Starting phenix.real_space_refine on Tue Feb 3 12:20:36 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jhi_61483/02_2026/9jhi_61483.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jhi_61483/02_2026/9jhi_61483.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.73 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9jhi_61483/02_2026/9jhi_61483.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jhi_61483/02_2026/9jhi_61483.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9jhi_61483/02_2026/9jhi_61483.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jhi_61483/02_2026/9jhi_61483.map" } resolution = 3.73 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= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 12 5.16 5 C 930 2.51 5 N 222 2.21 5 O 270 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 1434 Number of models: 1 Model: "" Number of chains: 1 Chain: "AE" Number of atoms: 239 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 239 Classifications: {'peptide': 32} Link IDs: {'TRANS': 31} Restraints were copied for chains: AA, AD, AB, AF, AC Time building chain proxies: 0.32, per 1000 atoms: 0.22 Number of scatterers: 1434 At special positions: 0 Unit cell: (82.17, 60.59, 29.88, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 12 16.00 O 270 8.00 N 222 7.00 C 930 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.14 Conformation dependent library (CDL) restraints added in 58.2 milliseconds 360 Ramachandran restraints generated. 180 Oldfield, 0 Emsley, 180 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 360 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 4 sheets defined 0.0% alpha, 65.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.05 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'AD' and resid 2 through 13 removed outlier: 7.001A pdb=" N VALAD 3 " --> pdb=" O ILEAE 2 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N THRAE 4 " --> pdb=" O VALAD 3 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N GLNAD 5 " --> pdb=" O THRAE 4 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N THRAE 6 " --> pdb=" O GLNAD 5 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N METAD 7 " --> pdb=" O THRAE 6 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N LYSAE 8 " --> pdb=" O METAD 7 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N GLYAD 9 " --> pdb=" O LYSAE 8 " (cutoff:3.500A) removed outlier: 9.162A pdb=" N VALAE 3 " --> pdb=" O THRAF 4 " (cutoff:3.500A) removed outlier: 9.971A pdb=" N THRAF 6 " --> pdb=" O VALAE 3 " (cutoff:3.500A) removed outlier: 8.712A pdb=" N GLNAE 5 " --> pdb=" O THRAF 6 " (cutoff:3.500A) removed outlier: 10.228A pdb=" N LYSAF 8 " --> pdb=" O GLNAE 5 " (cutoff:3.500A) removed outlier: 9.011A pdb=" N METAE 7 " --> pdb=" O LYSAF 8 " (cutoff:3.500A) removed outlier: 8.944A pdb=" N LEUAF 10 " --> pdb=" O METAE 7 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N GLYAE 9 " --> pdb=" O LEUAF 10 " (cutoff:3.500A) removed outlier: 7.937A pdb=" N ILEAF 12 " --> pdb=" O GLYAE 9 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N ASPAE 11 " --> pdb=" O ILEAF 12 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'AD' and resid 21 through 31 removed outlier: 5.337A pdb=" N SERAE 21 " --> pdb=" O LEUAD 22 " (cutoff:3.500A) removed outlier: 7.391A pdb=" N METAD 24 " --> pdb=" O SERAE 21 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N ALAAE 23 " --> pdb=" O METAD 24 " (cutoff:3.500A) removed outlier: 8.306A pdb=" N ALAAD 26 " --> pdb=" O ALAAE 23 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N ALAAE 25 " --> pdb=" O ALAAD 26 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N ASPAD 28 " --> pdb=" O ALAAE 25 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N SERAE 27 " --> pdb=" O ASPAD 28 " (cutoff:3.500A) removed outlier: 10.127A pdb=" N SERAD 30 " --> pdb=" O SERAE 27 " (cutoff:3.500A) removed outlier: 8.672A pdb=" N ILEAE 29 " --> pdb=" O SERAD 30 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N LEUAE 22 " --> pdb=" O SERAF 21 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N SERAF 27 " --> pdb=" O ALAAE 26 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N ASPAE 28 " --> pdb=" O SERAF 27 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N ILEAF 29 " --> pdb=" O ASPAE 28 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N SERAE 30 " --> pdb=" O ILEAF 29 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N LEUAF 31 " --> pdb=" O SERAE 30 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'AB' and resid 2 through 13 removed outlier: 7.001A pdb=" N VALAB 3 " --> pdb=" O ILEAA 2 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N THRAA 4 " --> pdb=" O VALAB 3 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N GLNAB 5 " --> pdb=" O THRAA 4 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N THRAA 6 " --> pdb=" O GLNAB 5 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N METAB 7 " --> pdb=" O THRAA 6 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N LYSAA 8 " --> pdb=" O METAB 7 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N GLYAB 9 " --> pdb=" O LYSAA 8 " (cutoff:3.500A) removed outlier: 9.161A pdb=" N VALAA 3 " --> pdb=" O THRAC 4 " (cutoff:3.500A) removed outlier: 9.970A pdb=" N THRAC 6 " --> pdb=" O VALAA 3 " (cutoff:3.500A) removed outlier: 8.712A pdb=" N GLNAA 5 " --> pdb=" O THRAC 6 " (cutoff:3.500A) removed outlier: 10.226A pdb=" N LYSAC 8 " --> pdb=" O GLNAA 5 " (cutoff:3.500A) removed outlier: 9.010A pdb=" N METAA 7 " --> pdb=" O LYSAC 8 " (cutoff:3.500A) removed outlier: 8.942A pdb=" N LEUAC 10 " --> pdb=" O METAA 7 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N GLYAA 9 " --> pdb=" O LEUAC 10 " (cutoff:3.500A) removed outlier: 7.936A pdb=" N ILEAC 12 " --> pdb=" O GLYAA 9 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N ASPAA 11 " --> pdb=" O ILEAC 12 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'AB' and resid 21 through 31 removed outlier: 5.338A pdb=" N SERAA 21 " --> pdb=" O LEUAB 22 " (cutoff:3.500A) removed outlier: 7.391A pdb=" N METAB 24 " --> pdb=" O SERAA 21 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N ALAAA 23 " --> pdb=" O METAB 24 " (cutoff:3.500A) removed outlier: 8.305A pdb=" N ALAAB 26 " --> pdb=" O ALAAA 23 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N ALAAA 25 " --> pdb=" O ALAAB 26 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N ASPAB 28 " --> pdb=" O ALAAA 25 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N SERAA 27 " --> pdb=" O ASPAB 28 " (cutoff:3.500A) removed outlier: 10.126A pdb=" N SERAB 30 " --> pdb=" O SERAA 27 " (cutoff:3.500A) removed outlier: 8.673A pdb=" N ILEAA 29 " --> pdb=" O SERAB 30 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N LEUAA 22 " --> pdb=" O SERAC 21 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N SERAC 27 " --> pdb=" O ALAAA 26 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N ASPAA 28 " --> pdb=" O SERAC 27 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N ILEAC 29 " --> pdb=" O ASPAA 28 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N SERAA 30 " --> pdb=" O ILEAC 29 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N LEUAC 31 " --> pdb=" O SERAA 30 " (cutoff:3.500A) 16 hydrogen bonds defined for protein. 48 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: 0.22 Time building geometry restraints manager: 0.15 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 426 1.34 - 1.46: 269 1.46 - 1.57: 727 1.57 - 1.68: 0 1.68 - 1.80: 24 Bond restraints: 1446 Sorted by residual: bond pdb=" N VALAA 15 " pdb=" CA VALAA 15 " ideal model delta sigma weight residual 1.459 1.493 -0.034 1.25e-02 6.40e+03 7.29e+00 bond pdb=" N VALAE 15 " pdb=" CA VALAE 15 " ideal model delta sigma weight residual 1.459 1.493 -0.034 1.25e-02 6.40e+03 7.29e+00 bond pdb=" N VALAB 15 " pdb=" CA VALAB 15 " ideal model delta sigma weight residual 1.459 1.492 -0.033 1.25e-02 6.40e+03 7.16e+00 bond pdb=" N LEUAC 31 " pdb=" CA LEUAC 31 " ideal model delta sigma weight residual 1.455 1.488 -0.033 1.25e-02 6.40e+03 7.13e+00 bond pdb=" N LEUAA 31 " pdb=" CA LEUAA 31 " ideal model delta sigma weight residual 1.455 1.488 -0.033 1.25e-02 6.40e+03 7.09e+00 ... (remaining 1441 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.10: 1706 1.10 - 2.20: 183 2.20 - 3.30: 37 3.30 - 4.40: 24 4.40 - 5.50: 6 Bond angle restraints: 1956 Sorted by residual: angle pdb=" CA VALAA 15 " pdb=" C VALAA 15 " pdb=" O VALAA 15 " ideal model delta sigma weight residual 120.78 117.88 2.90 1.25e+00 6.40e-01 5.38e+00 angle pdb=" CA VALAB 15 " pdb=" C VALAB 15 " pdb=" O VALAB 15 " ideal model delta sigma weight residual 120.78 117.90 2.88 1.25e+00 6.40e-01 5.30e+00 angle pdb=" CA VALAE 15 " pdb=" C VALAE 15 " pdb=" O VALAE 15 " ideal model delta sigma weight residual 120.78 117.95 2.83 1.25e+00 6.40e-01 5.12e+00 angle pdb=" CA VALAF 15 " pdb=" C VALAF 15 " pdb=" O VALAF 15 " ideal model delta sigma weight residual 120.78 117.96 2.82 1.25e+00 6.40e-01 5.10e+00 angle pdb=" CA VALAC 15 " pdb=" C VALAC 15 " pdb=" O VALAC 15 " ideal model delta sigma weight residual 120.78 117.99 2.79 1.25e+00 6.40e-01 5.00e+00 ... (remaining 1951 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 10.17: 720 10.17 - 20.34: 84 20.34 - 30.51: 42 30.51 - 40.67: 6 40.67 - 50.84: 12 Dihedral angle restraints: 864 sinusoidal: 312 harmonic: 552 Sorted by residual: dihedral pdb=" CA ILEAC 12 " pdb=" CB ILEAC 12 " pdb=" CG1 ILEAC 12 " pdb=" CD1 ILEAC 12 " ideal model delta sinusoidal sigma weight residual 180.00 129.16 50.84 3 1.50e+01 4.44e-03 8.95e+00 dihedral pdb=" CA ILEAF 12 " pdb=" CB ILEAF 12 " pdb=" CG1 ILEAF 12 " pdb=" CD1 ILEAF 12 " ideal model delta sinusoidal sigma weight residual 180.00 129.18 50.82 3 1.50e+01 4.44e-03 8.94e+00 dihedral pdb=" CA ILEAA 12 " pdb=" CB ILEAA 12 " pdb=" CG1 ILEAA 12 " pdb=" CD1 ILEAA 12 " ideal model delta sinusoidal sigma weight residual 180.00 129.19 50.81 3 1.50e+01 4.44e-03 8.94e+00 ... (remaining 861 not shown) Histogram of chiral volume deviations from ideal: 0.001 - 0.034: 156 0.034 - 0.066: 48 0.066 - 0.098: 18 0.098 - 0.131: 18 0.131 - 0.163: 18 Chirality restraints: 258 Sorted by residual: chirality pdb=" CA LEUAE 31 " pdb=" N LEUAE 31 " pdb=" C LEUAE 31 " pdb=" CB LEUAE 31 " both_signs ideal model delta sigma weight residual False 2.51 2.67 -0.16 2.00e-01 2.50e+01 6.63e-01 chirality pdb=" CA LEUAA 31 " pdb=" N LEUAA 31 " pdb=" C LEUAA 31 " pdb=" CB LEUAA 31 " both_signs ideal model delta sigma weight residual False 2.51 2.67 -0.16 2.00e-01 2.50e+01 6.63e-01 chirality pdb=" CA LEUAC 31 " pdb=" N LEUAC 31 " pdb=" C LEUAC 31 " pdb=" CB LEUAC 31 " both_signs ideal model delta sigma weight residual False 2.51 2.67 -0.16 2.00e-01 2.50e+01 6.49e-01 ... (remaining 255 not shown) Planarity restraints: 222 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASPAB 28 " -0.006 2.00e-02 2.50e+03 1.21e-02 1.46e+00 pdb=" C ASPAB 28 " 0.021 2.00e-02 2.50e+03 pdb=" O ASPAB 28 " -0.008 2.00e-02 2.50e+03 pdb=" N ILEAB 29 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASPAD 28 " 0.006 2.00e-02 2.50e+03 1.19e-02 1.43e+00 pdb=" C ASPAD 28 " -0.021 2.00e-02 2.50e+03 pdb=" O ASPAD 28 " 0.008 2.00e-02 2.50e+03 pdb=" N ILEAD 29 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASPAF 28 " 0.006 2.00e-02 2.50e+03 1.19e-02 1.42e+00 pdb=" C ASPAF 28 " -0.021 2.00e-02 2.50e+03 pdb=" O ASPAF 28 " 0.008 2.00e-02 2.50e+03 pdb=" N ILEAF 29 " 0.007 2.00e-02 2.50e+03 ... (remaining 219 not shown) Histogram of nonbonded interaction distances: 2.50 - 2.98: 823 2.98 - 3.46: 1339 3.46 - 3.94: 2154 3.94 - 4.42: 2235 4.42 - 4.90: 4552 Nonbonded interactions: 11103 Sorted by model distance: nonbonded pdb=" C LEUAC 31 " pdb=" CD1 LEUAC 32 " model vdw 2.504 3.690 nonbonded pdb=" C LEUAD 31 " pdb=" CD1 LEUAD 32 " model vdw 2.504 3.690 nonbonded pdb=" C LEUAB 31 " pdb=" CD1 LEUAB 32 " model vdw 2.504 3.690 nonbonded pdb=" C LEUAA 31 " pdb=" CD1 LEUAA 32 " model vdw 2.504 3.690 nonbonded pdb=" C LEUAF 31 " pdb=" CD1 LEUAF 32 " model vdw 2.504 3.690 ... (remaining 11098 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: 0.01 Found NCS groups: ncs_group { reference = chain 'AE' selection = chain 'AA' selection = chain 'AD' selection = chain 'AB' selection = chain 'AF' selection = chain 'AC' } 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: 0.730 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: 0.040 Check model and map are aligned: 0.010 Set scattering table: 0.000 Process input model: 3.840 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:1.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 5.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7572 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 : 0.009 0.034 1446 Z= 0.495 Angle : 0.893 5.500 1956 Z= 0.490 Chirality : 0.060 0.163 258 Planarity : 0.004 0.012 222 Dihedral : 13.105 50.843 504 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 44.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.56 % Favored : 84.44 % Rotamer: Outliers : 0.00 % Allowed : 15.38 % Favored : 84.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -4.42 (0.51), residues: 180 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.36 (0.39), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.005 0.002 TYRAD 20 TRP 0.009 0.003 TRPAF 19 Details of bonding type rmsd covalent geometry : bond 0.00917 ( 1446) covalent geometry : angle 0.89297 ( 1956) hydrogen bonds : bond 0.14828 ( 16) hydrogen bonds : angle 7.97237 ( 48) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 360 Ramachandran restraints generated. 180 Oldfield, 0 Emsley, 180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 360 Ramachandran restraints generated. 180 Oldfield, 0 Emsley, 180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 60 time to evaluate : 0.035 Fit side-chains REVERT: AE 7 MET cc_start: 0.7729 (mpp) cc_final: 0.7513 (mpp) REVERT: AE 8 LYS cc_start: 0.7677 (mttt) cc_final: 0.7324 (mttm) REVERT: AE 10 LEU cc_start: 0.8198 (mp) cc_final: 0.7994 (mt) REVERT: AA 7 MET cc_start: 0.7725 (mpp) cc_final: 0.7496 (mpp) REVERT: AA 8 LYS cc_start: 0.7693 (mttt) cc_final: 0.7333 (mttm) REVERT: AD 7 MET cc_start: 0.7551 (mpp) cc_final: 0.6679 (mtt) REVERT: AD 8 LYS cc_start: 0.7484 (mttt) cc_final: 0.6058 (mmmt) REVERT: AD 29 ILE cc_start: 0.7189 (pt) cc_final: 0.6808 (tp) REVERT: AB 7 MET cc_start: 0.7525 (mpp) cc_final: 0.6663 (mtt) REVERT: AB 8 LYS cc_start: 0.7495 (mttt) cc_final: 0.6063 (mmmt) REVERT: AB 29 ILE cc_start: 0.7195 (pt) cc_final: 0.6823 (tp) REVERT: AF 7 MET cc_start: 0.7414 (mpp) cc_final: 0.6358 (mtt) REVERT: AF 10 LEU cc_start: 0.8199 (mp) cc_final: 0.7943 (mt) REVERT: AC 7 MET cc_start: 0.7414 (mpp) cc_final: 0.6373 (mtt) REVERT: AC 10 LEU cc_start: 0.8196 (mp) cc_final: 0.7945 (mt) outliers start: 0 outliers final: 0 residues processed: 60 average time/residue: 0.0615 time to fit residues: 4.1188 Evaluate side-chains 43 residues out of total 156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 43 time to evaluate : 0.053 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 12 optimal weight: 5.9990 chunk 13 optimal weight: 5.9990 chunk 1 optimal weight: 2.9990 chunk 8 optimal weight: 7.9990 chunk 16 optimal weight: 0.9990 chunk 15 optimal weight: 5.9990 chunk 9 optimal weight: 0.8980 chunk 11 optimal weight: 0.7980 chunk 6 optimal weight: 2.9990 chunk 4 optimal weight: 0.7980 chunk 3 optimal weight: 0.9980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: AE 13 GLN AA 13 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4452 r_free = 0.4452 target = 0.151202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4267 r_free = 0.4267 target = 0.133120 restraints weight = 2100.006| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4304 r_free = 0.4304 target = 0.137117 restraints weight = 923.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4326 r_free = 0.4326 target = 0.139494 restraints weight = 526.140| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4341 r_free = 0.4341 target = 0.141032 restraints weight = 359.614| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4351 r_free = 0.4351 target = 0.142035 restraints weight = 277.823| |-----------------------------------------------------------------------------| r_work (final): 0.4359 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7514 moved from start: 0.3413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 1446 Z= 0.126 Angle : 0.732 8.016 1956 Z= 0.318 Chirality : 0.051 0.191 258 Planarity : 0.002 0.007 222 Dihedral : 3.508 10.413 192 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 11.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.22 % Favored : 87.78 % Rotamer: Outliers : 5.77 % Allowed : 16.03 % Favored : 78.21 % 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: -3.94 (0.54), residues: 180 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.00 (0.41), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.008 0.001 TYRAA 20 TRP 0.014 0.002 TRPAE 19 Details of bonding type rmsd covalent geometry : bond 0.00274 ( 1446) covalent geometry : angle 0.73167 ( 1956) hydrogen bonds : bond 0.02705 ( 16) hydrogen bonds : angle 5.85419 ( 48) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 360 Ramachandran restraints generated. 180 Oldfield, 0 Emsley, 180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 360 Ramachandran restraints generated. 180 Oldfield, 0 Emsley, 180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 49 time to evaluate : 0.055 Fit side-chains REVERT: AE 8 LYS cc_start: 0.7747 (mttt) cc_final: 0.7110 (mttm) REVERT: AA 8 LYS cc_start: 0.7761 (mttt) cc_final: 0.7155 (mttm) REVERT: AD 7 MET cc_start: 0.7786 (mpp) cc_final: 0.6813 (mtt) REVERT: AD 8 LYS cc_start: 0.7451 (mttt) cc_final: 0.5738 (mmmt) REVERT: AB 7 MET cc_start: 0.7732 (mpp) cc_final: 0.6770 (mtt) REVERT: AB 8 LYS cc_start: 0.7436 (mttt) cc_final: 0.5739 (mmmt) REVERT: AF 7 MET cc_start: 0.7300 (mpp) cc_final: 0.6940 (mtt) REVERT: AC 7 MET cc_start: 0.7282 (mpp) cc_final: 0.6975 (mtt) outliers start: 9 outliers final: 3 residues processed: 49 average time/residue: 0.0451 time to fit residues: 2.5767 Evaluate side-chains 42 residues out of total 156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 39 time to evaluate : 0.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AE residue 6 THR Chi-restraints excluded: chain AD residue 6 THR Chi-restraints excluded: chain AB residue 6 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 3 optimal weight: 9.9990 chunk 12 optimal weight: 2.9990 chunk 11 optimal weight: 9.9990 chunk 15 optimal weight: 0.9990 chunk 1 optimal weight: 10.0000 chunk 0 optimal weight: 3.9990 chunk 8 optimal weight: 9.9990 chunk 9 optimal weight: 9.9990 chunk 6 optimal weight: 2.9990 chunk 16 optimal weight: 6.9990 chunk 10 optimal weight: 6.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- 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 = 0.4483 r_free = 0.4483 target = 0.148464 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4310 r_free = 0.4310 target = 0.130834 restraints weight = 2113.617| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4340 r_free = 0.4340 target = 0.134119 restraints weight = 901.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4361 r_free = 0.4361 target = 0.136230 restraints weight = 507.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.4374 r_free = 0.4374 target = 0.137761 restraints weight = 349.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4382 r_free = 0.4382 target = 0.138579 restraints weight = 269.109| |-----------------------------------------------------------------------------| r_work (final): 0.4397 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7463 moved from start: 0.4858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 1446 Z= 0.230 Angle : 0.740 6.697 1956 Z= 0.353 Chirality : 0.049 0.230 258 Planarity : 0.003 0.010 222 Dihedral : 4.484 12.890 192 Min Nonbonded Distance : 2.628 Molprobity Statistics. All-atom Clashscore : 20.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.89 % Favored : 91.11 % Rotamer: Outliers : 5.13 % Allowed : 12.18 % Favored : 82.69 % 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: -4.11 (0.47), residues: 180 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.13 (0.36), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.004 0.001 TYRAC 20 TRP 0.009 0.003 TRPAD 19 Details of bonding type rmsd covalent geometry : bond 0.00527 ( 1446) covalent geometry : angle 0.73976 ( 1956) hydrogen bonds : bond 0.02220 ( 16) hydrogen bonds : angle 5.18626 ( 48) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 360 Ramachandran restraints generated. 180 Oldfield, 0 Emsley, 180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 360 Ramachandran restraints generated. 180 Oldfield, 0 Emsley, 180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 49 time to evaluate : 0.055 Fit side-chains REVERT: AE 8 LYS cc_start: 0.7678 (mttt) cc_final: 0.7100 (mttm) REVERT: AA 8 LYS cc_start: 0.7683 (mttt) cc_final: 0.7103 (mttm) REVERT: AD 7 MET cc_start: 0.7361 (mpp) cc_final: 0.6924 (mtt) REVERT: AD 8 LYS cc_start: 0.7518 (mttt) cc_final: 0.5833 (mmmt) REVERT: AB 7 MET cc_start: 0.7395 (mpp) cc_final: 0.6938 (mtt) REVERT: AB 8 LYS cc_start: 0.7554 (mttt) cc_final: 0.5878 (mmmt) REVERT: AC 22 LEU cc_start: 0.8087 (OUTLIER) cc_final: 0.7536 (tt) outliers start: 8 outliers final: 4 residues processed: 56 average time/residue: 0.0426 time to fit residues: 2.7888 Evaluate side-chains 51 residues out of total 156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 46 time to evaluate : 0.055 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AE residue 22 LEU Chi-restraints excluded: chain AA residue 22 LEU Chi-restraints excluded: chain AD residue 6 THR Chi-restraints excluded: chain AB residue 6 THR Chi-restraints excluded: chain AC residue 22 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 9 optimal weight: 0.1980 chunk 10 optimal weight: 3.9990 chunk 11 optimal weight: 8.9990 chunk 12 optimal weight: 3.9990 chunk 16 optimal weight: 7.9990 chunk 7 optimal weight: 7.9990 chunk 6 optimal weight: 6.9990 chunk 13 optimal weight: 0.0870 chunk 8 optimal weight: 3.9990 chunk 5 optimal weight: 7.9990 chunk 4 optimal weight: 2.9990 overall best weight: 2.2564 ------------------------------------------------------------------------------- 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 = 0.4597 r_free = 0.4597 target = 0.157413 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4413 r_free = 0.4413 target = 0.138376 restraints weight = 2080.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4446 r_free = 0.4446 target = 0.141733 restraints weight = 916.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4470 r_free = 0.4470 target = 0.144073 restraints weight = 533.586| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4485 r_free = 0.4485 target = 0.145664 restraints weight = 371.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.4497 r_free = 0.4497 target = 0.146766 restraints weight = 291.025| |-----------------------------------------------------------------------------| r_work (final): 0.4508 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7403 moved from start: 0.5596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 1446 Z= 0.156 Angle : 0.578 5.354 1956 Z= 0.293 Chirality : 0.046 0.191 258 Planarity : 0.002 0.008 222 Dihedral : 4.165 12.080 192 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 13.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.11 % Favored : 88.89 % Rotamer: Outliers : 6.41 % Allowed : 18.59 % Favored : 75.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -4.14 (0.45), residues: 180 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.15 (0.35), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.004 0.001 TYRAC 20 TRP 0.009 0.002 TRPAD 19 Details of bonding type rmsd covalent geometry : bond 0.00365 ( 1446) covalent geometry : angle 0.57810 ( 1956) hydrogen bonds : bond 0.01816 ( 16) hydrogen bonds : angle 5.34909 ( 48) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 360 Ramachandran restraints generated. 180 Oldfield, 0 Emsley, 180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 360 Ramachandran restraints generated. 180 Oldfield, 0 Emsley, 180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 50 time to evaluate : 0.066 Fit side-chains REVERT: AE 8 LYS cc_start: 0.7660 (mttt) cc_final: 0.7147 (mttm) REVERT: AA 8 LYS cc_start: 0.7705 (mttt) cc_final: 0.7134 (mttm) REVERT: AD 7 MET cc_start: 0.7311 (mpp) cc_final: 0.6815 (mtm) REVERT: AD 8 LYS cc_start: 0.7533 (mttt) cc_final: 0.5847 (mmmt) REVERT: AD 24 MET cc_start: 0.6781 (mtp) cc_final: 0.6316 (mtt) REVERT: AB 7 MET cc_start: 0.7382 (mpp) cc_final: 0.6585 (mtm) REVERT: AB 8 LYS cc_start: 0.7509 (mttt) cc_final: 0.5822 (mmmt) REVERT: AB 24 MET cc_start: 0.6783 (mtp) cc_final: 0.6351 (mtt) REVERT: AC 22 LEU cc_start: 0.8413 (OUTLIER) cc_final: 0.8110 (tt) outliers start: 10 outliers final: 8 residues processed: 56 average time/residue: 0.0285 time to fit residues: 1.8985 Evaluate side-chains 56 residues out of total 156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 47 time to evaluate : 0.032 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AE residue 22 LEU Chi-restraints excluded: chain AA residue 22 LEU Chi-restraints excluded: chain AD residue 6 THR Chi-restraints excluded: chain AD residue 28 ASP Chi-restraints excluded: chain AB residue 6 THR Chi-restraints excluded: chain AB residue 28 ASP Chi-restraints excluded: chain AF residue 6 THR Chi-restraints excluded: chain AC residue 6 THR Chi-restraints excluded: chain AC residue 22 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 5 optimal weight: 6.9990 chunk 10 optimal weight: 7.9990 chunk 12 optimal weight: 0.3980 chunk 7 optimal weight: 6.9990 chunk 17 optimal weight: 2.9990 chunk 6 optimal weight: 2.9990 chunk 1 optimal weight: 5.9990 chunk 14 optimal weight: 5.9990 chunk 11 optimal weight: 2.9990 chunk 3 optimal weight: 2.9990 chunk 0 optimal weight: 0.9990 overall best weight: 2.0788 ------------------------------------------------------------------------------- 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 = 0.4623 r_free = 0.4623 target = 0.159073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.4432 r_free = 0.4432 target = 0.139232 restraints weight = 2042.660| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4466 r_free = 0.4466 target = 0.142596 restraints weight = 930.375| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4491 r_free = 0.4491 target = 0.144951 restraints weight = 555.743| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4505 r_free = 0.4505 target = 0.146316 restraints weight = 391.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.4519 r_free = 0.4519 target = 0.147530 restraints weight = 314.432| |-----------------------------------------------------------------------------| r_work (final): 0.4523 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7386 moved from start: 0.5948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 1446 Z= 0.145 Angle : 0.582 4.978 1956 Z= 0.297 Chirality : 0.045 0.203 258 Planarity : 0.002 0.009 222 Dihedral : 4.127 12.314 192 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 12.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.00 % Favored : 90.00 % Rotamer: Outliers : 7.05 % Allowed : 23.72 % Favored : 69.23 % 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: -4.26 (0.44), residues: 180 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.24 (0.34), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.004 0.001 TYRAC 20 TRP 0.007 0.002 TRPAA 19 Details of bonding type rmsd covalent geometry : bond 0.00332 ( 1446) covalent geometry : angle 0.58232 ( 1956) hydrogen bonds : bond 0.01656 ( 16) hydrogen bonds : angle 5.54214 ( 48) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 360 Ramachandran restraints generated. 180 Oldfield, 0 Emsley, 180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 360 Ramachandran restraints generated. 180 Oldfield, 0 Emsley, 180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 50 time to evaluate : 0.054 Fit side-chains REVERT: AE 8 LYS cc_start: 0.7711 (mttt) cc_final: 0.7184 (mttm) REVERT: AA 8 LYS cc_start: 0.7699 (mttt) cc_final: 0.7203 (mttm) REVERT: AD 7 MET cc_start: 0.7220 (mpp) cc_final: 0.6754 (mtm) REVERT: AD 8 LYS cc_start: 0.7615 (mttt) cc_final: 0.5899 (mmmt) REVERT: AD 24 MET cc_start: 0.6862 (mtp) cc_final: 0.6419 (mtt) REVERT: AB 22 LEU cc_start: 0.8141 (OUTLIER) cc_final: 0.7856 (tp) REVERT: AB 24 MET cc_start: 0.6934 (mtp) cc_final: 0.6501 (mtt) REVERT: AF 29 ILE cc_start: 0.6075 (pt) cc_final: 0.5858 (mm) outliers start: 11 outliers final: 7 residues processed: 57 average time/residue: 0.0382 time to fit residues: 2.5972 Evaluate side-chains 58 residues out of total 156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 50 time to evaluate : 0.056 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AA residue 22 LEU Chi-restraints excluded: chain AD residue 6 THR Chi-restraints excluded: chain AD residue 28 ASP Chi-restraints excluded: chain AB residue 6 THR Chi-restraints excluded: chain AB residue 22 LEU Chi-restraints excluded: chain AB residue 28 ASP Chi-restraints excluded: chain AF residue 6 THR Chi-restraints excluded: chain AC residue 6 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 8 optimal weight: 7.9990 chunk 5 optimal weight: 5.9990 chunk 1 optimal weight: 6.9990 chunk 11 optimal weight: 0.9990 chunk 9 optimal weight: 9.9990 chunk 10 optimal weight: 4.9990 chunk 7 optimal weight: 0.8980 chunk 12 optimal weight: 8.9990 chunk 0 optimal weight: 9.9990 chunk 3 optimal weight: 3.9990 chunk 4 optimal weight: 0.9980 overall best weight: 2.3786 ------------------------------------------------------------------------------- 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 = 0.4648 r_free = 0.4648 target = 0.159755 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.4460 r_free = 0.4460 target = 0.140256 restraints weight = 2062.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4497 r_free = 0.4497 target = 0.143806 restraints weight = 925.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4519 r_free = 0.4519 target = 0.145909 restraints weight = 542.252| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.4537 r_free = 0.4537 target = 0.147648 restraints weight = 386.977| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.4549 r_free = 0.4549 target = 0.148727 restraints weight = 302.717| |-----------------------------------------------------------------------------| r_work (final): 0.4549 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7384 moved from start: 0.6206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.023 1446 Z= 0.161 Angle : 0.604 5.352 1956 Z= 0.308 Chirality : 0.046 0.216 258 Planarity : 0.002 0.009 222 Dihedral : 4.318 11.879 192 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 13.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.11 % Favored : 88.89 % Rotamer: Outliers : 7.05 % Allowed : 32.05 % Favored : 60.90 % 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: -4.54 (0.41), residues: 180 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.45 (0.31), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.003 0.001 TYRAE 20 TRP 0.015 0.002 TRPAF 19 Details of bonding type rmsd covalent geometry : bond 0.00369 ( 1446) covalent geometry : angle 0.60432 ( 1956) hydrogen bonds : bond 0.01564 ( 16) hydrogen bonds : angle 5.75428 ( 48) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 360 Ramachandran restraints generated. 180 Oldfield, 0 Emsley, 180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 360 Ramachandran restraints generated. 180 Oldfield, 0 Emsley, 180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 49 time to evaluate : 0.069 Fit side-chains REVERT: AE 8 LYS cc_start: 0.7757 (mttt) cc_final: 0.7261 (mttm) REVERT: AA 8 LYS cc_start: 0.7736 (mttt) cc_final: 0.7221 (mttm) REVERT: AD 7 MET cc_start: 0.7190 (mpp) cc_final: 0.6742 (mtm) REVERT: AD 8 LYS cc_start: 0.7502 (mttt) cc_final: 0.5836 (mmmt) REVERT: AD 22 LEU cc_start: 0.8200 (OUTLIER) cc_final: 0.7977 (tp) REVERT: AD 24 MET cc_start: 0.6796 (mtp) cc_final: 0.6419 (mtt) REVERT: AB 8 LYS cc_start: 0.7407 (mttt) cc_final: 0.5809 (mmmt) REVERT: AB 24 MET cc_start: 0.6896 (mtp) cc_final: 0.6491 (mtt) outliers start: 11 outliers final: 9 residues processed: 56 average time/residue: 0.0427 time to fit residues: 2.7733 Evaluate side-chains 58 residues out of total 156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 48 time to evaluate : 0.057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AE residue 22 LEU Chi-restraints excluded: chain AA residue 22 LEU Chi-restraints excluded: chain AD residue 6 THR Chi-restraints excluded: chain AD residue 22 LEU Chi-restraints excluded: chain AD residue 28 ASP Chi-restraints excluded: chain AB residue 6 THR Chi-restraints excluded: chain AB residue 28 ASP Chi-restraints excluded: chain AF residue 6 THR Chi-restraints excluded: chain AF residue 24 MET Chi-restraints excluded: chain AC residue 6 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 6 optimal weight: 0.5980 chunk 2 optimal weight: 5.9990 chunk 11 optimal weight: 7.9990 chunk 12 optimal weight: 4.9990 chunk 4 optimal weight: 3.9990 chunk 13 optimal weight: 9.9990 chunk 17 optimal weight: 10.0000 chunk 15 optimal weight: 0.7980 chunk 3 optimal weight: 0.9980 chunk 8 optimal weight: 0.9990 chunk 0 optimal weight: 0.9980 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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 = 0.4764 r_free = 0.4764 target = 0.171356 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4566 r_free = 0.4566 target = 0.150685 restraints weight = 2019.182| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4602 r_free = 0.4602 target = 0.154444 restraints weight = 917.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4625 r_free = 0.4625 target = 0.156835 restraints weight = 543.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.4645 r_free = 0.4645 target = 0.158657 restraints weight = 386.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.4653 r_free = 0.4653 target = 0.159516 restraints weight = 302.980| |-----------------------------------------------------------------------------| r_work (final): 0.4646 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7335 moved from start: 0.6490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.015 1446 Z= 0.095 Angle : 0.545 5.435 1956 Z= 0.277 Chirality : 0.046 0.201 258 Planarity : 0.002 0.008 222 Dihedral : 3.587 10.850 192 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.78 % Favored : 92.22 % Rotamer: Outliers : 5.77 % Allowed : 36.54 % Favored : 57.69 % 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: -4.37 (0.43), residues: 180 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.32 (0.33), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.004 0.000 TYRAB 20 TRP 0.012 0.002 TRPAF 19 Details of bonding type rmsd covalent geometry : bond 0.00206 ( 1446) covalent geometry : angle 0.54533 ( 1956) hydrogen bonds : bond 0.01165 ( 16) hydrogen bonds : angle 5.41924 ( 48) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 360 Ramachandran restraints generated. 180 Oldfield, 0 Emsley, 180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 360 Ramachandran restraints generated. 180 Oldfield, 0 Emsley, 180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 47 time to evaluate : 0.034 Fit side-chains REVERT: AE 7 MET cc_start: 0.7105 (mpp) cc_final: 0.6898 (mtt) REVERT: AE 8 LYS cc_start: 0.7694 (mttt) cc_final: 0.7241 (mttm) REVERT: AA 7 MET cc_start: 0.7146 (mpp) cc_final: 0.6944 (mtt) REVERT: AA 8 LYS cc_start: 0.7715 (mttt) cc_final: 0.7229 (mttm) REVERT: AD 7 MET cc_start: 0.7287 (mpp) cc_final: 0.6962 (mtm) REVERT: AD 8 LYS cc_start: 0.7503 (mttt) cc_final: 0.5882 (mmmt) REVERT: AD 24 MET cc_start: 0.6788 (mtp) cc_final: 0.6377 (mtt) REVERT: AB 8 LYS cc_start: 0.7505 (mttt) cc_final: 0.5920 (mmmt) REVERT: AB 24 MET cc_start: 0.6912 (mtp) cc_final: 0.6478 (mtt) outliers start: 9 outliers final: 8 residues processed: 53 average time/residue: 0.0416 time to fit residues: 2.5606 Evaluate side-chains 53 residues out of total 156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 45 time to evaluate : 0.055 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AE residue 22 LEU Chi-restraints excluded: chain AD residue 6 THR Chi-restraints excluded: chain AD residue 28 ASP Chi-restraints excluded: chain AB residue 6 THR Chi-restraints excluded: chain AB residue 32 LEU Chi-restraints excluded: chain AF residue 6 THR Chi-restraints excluded: chain AF residue 24 MET Chi-restraints excluded: chain AC residue 6 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 1 optimal weight: 10.0000 chunk 9 optimal weight: 0.0980 chunk 6 optimal weight: 3.9990 chunk 3 optimal weight: 3.9990 chunk 8 optimal weight: 9.9990 chunk 14 optimal weight: 9.9990 chunk 15 optimal weight: 0.1980 chunk 7 optimal weight: 3.9990 chunk 17 optimal weight: 5.9990 chunk 13 optimal weight: 2.9990 chunk 12 optimal weight: 4.9990 overall best weight: 2.2586 ------------------------------------------------------------------------------- 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 = 0.4973 r_free = 0.4973 target = 0.287696 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.5268 r_free = 0.5268 target = 0.233114 restraints weight = 2341.683| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.5293 r_free = 0.5293 target = 0.235757 restraints weight = 1198.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.5306 r_free = 0.5306 target = 0.237383 restraints weight = 749.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.5333 r_free = 0.5333 target = 0.238592 restraints weight = 542.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.5336 r_free = 0.5336 target = 0.238937 restraints weight = 420.273| |-----------------------------------------------------------------------------| r_work (final): 0.4605 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7388 moved from start: 0.6568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.021 1446 Z= 0.153 Angle : 0.606 5.763 1956 Z= 0.307 Chirality : 0.046 0.190 258 Planarity : 0.002 0.009 222 Dihedral : 4.134 11.744 192 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 11.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.56 % Favored : 89.44 % Rotamer: Outliers : 6.41 % Allowed : 36.54 % Favored : 57.05 % 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: -4.52 (0.41), residues: 180 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.43 (0.32), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.003 0.001 TYRAF 20 TRP 0.012 0.002 TRPAF 19 Details of bonding type rmsd covalent geometry : bond 0.00357 ( 1446) covalent geometry : angle 0.60595 ( 1956) hydrogen bonds : bond 0.01476 ( 16) hydrogen bonds : angle 5.83836 ( 48) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 360 Ramachandran restraints generated. 180 Oldfield, 0 Emsley, 180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 360 Ramachandran restraints generated. 180 Oldfield, 0 Emsley, 180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 50 time to evaluate : 0.062 Fit side-chains REVERT: AE 8 LYS cc_start: 0.7784 (mttt) cc_final: 0.7314 (mttm) REVERT: AA 7 MET cc_start: 0.7427 (mpp) cc_final: 0.7039 (mtt) REVERT: AA 8 LYS cc_start: 0.7775 (mttt) cc_final: 0.7284 (mttm) REVERT: AD 7 MET cc_start: 0.7075 (mpp) cc_final: 0.6729 (mtm) REVERT: AD 8 LYS cc_start: 0.7504 (mttt) cc_final: 0.5848 (mmmt) REVERT: AD 24 MET cc_start: 0.6775 (mtp) cc_final: 0.6452 (mtt) REVERT: AB 8 LYS cc_start: 0.7535 (mttt) cc_final: 0.5976 (mmmt) REVERT: AB 24 MET cc_start: 0.6821 (mtp) cc_final: 0.6480 (mtt) outliers start: 10 outliers final: 9 residues processed: 56 average time/residue: 0.0470 time to fit residues: 3.0834 Evaluate side-chains 58 residues out of total 156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 49 time to evaluate : 0.061 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AE residue 22 LEU Chi-restraints excluded: chain AD residue 6 THR Chi-restraints excluded: chain AD residue 28 ASP Chi-restraints excluded: chain AB residue 6 THR Chi-restraints excluded: chain AB residue 28 ASP Chi-restraints excluded: chain AB residue 32 LEU Chi-restraints excluded: chain AF residue 6 THR Chi-restraints excluded: chain AF residue 24 MET Chi-restraints excluded: chain AC residue 6 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 3 optimal weight: 9.9990 chunk 12 optimal weight: 6.9990 chunk 6 optimal weight: 6.9990 chunk 1 optimal weight: 7.9990 chunk 15 optimal weight: 6.9990 chunk 10 optimal weight: 6.9990 chunk 16 optimal weight: 0.7980 chunk 7 optimal weight: 3.9990 chunk 17 optimal weight: 0.9990 chunk 4 optimal weight: 2.9990 chunk 8 optimal weight: 0.5980 overall best weight: 1.8786 ------------------------------------------------------------------------------- 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 = 0.4700 r_free = 0.4700 target = 0.163358 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4491 r_free = 0.4491 target = 0.143581 restraints weight = 2072.158| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4531 r_free = 0.4531 target = 0.147126 restraints weight = 961.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4555 r_free = 0.4555 target = 0.149348 restraints weight = 580.260| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4569 r_free = 0.4569 target = 0.150691 restraints weight = 418.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4586 r_free = 0.4586 target = 0.151947 restraints weight = 340.269| |-----------------------------------------------------------------------------| r_work (final): 0.4586 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7361 moved from start: 0.6683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 1446 Z= 0.139 Angle : 0.601 5.514 1956 Z= 0.304 Chirality : 0.047 0.225 258 Planarity : 0.002 0.009 222 Dihedral : 3.981 12.032 192 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.56 % Favored : 89.44 % Rotamer: Outliers : 6.41 % Allowed : 38.46 % Favored : 55.13 % 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: -4.57 (0.41), residues: 180 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.47 (0.31), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.004 0.001 TYRAF 20 TRP 0.012 0.002 TRPAF 19 Details of bonding type rmsd covalent geometry : bond 0.00329 ( 1446) covalent geometry : angle 0.60053 ( 1956) hydrogen bonds : bond 0.01527 ( 16) hydrogen bonds : angle 5.73647 ( 48) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 360 Ramachandran restraints generated. 180 Oldfield, 0 Emsley, 180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 360 Ramachandran restraints generated. 180 Oldfield, 0 Emsley, 180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 48 time to evaluate : 0.076 Fit side-chains REVERT: AE 8 LYS cc_start: 0.7686 (mttt) cc_final: 0.7194 (mttm) REVERT: AA 7 MET cc_start: 0.7371 (mpp) cc_final: 0.7017 (mtt) REVERT: AA 8 LYS cc_start: 0.7685 (mttt) cc_final: 0.7189 (mttm) REVERT: AD 7 MET cc_start: 0.7209 (mpp) cc_final: 0.6755 (mtm) REVERT: AD 8 LYS cc_start: 0.7413 (mttt) cc_final: 0.5789 (mmmt) REVERT: AD 24 MET cc_start: 0.6808 (mtp) cc_final: 0.6412 (mtt) REVERT: AB 8 LYS cc_start: 0.7512 (mttt) cc_final: 0.5888 (mmmt) REVERT: AB 24 MET cc_start: 0.6876 (mtp) cc_final: 0.6464 (mtt) outliers start: 10 outliers final: 9 residues processed: 53 average time/residue: 0.0491 time to fit residues: 3.0523 Evaluate side-chains 56 residues out of total 156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 47 time to evaluate : 0.055 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AE residue 22 LEU Chi-restraints excluded: chain AD residue 6 THR Chi-restraints excluded: chain AD residue 28 ASP Chi-restraints excluded: chain AB residue 6 THR Chi-restraints excluded: chain AB residue 28 ASP Chi-restraints excluded: chain AB residue 32 LEU Chi-restraints excluded: chain AF residue 6 THR Chi-restraints excluded: chain AF residue 24 MET Chi-restraints excluded: chain AC residue 6 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 12 optimal weight: 0.0970 chunk 3 optimal weight: 9.9990 chunk 13 optimal weight: 10.0000 chunk 14 optimal weight: 0.5980 chunk 2 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 chunk 6 optimal weight: 8.9990 chunk 9 optimal weight: 2.9990 chunk 7 optimal weight: 0.9980 chunk 4 optimal weight: 0.8980 chunk 5 optimal weight: 4.9990 overall best weight: 1.1180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: AB 13 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4829 r_free = 0.4829 target = 0.172534 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4594 r_free = 0.4594 target = 0.150805 restraints weight = 1953.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4638 r_free = 0.4638 target = 0.154743 restraints weight = 902.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4673 r_free = 0.4673 target = 0.157440 restraints weight = 545.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.4694 r_free = 0.4694 target = 0.159281 restraints weight = 385.522| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4706 r_free = 0.4706 target = 0.160515 restraints weight = 303.148| |-----------------------------------------------------------------------------| r_work (final): 0.4685 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7252 moved from start: 0.6874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.017 1446 Z= 0.108 Angle : 0.571 5.746 1956 Z= 0.290 Chirality : 0.047 0.230 258 Planarity : 0.002 0.013 222 Dihedral : 3.579 10.905 192 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.33 % Favored : 91.67 % Rotamer: Outliers : 6.41 % Allowed : 41.03 % Favored : 52.56 % 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: -4.54 (0.41), residues: 180 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.46 (0.32), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.003 0.001 TYRAF 20 TRP 0.012 0.002 TRPAF 19 Details of bonding type rmsd covalent geometry : bond 0.00250 ( 1446) covalent geometry : angle 0.57131 ( 1956) hydrogen bonds : bond 0.01384 ( 16) hydrogen bonds : angle 5.51022 ( 48) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 360 Ramachandran restraints generated. 180 Oldfield, 0 Emsley, 180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 360 Ramachandran restraints generated. 180 Oldfield, 0 Emsley, 180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 48 time to evaluate : 0.055 Fit side-chains REVERT: AE 8 LYS cc_start: 0.7584 (mttt) cc_final: 0.7211 (mttm) REVERT: AA 7 MET cc_start: 0.7313 (mpp) cc_final: 0.7017 (mtt) REVERT: AA 8 LYS cc_start: 0.7586 (mttt) cc_final: 0.7083 (mttm) REVERT: AD 7 MET cc_start: 0.7322 (mpp) cc_final: 0.6835 (mtm) REVERT: AD 8 LYS cc_start: 0.7450 (mttt) cc_final: 0.5800 (mmmt) REVERT: AD 24 MET cc_start: 0.6794 (mtp) cc_final: 0.6591 (mtp) REVERT: AB 8 LYS cc_start: 0.7384 (mttt) cc_final: 0.5792 (mmmt) REVERT: AB 24 MET cc_start: 0.6936 (mtp) cc_final: 0.6691 (mtp) outliers start: 10 outliers final: 8 residues processed: 54 average time/residue: 0.0401 time to fit residues: 2.5222 Evaluate side-chains 56 residues out of total 156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 48 time to evaluate : 0.033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AA residue 22 LEU Chi-restraints excluded: chain AD residue 6 THR Chi-restraints excluded: chain AD residue 28 ASP Chi-restraints excluded: chain AB residue 6 THR Chi-restraints excluded: chain AB residue 28 ASP Chi-restraints excluded: chain AB residue 32 LEU Chi-restraints excluded: chain AF residue 6 THR Chi-restraints excluded: chain AC residue 6 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 8 optimal weight: 8.9990 chunk 4 optimal weight: 8.9990 chunk 9 optimal weight: 2.9990 chunk 14 optimal weight: 10.0000 chunk 15 optimal weight: 4.9990 chunk 0 optimal weight: 9.9990 chunk 3 optimal weight: 7.9990 chunk 5 optimal weight: 3.9990 chunk 1 optimal weight: 6.9990 chunk 7 optimal weight: 0.0050 chunk 13 optimal weight: 3.9990 overall best weight: 3.2002 ------------------------------------------------------------------------------- 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 = 0.4653 r_free = 0.4653 target = 0.155755 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4417 r_free = 0.4417 target = 0.135143 restraints weight = 2174.581| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4455 r_free = 0.4455 target = 0.138506 restraints weight = 1001.211| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4483 r_free = 0.4483 target = 0.140771 restraints weight = 618.178| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4499 r_free = 0.4499 target = 0.142200 restraints weight = 450.220| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.4511 r_free = 0.4511 target = 0.143356 restraints weight = 365.153| |-----------------------------------------------------------------------------| r_work (final): 0.4498 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7358 moved from start: 0.6837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.028 1446 Z= 0.207 Angle : 0.694 5.557 1956 Z= 0.356 Chirality : 0.048 0.245 258 Planarity : 0.003 0.010 222 Dihedral : 4.577 13.317 192 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 14.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.67 % Favored : 88.33 % Rotamer: Outliers : 5.77 % Allowed : 42.95 % Favored : 51.28 % 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: -4.74 (0.39), residues: 180 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.61 (0.30), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.005 0.001 TYRAF 20 TRP 0.010 0.002 TRPAF 19 Details of bonding type rmsd covalent geometry : bond 0.00489 ( 1446) covalent geometry : angle 0.69444 ( 1956) hydrogen bonds : bond 0.01680 ( 16) hydrogen bonds : angle 6.27269 ( 48) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 542.06 seconds wall clock time: 9 minutes 56.34 seconds (596.34 seconds total)