 6 LYS cc_start: 0.8394 (mmmt) cc_final: 0.8097 (mmtm) REVERT: S 2 LYS cc_start: 0.9099 (mttt) cc_final: 0.8660 (mmmt) REVERT: T 6 LYS cc_start: 0.8356 (mmtt) cc_final: 0.8112 (mmmt) REVERT: U 2 LYS cc_start: 0.3752 (OUTLIER) cc_final: 0.2474 (tptt) REVERT: F 2 LYS cc_start: 0.6128 (OUTLIER) cc_final: 0.5129 (pttm) REVERT: W 2 LYS cc_start: 0.8627 (mttt) cc_final: 0.8056 (tppt) outliers start: 10 outliers final: 6 residues processed: 33 average time/residue: 0.1176 time to fit residues: 4.1151 Evaluate side-chains 31 residues out of total 126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 23 time to evaluate : 0.037 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 3 PHE Chi-restraints excluded: chain L residue 5 PHE Chi-restraints excluded: chain T residue 5 PHE Chi-restraints excluded: chain T residue 7 PHE Chi-restraints excluded: chain U residue 2 LYS Chi-restraints excluded: chain F residue 2 LYS Chi-restraints excluded: chain X residue 3 PHE Chi-restraints excluded: chain X residue 5 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: [0] chunk 0 optimal weight: 6.9990 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.079906 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.073453 restraints weight = 10051.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.075001 restraints weight = 4147.307| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.076067 restraints weight = 2262.071| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.076774 restraints weight = 1435.113| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.077238 restraints weight = 1026.001| |-----------------------------------------------------------------------------| r_work (final): 0.3574 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7597 moved from start: 1.0681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.041 1476 Z= 0.406 Angle : 1.593 13.899 1872 Z= 0.657 Chirality : 0.062 0.180 126 Planarity : 0.005 0.038 234 Dihedral : 58.899 179.056 162 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 19.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.48 % Favored : 93.52 % Rotamer: Outliers : 8.73 % Allowed : 23.81 % Favored : 67.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.36 (0.56), residues: 108 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.31 (0.43), residues: 108 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.015 0.002 PHE U 5 Details of bonding type rmsd/Z covalent geometry : bond 0.00991 / 0.41 ( 1458) covalent geometry : angle 1.59256 / 0.66 ( 1872) hydrogen bonds : bond 0.04351 / 2.72 ( 32) hydrogen bonds : angle 10.16572 / 6.24 ( 72) Misc. bond : bond 0.00033 / 0.02 ( 18) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 216 Ramachandran restraints generated. 108 Oldfield, 0 Emsley, 108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 216 Ramachandran restraints generated. 108 Oldfield, 0 Emsley, 108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 23 time to evaluate : 0.037 Fit side-chains REVERT: D 2 LYS cc_start: 0.9063 (mttt) cc_final: 0.8464 (pptt) REVERT: Q 6 LYS cc_start: 0.8571 (mmtp) cc_final: 0.8238 (mmtm) REVERT: R 6 LYS cc_start: 0.8372 (mmmt) cc_final: 0.8107 (mmtm) REVERT: S 2 LYS cc_start: 0.9122 (mttt) cc_final: 0.8748 (mmmt) REVERT: T 6 LYS cc_start: 0.8360 (mmtt) cc_final: 0.8135 (mmmt) REVERT: U 2 LYS cc_start: 0.3682 (OUTLIER) cc_final: 0.2319 (tptt) REVERT: F 2 LYS cc_start: 0.6068 (OUTLIER) cc_final: 0.5052 (pttm) REVERT: W 2 LYS cc_start: 0.8655 (mttt) cc_final: 0.8067 (tppt) REVERT: W 4 GLU cc_start: 0.7886 (mp0) cc_final: 0.7580 (mp0) REVERT: W 5 PHE cc_start: 0.8603 (OUTLIER) cc_final: 0.8247 (m-10) outliers start: 11 outliers final: 7 residues processed: 33 average time/residue: 0.1310 time to fit residues: 4.5863 Evaluate side-chains 31 residues out of total 126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 21 time to evaluate : 0.059 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 3 PHE Chi-restraints excluded: chain L residue 5 PHE Chi-restraints excluded: chain T residue 5 PHE Chi-restraints excluded: chain T residue 7 PHE Chi-restraints excluded: chain U residue 2 LYS Chi-restraints excluded: chain F residue 2 LYS Chi-restraints excluded: chain X residue 3 PHE Chi-restraints excluded: chain X residue 5 PHE Chi-restraints excluded: chain W residue 5 PHE Chi-restraints excluded: chain Y residue 5 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: [0] chunk 0 optimal weight: 6.9990 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.080282 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.074099 restraints weight = 8756.991| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.075702 restraints weight = 3674.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.076710 restraints weight = 2046.721| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.077394 restraints weight = 1304.980| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.077724 restraints weight = 933.701| |-----------------------------------------------------------------------------| r_work (final): 0.3577 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7533 moved from start: 1.0938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.041 1476 Z= 0.400 Angle : 1.599 13.873 1872 Z= 0.658 Chirality : 0.061 0.174 126 Planarity : 0.005 0.037 234 Dihedral : 58.903 179.613 162 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 21.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.48 % Favored : 93.52 % Rotamer: Outliers : 9.52 % Allowed : 24.60 % Favored : 65.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.65 (0.53), residues: 108 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.54 (0.40), residues: 108 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.016 0.002 PHE U 5 Details of bonding type rmsd/Z covalent geometry : bond 0.00981 / 0.40 ( 1458) covalent geometry : angle 1.59937 / 0.66 ( 1872) hydrogen bonds : bond 0.04439 / 2.73 ( 32) hydrogen bonds : angle 10.32516 / 6.26 ( 72) Misc. bond : bond 0.00036 / 0.02 ( 18) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 216 Ramachandran restraints generated. 108 Oldfield, 0 Emsley, 108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 216 Ramachandran restraints generated. 108 Oldfield, 0 Emsley, 108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 23 time to evaluate : 0.035 Fit side-chains REVERT: D 2 LYS cc_start: 0.9089 (mttt) cc_final: 0.8440 (pptt) REVERT: Q 6 LYS cc_start: 0.8572 (mmtp) cc_final: 0.8224 (mmtm) REVERT: R 6 LYS cc_start: 0.8352 (mmmt) cc_final: 0.8039 (mmtm) REVERT: S 2 LYS cc_start: 0.9118 (mttt) cc_final: 0.8679 (mmmt) REVERT: T 6 LYS cc_start: 0.8367 (mmtt) cc_final: 0.8145 (mmmt) REVERT: U 2 LYS cc_start: 0.3511 (OUTLIER) cc_final: 0.2300 (tptt) REVERT: F 2 LYS cc_start: 0.5832 (OUTLIER) cc_final: 0.4842 (pttm) REVERT: E 4 GLU cc_start: 0.3375 (OUTLIER) cc_final: 0.2401 (pm20) REVERT: E 6 LYS cc_start: 0.5757 (OUTLIER) cc_final: 0.5295 (pttm) REVERT: W 2 LYS cc_start: 0.8563 (mttt) cc_final: 0.7917 (tppt) REVERT: W 4 GLU cc_start: 0.7924 (mp0) cc_final: 0.7707 (mp0) outliers start: 12 outliers final: 7 residues processed: 34 average time/residue: 0.1423 time to fit residues: 5.0880 Evaluate side-chains 31 residues out of total 126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 20 time to evaluate : 0.059 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 3 PHE Chi-restraints excluded: chain L residue 5 PHE Chi-restraints excluded: chain T residue 5 PHE Chi-restraints excluded: chain T residue 7 PHE Chi-restraints excluded: chain U residue 2 LYS Chi-restraints excluded: chain F residue 2 LYS Chi-restraints excluded: chain X residue 3 PHE Chi-restraints excluded: chain X residue 5 PHE Chi-restraints excluded: chain E residue 4 GLU Chi-restraints excluded: chain E residue 6 LYS Chi-restraints excluded: chain Y residue 5 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: [0] chunk 0 optimal weight: 6.9990 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.080131 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.073706 restraints weight = 10070.998| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.075352 restraints weight = 4061.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.076300 restraints weight = 2245.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.077040 restraints weight = 1502.311| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.077516 restraints weight = 1042.013| |-----------------------------------------------------------------------------| r_work (final): 0.3570 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7534 moved from start: 1.1141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.041 1476 Z= 0.400 Angle : 1.607 13.867 1872 Z= 0.661 Chirality : 0.062 0.175 126 Planarity : 0.005 0.038 234 Dihedral : 58.930 179.916 162 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 19.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.41 % Favored : 92.59 % Rotamer: Outliers : 10.32 % Allowed : 23.02 % Favored : 66.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.67 (0.55), residues: 108 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.56 (0.42), residues: 108 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.016 0.002 PHE M 5 Details of bonding type rmsd/Z covalent geometry : bond 0.00982 / 0.40 ( 1458) covalent geometry : angle 1.60685 / 0.66 ( 1872) hydrogen bonds : bond 0.04453 / 2.74 ( 32) hydrogen bonds : angle 10.22557 / 6.18 ( 72) Misc. bond : bond 0.00036 / 0.02 ( 18) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 216 Ramachandran restraints generated. 108 Oldfield, 0 Emsley, 108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 216 Ramachandran restraints generated. 108 Oldfield, 0 Emsley, 108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 24 time to evaluate : 0.063 Fit side-chains REVERT: D 2 LYS cc_start: 0.9084 (mttt) cc_final: 0.8440 (pptt) REVERT: Q 6 LYS cc_start: 0.8520 (mmtp) cc_final: 0.8191 (mmtm) REVERT: R 6 LYS cc_start: 0.8348 (mmmt) cc_final: 0.8035 (mmtm) REVERT: S 2 LYS cc_start: 0.9093 (mttt) cc_final: 0.8660 (mmmt) REVERT: S 6 LYS cc_start: 0.8728 (mmtm) cc_final: 0.8468 (mmtm) REVERT: T 6 LYS cc_start: 0.8376 (mmtt) cc_final: 0.8154 (mmmt) REVERT: U 2 LYS cc_start: 0.3715 (OUTLIER) cc_final: 0.2469 (tptt) REVERT: F 2 LYS cc_start: 0.5849 (OUTLIER) cc_final: 0.4832 (pttm) REVERT: F 4 GLU cc_start: 0.3935 (OUTLIER) cc_final: 0.2625 (pm20) REVERT: E 4 GLU cc_start: 0.3486 (OUTLIER) cc_final: 0.2497 (pm20) REVERT: E 6 LYS cc_start: 0.5794 (OUTLIER) cc_final: 0.5338 (pttm) REVERT: W 2 LYS cc_start: 0.8563 (mttt) cc_final: 0.7904 (tppt) REVERT: W 4 GLU cc_start: 0.7965 (mp0) cc_final: 0.7745 (mp0) outliers start: 13 outliers final: 7 residues processed: 35 average time/residue: 0.1338 time to fit residues: 4.9215 Evaluate side-chains 35 residues out of total 126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 23 time to evaluate : 0.065 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 3 PHE Chi-restraints excluded: chain L residue 5 PHE Chi-restraints excluded: chain T residue 5 PHE Chi-restraints excluded: chain T residue 7 PHE Chi-restraints excluded: chain U residue 2 LYS Chi-restraints excluded: chain F residue 2 LYS Chi-restraints excluded: chain F residue 4 GLU Chi-restraints excluded: chain X residue 3 PHE Chi-restraints excluded: chain X residue 5 PHE Chi-restraints excluded: chain E residue 4 GLU Chi-restraints excluded: chain E residue 6 LYS Chi-restraints excluded: chain Y residue 5 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: [0] chunk 0 optimal weight: 6.9990 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.079982 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.073877 restraints weight = 8352.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.075394 restraints weight = 3600.527| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.076393 restraints weight = 2044.419| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.076982 restraints weight = 1327.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.077414 restraints weight = 967.215| |-----------------------------------------------------------------------------| r_work (final): 0.3564 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7525 moved from start: 1.1211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.041 1476 Z= 0.399 Angle : 1.632 13.894 1872 Z= 0.673 Chirality : 0.062 0.176 126 Planarity : 0.005 0.038 234 Dihedral : 58.967 179.751 162 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 22.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.41 % Favored : 92.59 % Rotamer: Outliers : 9.52 % Allowed : 24.60 % Favored : 65.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.80 (0.55), residues: 108 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.65 (0.42), residues: 108 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.017 0.002 PHE M 5 Details of bonding type rmsd/Z covalent geometry : bond 0.00980 / 0.40 ( 1458) covalent geometry : angle 1.63162 / 0.67 ( 1872) hydrogen bonds : bond 0.04551 / 2.77 ( 32) hydrogen bonds : angle 10.26997 / 6.20 ( 72) Misc. bond : bond 0.00034 / 0.02 ( 18) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 216 Ramachandran restraints generated. 108 Oldfield, 0 Emsley, 108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 216 Ramachandran restraints generated. 108 Oldfield, 0 Emsley, 108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 24 time to evaluate : 0.044 Fit side-chains REVERT: D 2 LYS cc_start: 0.9081 (mttt) cc_final: 0.8415 (pptt) REVERT: Q 6 LYS cc_start: 0.8541 (mmtp) cc_final: 0.8205 (mmtm) REVERT: R 6 LYS cc_start: 0.8341 (mmmt) cc_final: 0.8018 (mmtm) REVERT: S 2 LYS cc_start: 0.9101 (mttt) cc_final: 0.8648 (mmmt) REVERT: S 6 LYS cc_start: 0.8719 (mmtm) cc_final: 0.8461 (mmtm) REVERT: T 6 LYS cc_start: 0.8365 (mmtt) cc_final: 0.8144 (mmmt) REVERT: U 2 LYS cc_start: 0.3704 (OUTLIER) cc_final: 0.2461 (tptt) REVERT: F 2 LYS cc_start: 0.5854 (OUTLIER) cc_final: 0.4846 (pttm) REVERT: F 4 GLU cc_start: 0.3915 (OUTLIER) cc_final: 0.2610 (pm20) REVERT: E 4 GLU cc_start: 0.3545 (OUTLIER) cc_final: 0.2549 (pm20) REVERT: E 6 LYS cc_start: 0.5778 (OUTLIER) cc_final: 0.5326 (pttm) REVERT: W 2 LYS cc_start: 0.8528 (mttt) cc_final: 0.7859 (tppt) REVERT: W 4 GLU cc_start: 0.7953 (mp0) cc_final: 0.7728 (mp0) outliers start: 12 outliers final: 7 residues processed: 34 average time/residue: 0.1393 time to fit residues: 4.9846 Evaluate side-chains 34 residues out of total 126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 22 time to evaluate : 0.059 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 3 PHE Chi-restraints excluded: chain L residue 5 PHE Chi-restraints excluded: chain T residue 5 PHE Chi-restraints excluded: chain T residue 7 PHE Chi-restraints excluded: chain U residue 2 LYS Chi-restraints excluded: chain F residue 2 LYS Chi-restraints excluded: chain F residue 4 GLU Chi-restraints excluded: chain X residue 3 PHE Chi-restraints excluded: chain X residue 5 PHE Chi-restraints excluded: chain E residue 4 GLU Chi-restraints excluded: chain E residue 6 LYS Chi-restraints excluded: chain Y residue 5 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: [0] chunk 0 optimal weight: 6.9990 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.080421 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.074027 restraints weight = 9200.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.075593 restraints weight = 3886.137| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.076593 restraints weight = 2192.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.077213 restraints weight = 1444.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.077664 restraints weight = 1055.872| |-----------------------------------------------------------------------------| r_work (final): 0.3560 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7574 moved from start: 1.1327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.041 1476 Z= 0.398 Angle : 1.636 13.902 1872 Z= 0.675 Chirality : 0.063 0.176 126 Planarity : 0.005 0.038 234 Dihedral : 58.950 179.585 162 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 23.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.33 % Favored : 91.67 % Rotamer: Outliers : 11.11 % Allowed : 25.40 % Favored : 63.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.78 (0.56), residues: 108 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.63 (0.43), residues: 108 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.017 0.002 PHE M 5 Details of bonding type rmsd/Z covalent geometry : bond 0.00984 / 0.40 ( 1458) covalent geometry : angle 1.63646 / 0.68 ( 1872) hydrogen bonds : bond 0.04608 / 2.76 ( 32) hydrogen bonds : angle 10.04425 / 6.01 ( 72) Misc. bond : bond 0.00037 / 0.02 ( 18) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 306.48 seconds wall clock time: 6 minutes 5.74 seconds (365.74 seconds total)