Starting phenix.real_space_refine on Tue Feb 3 12:19:58 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jhf_61480/02_2026/9jhf_61480.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jhf_61480/02_2026/9jhf_61480.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.06 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9jhf_61480/02_2026/9jhf_61480.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jhf_61480/02_2026/9jhf_61480.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9jhf_61480/02_2026/9jhf_61480.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jhf_61480/02_2026/9jhf_61480.map" } resolution = 4.06 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 12 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: "AA" 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: AB, AC, AE, AD, AF Time building chain proxies: 0.18, per 1000 atoms: 0.13 Number of scatterers: 1434 At special positions: 0 Unit cell: (71.38, 71.38, 32.37, 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: 0.06 Conformation dependent library (CDL) restraints added in 36.2 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 5 sheets defined 0.0% alpha, 54.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.03 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'AC' and resid 2 through 13 removed outlier: 6.926A pdb=" N VALAC 3 " --> pdb=" O ILEAA 2 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N THRAA 4 " --> pdb=" O VALAC 3 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N GLNAC 5 " --> pdb=" O THRAA 4 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N THRAA 6 " --> pdb=" O GLNAC 5 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N METAC 7 " --> pdb=" O THRAA 6 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N LYSAA 8 " --> pdb=" O METAC 7 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N GLYAC 9 " --> pdb=" O LYSAA 8 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N ILEAA 2 " --> pdb=" O VALAD 3 " (cutoff:3.500A) removed outlier: 7.796A pdb=" N GLNAD 5 " --> pdb=" O ILEAA 2 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N THRAA 4 " --> pdb=" O GLNAD 5 " (cutoff:3.500A) removed outlier: 7.504A pdb=" N METAD 7 " --> pdb=" O THRAA 4 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N THRAA 6 " --> pdb=" O METAD 7 " (cutoff:3.500A) removed outlier: 8.108A pdb=" N GLYAD 9 " --> pdb=" O THRAA 6 " (cutoff:3.500A) removed outlier: 8.464A pdb=" N LYSAA 8 " --> pdb=" O GLYAD 9 " (cutoff:3.500A) removed outlier: 8.466A pdb=" N ASPAD 11 " --> pdb=" O LYSAA 8 " (cutoff:3.500A) removed outlier: 9.409A pdb=" N LEUAA 10 " --> pdb=" O ASPAD 11 " (cutoff:3.500A) removed outlier: 9.910A pdb=" N GLNAD 13 " --> pdb=" O LEUAA 10 " (cutoff:3.500A) removed outlier: 8.691A pdb=" N ILEAA 12 " --> pdb=" O GLNAD 13 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'AC' and resid 23 through 25 removed outlier: 6.327A pdb=" N ALAAA 23 " --> pdb=" O METAC 24 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'AC' and resid 28 through 31 removed outlier: 6.189A pdb=" N ASPAA 28 " --> pdb=" O ILEAC 29 " (cutoff:3.500A) removed outlier: 7.996A pdb=" N LEUAC 31 " --> pdb=" O ASPAA 28 " (cutoff:3.500A) removed outlier: 7.134A pdb=" N SERAA 30 " --> pdb=" O LEUAC 31 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'AE' and resid 2 through 13 removed outlier: 6.888A pdb=" N VALAE 3 " --> pdb=" O ILEAB 2 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N THRAB 4 " --> pdb=" O VALAE 3 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N GLNAE 5 " --> pdb=" O THRAB 4 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N THRAB 6 " --> pdb=" O GLNAE 5 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N METAE 7 " --> pdb=" O THRAB 6 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N LYSAB 8 " --> pdb=" O METAE 7 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N GLYAE 9 " --> pdb=" O LYSAB 8 " (cutoff:3.500A) removed outlier: 9.236A pdb=" N VALAB 3 " --> pdb=" O THRAF 4 " (cutoff:3.500A) removed outlier: 9.950A pdb=" N THRAF 6 " --> pdb=" O VALAB 3 " (cutoff:3.500A) removed outlier: 8.666A pdb=" N GLNAB 5 " --> pdb=" O THRAF 6 " (cutoff:3.500A) removed outlier: 10.104A pdb=" N LYSAF 8 " --> pdb=" O GLNAB 5 " (cutoff:3.500A) removed outlier: 9.129A pdb=" N METAB 7 " --> pdb=" O LYSAF 8 " (cutoff:3.500A) removed outlier: 8.999A pdb=" N LEUAF 10 " --> pdb=" O METAB 7 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N GLYAB 9 " --> pdb=" O LEUAF 10 " (cutoff:3.500A) removed outlier: 7.961A pdb=" N ILEAF 12 " --> pdb=" O GLYAB 9 " (cutoff:3.500A) removed outlier: 5.849A pdb=" N ASPAB 11 " --> pdb=" O ILEAF 12 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'AE' and resid 23 through 31 removed outlier: 6.418A pdb=" N ALAAB 23 " --> pdb=" O METAE 24 " (cutoff:3.500A) removed outlier: 8.675A pdb=" N ALAAE 26 " --> pdb=" O ALAAB 23 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N ALAAB 25 " --> pdb=" O ALAAE 26 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N ASPAE 28 " --> pdb=" O ALAAB 25 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N SERAB 27 " --> pdb=" O ASPAE 28 " (cutoff:3.500A) removed outlier: 10.037A pdb=" N SERAE 30 " --> pdb=" O SERAB 27 " (cutoff:3.500A) removed outlier: 8.659A pdb=" N ILEAB 29 " --> pdb=" O SERAE 30 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N METAF 24 " --> pdb=" O ALAAB 23 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N ALAAB 25 " --> pdb=" O METAF 24 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N ALAAF 26 " --> pdb=" O ALAAB 25 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N SERAB 27 " --> pdb=" O ALAAF 26 " (cutoff:3.500A) 17 hydrogen bonds defined for protein. 51 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: 0.12 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: 1.22 - 1.34: 426 1.34 - 1.46: 211 1.46 - 1.58: 785 1.58 - 1.69: 0 1.69 - 1.81: 24 Bond restraints: 1446 Sorted by residual: bond pdb=" N ILEAD 29 " pdb=" CA ILEAD 29 " ideal model delta sigma weight residual 1.459 1.495 -0.036 1.29e-02 6.01e+03 7.92e+00 bond pdb=" N ILEAB 29 " pdb=" CA ILEAB 29 " ideal model delta sigma weight residual 1.459 1.495 -0.036 1.29e-02 6.01e+03 7.86e+00 bond pdb=" N METAC 24 " pdb=" CA METAC 24 " ideal model delta sigma weight residual 1.455 1.490 -0.035 1.26e-02 6.30e+03 7.81e+00 bond pdb=" N ILEAA 29 " pdb=" CA ILEAA 29 " ideal model delta sigma weight residual 1.459 1.495 -0.036 1.29e-02 6.01e+03 7.71e+00 bond pdb=" N METAA 24 " pdb=" CA METAA 24 " ideal model delta sigma weight residual 1.455 1.489 -0.035 1.26e-02 6.30e+03 7.67e+00 ... (remaining 1441 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.05: 1369 1.05 - 2.10: 408 2.10 - 3.16: 155 3.16 - 4.21: 12 4.21 - 5.26: 12 Bond angle restraints: 1956 Sorted by residual: angle pdb=" C TRPAD 19 " pdb=" CA TRPAD 19 " pdb=" CB TRPAD 19 " ideal model delta sigma weight residual 110.06 115.32 -5.26 1.39e+00 5.18e-01 1.43e+01 angle pdb=" C TRPAE 19 " pdb=" CA TRPAE 19 " pdb=" CB TRPAE 19 " ideal model delta sigma weight residual 110.06 115.30 -5.24 1.39e+00 5.18e-01 1.42e+01 angle pdb=" C TRPAC 19 " pdb=" CA TRPAC 19 " pdb=" CB TRPAC 19 " ideal model delta sigma weight residual 110.06 115.27 -5.21 1.39e+00 5.18e-01 1.40e+01 angle pdb=" C TRPAB 19 " pdb=" CA TRPAB 19 " pdb=" CB TRPAB 19 " ideal model delta sigma weight residual 110.06 115.25 -5.19 1.39e+00 5.18e-01 1.39e+01 angle pdb=" C TRPAF 19 " pdb=" CA TRPAF 19 " pdb=" CB TRPAF 19 " ideal model delta sigma weight residual 110.06 115.24 -5.18 1.39e+00 5.18e-01 1.39e+01 ... (remaining 1951 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 10.77: 710 10.77 - 21.53: 64 21.53 - 32.29: 54 32.29 - 43.06: 18 43.06 - 53.82: 18 Dihedral angle restraints: 864 sinusoidal: 312 harmonic: 552 Sorted by residual: dihedral pdb=" CA ASPAD 28 " pdb=" CB ASPAD 28 " pdb=" CG ASPAD 28 " pdb=" OD1 ASPAD 28 " ideal model delta sinusoidal sigma weight residual -30.00 -83.82 53.82 1 2.00e+01 2.50e-03 9.83e+00 dihedral pdb=" CA ASPAA 28 " pdb=" CB ASPAA 28 " pdb=" CG ASPAA 28 " pdb=" OD1 ASPAA 28 " ideal model delta sinusoidal sigma weight residual -30.00 -83.79 53.79 1 2.00e+01 2.50e-03 9.82e+00 dihedral pdb=" CA ASPAB 28 " pdb=" CB ASPAB 28 " pdb=" CG ASPAB 28 " pdb=" OD1 ASPAB 28 " ideal model delta sinusoidal sigma weight residual -30.00 -83.78 53.78 1 2.00e+01 2.50e-03 9.82e+00 ... (remaining 861 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 120 0.035 - 0.070: 53 0.070 - 0.104: 37 0.104 - 0.139: 24 0.139 - 0.174: 24 Chirality restraints: 258 Sorted by residual: chirality pdb=" CA ILEAD 29 " pdb=" N ILEAD 29 " pdb=" C ILEAD 29 " pdb=" CB ILEAD 29 " both_signs ideal model delta sigma weight residual False 2.43 2.61 -0.17 2.00e-01 2.50e+01 7.53e-01 chirality pdb=" CA ILEAF 29 " pdb=" N ILEAF 29 " pdb=" C ILEAF 29 " pdb=" CB ILEAF 29 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.17 2.00e-01 2.50e+01 7.27e-01 chirality pdb=" CA ILEAA 29 " pdb=" N ILEAA 29 " pdb=" C ILEAA 29 " pdb=" CB ILEAA 29 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.17 2.00e-01 2.50e+01 7.24e-01 ... (remaining 255 not shown) Planarity restraints: 222 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA METAE 7 " -0.004 2.00e-02 2.50e+03 8.86e-03 7.85e-01 pdb=" C METAE 7 " 0.015 2.00e-02 2.50e+03 pdb=" O METAE 7 " -0.006 2.00e-02 2.50e+03 pdb=" N LYSAE 8 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA METAA 7 " 0.004 2.00e-02 2.50e+03 8.64e-03 7.47e-01 pdb=" C METAA 7 " -0.015 2.00e-02 2.50e+03 pdb=" O METAA 7 " 0.006 2.00e-02 2.50e+03 pdb=" N LYSAA 8 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA METAF 7 " -0.004 2.00e-02 2.50e+03 8.41e-03 7.07e-01 pdb=" C METAF 7 " 0.015 2.00e-02 2.50e+03 pdb=" O METAF 7 " -0.005 2.00e-02 2.50e+03 pdb=" N LYSAF 8 " -0.005 2.00e-02 2.50e+03 ... (remaining 219 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 290 2.81 - 3.33: 1350 3.33 - 3.85: 2246 3.85 - 4.38: 2300 4.38 - 4.90: 4657 Nonbonded interactions: 10843 Sorted by model distance: nonbonded pdb=" OG SERAB 21 " pdb=" O SERAE 21 " model vdw 2.285 3.040 nonbonded pdb=" O SERAB 21 " pdb=" OG SERAF 21 " model vdw 2.289 3.040 nonbonded pdb=" O SERAB 21 " pdb=" CB SERAF 21 " model vdw 2.318 3.440 nonbonded pdb=" CB SERAB 21 " pdb=" O SERAE 21 " model vdw 2.361 3.440 nonbonded pdb=" O SERAA 21 " pdb=" OG SERAD 21 " model vdw 2.368 3.040 ... (remaining 10838 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 'AA' selection = chain 'AB' selection = chain 'AC' selection = chain 'AE' selection = chain 'AD' selection = chain 'AF' } 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: 0.840 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: 0.010 Set scattering table: 0.000 Process input model: 2.500 Find NCS groups from input model: 0.010 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:1.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 4.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7529 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 : 0.011 0.036 1446 Z= 0.769 Angle : 1.155 5.260 1956 Z= 0.810 Chirality : 0.072 0.174 258 Planarity : 0.003 0.009 222 Dihedral : 16.298 53.820 504 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 70.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.67 % Favored : 83.33 % Rotamer: Outliers : 0.00 % Allowed : 19.23 % Favored : 80.77 % 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: -3.63 (0.59), residues: 180 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.76 (0.45), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.004 0.001 TYRAC 20 TRP 0.002 0.000 TRPAC 19 Details of bonding type rmsd covalent geometry : bond 0.01129 ( 1446) covalent geometry : angle 1.15484 ( 1956) hydrogen bonds : bond 0.25968 ( 17) hydrogen bonds : angle 10.96548 ( 51) *********************** 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 45 residues out of total 156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 45 time to evaluate : 0.032 Fit side-chains REVERT: AD 19 TRP cc_start: 0.8813 (t60) cc_final: 0.6428 (t-100) REVERT: AF 19 TRP cc_start: 0.8865 (t60) cc_final: 0.7055 (t-100) outliers start: 0 outliers final: 0 residues processed: 45 average time/residue: 0.0481 time to fit residues: 2.4501 Evaluate side-chains 34 residues out of total 156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 34 time to evaluate : 0.033 ------------------------------------------------------------------------------- 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: 1.9990 chunk 13 optimal weight: 0.8980 chunk 1 optimal weight: 2.9990 chunk 8 optimal weight: 0.9990 chunk 16 optimal weight: 3.9990 chunk 15 optimal weight: 0.9980 chunk 9 optimal weight: 10.0000 chunk 11 optimal weight: 2.9990 chunk 6 optimal weight: 2.9990 chunk 4 optimal weight: 1.9990 chunk 3 optimal weight: 0.9980 overall best weight: 1.1784 ------------------------------------------------------------------------------- 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 = 0.4622 r_free = 0.4622 target = 0.185238 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4336 r_free = 0.4336 target = 0.149360 restraints weight = 1429.470| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4350 r_free = 0.4350 target = 0.151854 restraints weight = 942.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4361 r_free = 0.4361 target = 0.153427 restraints weight = 766.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.4361 r_free = 0.4361 target = 0.153427 restraints weight = 681.696| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.4361 r_free = 0.4361 target = 0.153427 restraints weight = 681.696| |-----------------------------------------------------------------------------| r_work (final): 0.4361 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7992 moved from start: 0.3940 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 : 0.509 3.504 1956 Z= 0.275 Chirality : 0.049 0.141 258 Planarity : 0.002 0.011 222 Dihedral : 3.611 12.004 192 Min Nonbonded Distance : 2.642 Molprobity Statistics. All-atom Clashscore : 3.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.56 % Favored : 84.44 % Rotamer: Outliers : 0.00 % Allowed : 0.64 % Favored : 99.36 % 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: -2.84 (0.61), residues: 180 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.15 (0.47), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.008 0.002 TYRAC 20 TRP 0.014 0.002 TRPAB 19 Details of bonding type rmsd covalent geometry : bond 0.00288 ( 1446) covalent geometry : angle 0.50913 ( 1956) hydrogen bonds : bond 0.02941 ( 17) hydrogen bonds : angle 5.96091 ( 51) *********************** 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 43 residues out of total 156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 43 time to evaluate : 0.034 Fit side-chains REVERT: AA 12 ILE cc_start: 0.8298 (mm) cc_final: 0.8007 (tp) REVERT: AC 19 TRP cc_start: 0.8390 (t60) cc_final: 0.8128 (t60) REVERT: AD 19 TRP cc_start: 0.8477 (t60) cc_final: 0.6374 (t-100) REVERT: AF 19 TRP cc_start: 0.8840 (t60) cc_final: 0.6728 (t-100) outliers start: 0 outliers final: 0 residues processed: 43 average time/residue: 0.0375 time to fit residues: 1.8306 Evaluate side-chains 32 residues out of total 156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 32 time to evaluate : 0.032 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 3 optimal weight: 5.9990 chunk 12 optimal weight: 0.3980 chunk 11 optimal weight: 5.9990 chunk 15 optimal weight: 3.9990 chunk 1 optimal weight: 9.9990 chunk 0 optimal weight: 7.9990 chunk 8 optimal weight: 7.9990 chunk 9 optimal weight: 0.8980 chunk 6 optimal weight: 0.9990 chunk 16 optimal weight: 0.9980 chunk 10 optimal weight: 9.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- 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 = 0.4447 r_free = 0.4447 target = 0.165707 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4180 r_free = 0.4180 target = 0.136875 restraints weight = 1488.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4194 r_free = 0.4194 target = 0.138933 restraints weight = 1021.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4206 r_free = 0.4206 target = 0.140443 restraints weight = 822.570| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4211 r_free = 0.4211 target = 0.141114 restraints weight = 719.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.4211 r_free = 0.4211 target = 0.141114 restraints weight = 675.583| |-----------------------------------------------------------------------------| r_work (final): 0.4217 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8116 moved from start: 0.4534 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= 0.124 Angle : 0.477 5.922 1956 Z= 0.258 Chirality : 0.046 0.144 258 Planarity : 0.002 0.008 222 Dihedral : 2.961 9.294 192 Min Nonbonded Distance : 2.635 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.67 % Favored : 88.33 % Rotamer: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % 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: -2.70 (0.63), residues: 180 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.05 (0.48), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.009 0.001 TYRAE 20 TRP 0.009 0.001 TRPAE 19 Details of bonding type rmsd covalent geometry : bond 0.00277 ( 1446) covalent geometry : angle 0.47722 ( 1956) hydrogen bonds : bond 0.02340 ( 17) hydrogen bonds : angle 4.92570 ( 51) *********************** 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 40 residues out of total 156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 40 time to evaluate : 0.034 Fit side-chains REVERT: AA 11 ASP cc_start: 0.8394 (t0) cc_final: 0.7965 (t0) REVERT: AA 12 ILE cc_start: 0.8549 (mm) cc_final: 0.8078 (tp) REVERT: AB 19 TRP cc_start: 0.9133 (t60) cc_final: 0.8916 (t60) REVERT: AD 19 TRP cc_start: 0.8561 (t60) cc_final: 0.6147 (t-100) REVERT: AF 19 TRP cc_start: 0.8708 (t60) cc_final: 0.6840 (t-100) outliers start: 0 outliers final: 0 residues processed: 40 average time/residue: 0.0266 time to fit residues: 1.2719 Evaluate side-chains 34 residues out of total 156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 34 time to evaluate : 0.033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 9 optimal weight: 4.9990 chunk 10 optimal weight: 8.9990 chunk 11 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 chunk 16 optimal weight: 0.6980 chunk 7 optimal weight: 7.9990 chunk 6 optimal weight: 5.9990 chunk 13 optimal weight: 10.0000 chunk 8 optimal weight: 2.9990 chunk 5 optimal weight: 4.9990 chunk 4 optimal weight: 5.9990 overall best weight: 2.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: AE 13 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4315 r_free = 0.4315 target = 0.152364 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.125477 restraints weight = 1616.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.127300 restraints weight = 1093.819| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.128578 restraints weight = 879.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4082 r_free = 0.4082 target = 0.128612 restraints weight = 774.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.4082 r_free = 0.4082 target = 0.128612 restraints weight = 768.682| |-----------------------------------------------------------------------------| r_work (final): 0.4084 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 moved from start: 0.4950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 1446 Z= 0.192 Angle : 0.550 5.034 1956 Z= 0.301 Chirality : 0.047 0.161 258 Planarity : 0.002 0.008 222 Dihedral : 3.300 9.935 192 Min Nonbonded Distance : 2.637 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.89 % Favored : 86.11 % Rotamer: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % 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: -2.81 (0.61), residues: 180 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.13 (0.46), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.016 0.003 TYRAE 20 TRP 0.007 0.001 TRPAB 19 Details of bonding type rmsd covalent geometry : bond 0.00438 ( 1446) covalent geometry : angle 0.55049 ( 1956) hydrogen bonds : bond 0.02848 ( 17) hydrogen bonds : angle 5.04333 ( 51) *********************** 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 39 residues out of total 156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 39 time to evaluate : 0.032 Fit side-chains REVERT: AA 12 ILE cc_start: 0.8729 (mm) cc_final: 0.8433 (tp) REVERT: AC 19 TRP cc_start: 0.8431 (t60) cc_final: 0.8224 (t60) REVERT: AD 30 SER cc_start: 0.9153 (t) cc_final: 0.8685 (m) REVERT: AF 21 SER cc_start: 0.8496 (p) cc_final: 0.8150 (p) outliers start: 0 outliers final: 0 residues processed: 39 average time/residue: 0.0275 time to fit residues: 1.2689 Evaluate side-chains 35 residues out of total 156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 35 time to evaluate : 0.032 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 5 optimal weight: 8.9990 chunk 10 optimal weight: 10.0000 chunk 12 optimal weight: 1.9990 chunk 7 optimal weight: 9.9990 chunk 17 optimal weight: 2.9990 chunk 6 optimal weight: 6.9990 chunk 1 optimal weight: 2.9990 chunk 14 optimal weight: 9.9990 chunk 11 optimal weight: 0.9980 chunk 3 optimal weight: 1.9990 chunk 0 optimal weight: 0.7980 overall best weight: 1.7586 ------------------------------------------------------------------------------- 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 = 0.4374 r_free = 0.4374 target = 0.155561 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4118 r_free = 0.4118 target = 0.128831 restraints weight = 1543.638| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4133 r_free = 0.4133 target = 0.130550 restraints weight = 1081.539| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4141 r_free = 0.4141 target = 0.131286 restraints weight = 877.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.4148 r_free = 0.4148 target = 0.132268 restraints weight = 802.029| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4149 r_free = 0.4149 target = 0.132289 restraints weight = 734.481| |-----------------------------------------------------------------------------| r_work (final): 0.4150 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 moved from start: 0.5260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 1446 Z= 0.131 Angle : 0.497 4.686 1956 Z= 0.264 Chirality : 0.047 0.156 258 Planarity : 0.002 0.010 222 Dihedral : 2.996 9.963 192 Min Nonbonded Distance : 2.640 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.00 % Favored : 85.00 % Rotamer: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % 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: -2.92 (0.59), residues: 180 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.22 (0.45), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.010 0.002 TYRAD 20 TRP 0.004 0.001 TRPAB 19 Details of bonding type rmsd covalent geometry : bond 0.00294 ( 1446) covalent geometry : angle 0.49733 ( 1956) hydrogen bonds : bond 0.02462 ( 17) hydrogen bonds : angle 4.87336 ( 51) *********************** 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 38 residues out of total 156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 38 time to evaluate : 0.033 Fit side-chains REVERT: AA 12 ILE cc_start: 0.8769 (mm) cc_final: 0.8468 (tp) REVERT: AC 19 TRP cc_start: 0.8283 (t60) cc_final: 0.8020 (t60) REVERT: AD 30 SER cc_start: 0.9138 (t) cc_final: 0.8752 (m) REVERT: AF 24 MET cc_start: 0.8178 (ptm) cc_final: 0.7816 (ptm) REVERT: AF 30 SER cc_start: 0.8860 (t) cc_final: 0.8517 (m) outliers start: 0 outliers final: 0 residues processed: 38 average time/residue: 0.0281 time to fit residues: 1.2620 Evaluate side-chains 34 residues out of total 156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 34 time to evaluate : 0.034 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 8 optimal weight: 9.9990 chunk 5 optimal weight: 2.9990 chunk 1 optimal weight: 9.9990 chunk 11 optimal weight: 1.9990 chunk 9 optimal weight: 6.9990 chunk 10 optimal weight: 0.1980 chunk 7 optimal weight: 5.9990 chunk 12 optimal weight: 0.9980 chunk 0 optimal weight: 3.9990 chunk 3 optimal weight: 4.9990 chunk 4 optimal weight: 6.9990 overall best weight: 2.0386 ------------------------------------------------------------------------------- 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 = 0.4371 r_free = 0.4371 target = 0.154056 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4105 r_free = 0.4105 target = 0.127363 restraints weight = 1579.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4120 r_free = 0.4120 target = 0.129046 restraints weight = 1098.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4127 r_free = 0.4127 target = 0.129719 restraints weight = 888.946| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4135 r_free = 0.4135 target = 0.130658 restraints weight = 813.800| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.4136 r_free = 0.4136 target = 0.130798 restraints weight = 747.698| |-----------------------------------------------------------------------------| r_work (final): 0.4134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.5479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 1446 Z= 0.149 Angle : 0.517 5.476 1956 Z= 0.275 Chirality : 0.047 0.153 258 Planarity : 0.002 0.009 222 Dihedral : 3.158 10.769 192 Min Nonbonded Distance : 2.641 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.89 % Favored : 86.11 % Rotamer: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % 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: -2.89 (0.59), residues: 180 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.20 (0.45), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.011 0.002 TYRAD 20 TRP 0.008 0.001 TRPAD 19 Details of bonding type rmsd covalent geometry : bond 0.00342 ( 1446) covalent geometry : angle 0.51728 ( 1956) hydrogen bonds : bond 0.02370 ( 17) hydrogen bonds : angle 4.60191 ( 51) *********************** 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 39 residues out of total 156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 39 time to evaluate : 0.058 Fit side-chains revert: symmetry clash REVERT: AA 12 ILE cc_start: 0.8795 (mm) cc_final: 0.8440 (tp) REVERT: AC 19 TRP cc_start: 0.8272 (t60) cc_final: 0.8063 (t60) REVERT: AD 30 SER cc_start: 0.9119 (t) cc_final: 0.8773 (m) REVERT: AF 8 LYS cc_start: 0.8459 (ttmt) cc_final: 0.8204 (tttp) REVERT: AF 24 MET cc_start: 0.8218 (ptm) cc_final: 0.7924 (ptm) REVERT: AF 30 SER cc_start: 0.8976 (t) cc_final: 0.8595 (m) outliers start: 0 outliers final: 0 residues processed: 39 average time/residue: 0.0319 time to fit residues: 1.4922 Evaluate side-chains 36 residues out of total 156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 36 time to evaluate : 0.066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 6 optimal weight: 6.9990 chunk 2 optimal weight: 5.9990 chunk 11 optimal weight: 3.9990 chunk 12 optimal weight: 1.9990 chunk 4 optimal weight: 10.0000 chunk 13 optimal weight: 7.9990 chunk 17 optimal weight: 0.0770 chunk 15 optimal weight: 0.0870 chunk 3 optimal weight: 0.9980 chunk 8 optimal weight: 2.9990 chunk 0 optimal weight: 0.8980 overall best weight: 0.8118 ------------------------------------------------------------------------------- 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 = 0.4448 r_free = 0.4448 target = 0.161907 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4196 r_free = 0.4196 target = 0.134790 restraints weight = 1572.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4211 r_free = 0.4211 target = 0.136560 restraints weight = 1080.241| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4220 r_free = 0.4220 target = 0.137618 restraints weight = 877.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.4220 r_free = 0.4220 target = 0.137618 restraints weight = 784.793| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.4220 r_free = 0.4220 target = 0.137618 restraints weight = 784.793| |-----------------------------------------------------------------------------| r_work (final): 0.4203 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.5757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 1446 Z= 0.106 Angle : 0.525 5.777 1956 Z= 0.272 Chirality : 0.049 0.145 258 Planarity : 0.002 0.008 222 Dihedral : 2.640 8.357 192 Min Nonbonded Distance : 2.646 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.22 % Favored : 87.78 % Rotamer: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % 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: -2.85 (0.58), residues: 180 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.17 (0.45), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.006 0.001 TYRAD 20 TRP 0.006 0.001 TRPAD 19 Details of bonding type rmsd covalent geometry : bond 0.00245 ( 1446) covalent geometry : angle 0.52548 ( 1956) hydrogen bonds : bond 0.01910 ( 17) hydrogen bonds : angle 4.24770 ( 51) *********************** 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 41 residues out of total 156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 41 time to evaluate : 0.053 Fit side-chains REVERT: AA 12 ILE cc_start: 0.8667 (mm) cc_final: 0.8398 (tp) REVERT: AC 19 TRP cc_start: 0.8049 (t60) cc_final: 0.7845 (t60) REVERT: AD 30 SER cc_start: 0.9096 (t) cc_final: 0.8875 (m) REVERT: AF 24 MET cc_start: 0.7957 (ptm) cc_final: 0.7643 (ptm) REVERT: AF 30 SER cc_start: 0.8949 (t) cc_final: 0.8608 (m) outliers start: 0 outliers final: 0 residues processed: 41 average time/residue: 0.0380 time to fit residues: 1.8557 Evaluate side-chains 36 residues out of total 156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 36 time to evaluate : 0.058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 1 optimal weight: 9.9990 chunk 9 optimal weight: 0.0060 chunk 6 optimal weight: 3.9990 chunk 3 optimal weight: 0.2980 chunk 8 optimal weight: 0.5980 chunk 14 optimal weight: 7.9990 chunk 15 optimal weight: 2.9990 chunk 7 optimal weight: 2.9990 chunk 17 optimal weight: 8.9990 chunk 13 optimal weight: 8.9990 chunk 12 optimal weight: 0.9980 overall best weight: 0.9798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: AC 13 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4442 r_free = 0.4442 target = 0.159479 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4174 r_free = 0.4174 target = 0.132670 restraints weight = 1563.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4190 r_free = 0.4190 target = 0.134506 restraints weight = 1082.413| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4200 r_free = 0.4200 target = 0.135705 restraints weight = 877.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.4208 r_free = 0.4208 target = 0.136449 restraints weight = 780.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.4208 r_free = 0.4208 target = 0.136456 restraints weight = 731.026| |-----------------------------------------------------------------------------| r_work (final): 0.4215 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.5854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 1446 Z= 0.109 Angle : 0.521 6.452 1956 Z= 0.267 Chirality : 0.048 0.156 258 Planarity : 0.002 0.009 222 Dihedral : 2.547 8.054 192 Min Nonbonded Distance : 2.645 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.56 % Favored : 89.44 % Rotamer: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % 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: -2.83 (0.58), residues: 180 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.15 (0.44), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.005 0.001 TYRAD 20 TRP 0.004 0.001 TRPAE 19 Details of bonding type rmsd covalent geometry : bond 0.00256 ( 1446) covalent geometry : angle 0.52127 ( 1956) hydrogen bonds : bond 0.02014 ( 17) hydrogen bonds : angle 4.17752 ( 51) *********************** 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 43 residues out of total 156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 43 time to evaluate : 0.038 Fit side-chains REVERT: AA 12 ILE cc_start: 0.8702 (mm) cc_final: 0.8396 (tp) REVERT: AF 21 SER cc_start: 0.8140 (p) cc_final: 0.7882 (p) REVERT: AF 30 SER cc_start: 0.8979 (t) cc_final: 0.8642 (m) outliers start: 0 outliers final: 0 residues processed: 43 average time/residue: 0.0315 time to fit residues: 1.6149 Evaluate side-chains 38 residues out of total 156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 38 time to evaluate : 0.036 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 3 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 6 optimal weight: 3.9990 chunk 1 optimal weight: 10.0000 chunk 15 optimal weight: 4.9990 chunk 10 optimal weight: 9.9990 chunk 16 optimal weight: 3.9990 chunk 7 optimal weight: 1.9990 chunk 17 optimal weight: 9.9990 chunk 4 optimal weight: 0.9980 chunk 8 optimal weight: 2.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- 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 = 0.4387 r_free = 0.4387 target = 0.154891 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4102 r_free = 0.4102 target = 0.126035 restraints weight = 1593.571| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4121 r_free = 0.4121 target = 0.127960 restraints weight = 1047.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4134 r_free = 0.4134 target = 0.129251 restraints weight = 841.227| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4136 r_free = 0.4136 target = 0.129415 restraints weight = 741.549| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4144 r_free = 0.4144 target = 0.130212 restraints weight = 720.243| |-----------------------------------------------------------------------------| r_work (final): 0.4147 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 moved from start: 0.5837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 1446 Z= 0.154 Angle : 0.568 6.895 1956 Z= 0.295 Chirality : 0.048 0.148 258 Planarity : 0.002 0.011 222 Dihedral : 2.804 8.360 192 Min Nonbonded Distance : 2.644 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.89 % Favored : 86.11 % Rotamer: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % 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: -2.85 (0.58), residues: 180 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.16 (0.44), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.010 0.002 TYRAD 20 TRP 0.005 0.001 TRPAB 19 Details of bonding type rmsd covalent geometry : bond 0.00359 ( 1446) covalent geometry : angle 0.56782 ( 1956) hydrogen bonds : bond 0.02128 ( 17) hydrogen bonds : angle 4.09191 ( 51) *********************** 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 37 residues out of total 156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 37 time to evaluate : 0.043 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 37 average time/residue: 0.0307 time to fit residues: 1.3483 Evaluate side-chains 34 residues out of total 156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 34 time to evaluate : 0.045 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 12 optimal weight: 4.9990 chunk 3 optimal weight: 1.9990 chunk 13 optimal weight: 10.0000 chunk 14 optimal weight: 9.9990 chunk 2 optimal weight: 7.9990 chunk 0 optimal weight: 3.9990 chunk 6 optimal weight: 4.9990 chunk 9 optimal weight: 2.9990 chunk 7 optimal weight: 0.5980 chunk 4 optimal weight: 1.9990 chunk 5 optimal weight: 9.9990 overall best weight: 2.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: AA 13 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4502 r_free = 0.4502 target = 0.226999 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4559 r_free = 0.4559 target = 0.192137 restraints weight = 1706.149| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4565 r_free = 0.4565 target = 0.193576 restraints weight = 1153.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.4586 r_free = 0.4586 target = 0.194913 restraints weight = 898.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.4590 r_free = 0.4590 target = 0.195549 restraints weight = 763.181| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.4590 r_free = 0.4590 target = 0.195549 restraints weight = 686.557| |-----------------------------------------------------------------------------| r_work (final): 0.4312 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.5912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 1446 Z= 0.172 Angle : 0.606 7.263 1956 Z= 0.311 Chirality : 0.049 0.156 258 Planarity : 0.002 0.011 222 Dihedral : 2.959 9.300 192 Min Nonbonded Distance : 2.645 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.78 % Favored : 87.22 % Rotamer: Outliers : 0.00 % Allowed : 0.64 % Favored : 99.36 % 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: -2.84 (0.58), residues: 180 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.16 (0.44), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.011 0.002 TYRAE 20 TRP 0.006 0.001 TRPAB 19 Details of bonding type rmsd covalent geometry : bond 0.00401 ( 1446) covalent geometry : angle 0.60591 ( 1956) hydrogen bonds : bond 0.01942 ( 17) hydrogen bonds : angle 4.23881 ( 51) ********************** 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 36 residues out of total 156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 36 time to evaluate : 0.053 Fit side-chains REVERT: AB 24 MET cc_start: 0.8246 (ptp) cc_final: 0.7945 (ptp) REVERT: AF 8 LYS cc_start: 0.8518 (ttmt) cc_final: 0.8314 (tttp) outliers start: 0 outliers final: 0 residues processed: 36 average time/residue: 0.0402 time to fit residues: 1.6725 Evaluate side-chains 33 residues out of total 156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 33 time to evaluate : 0.033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 8 optimal weight: 9.9990 chunk 4 optimal weight: 10.0000 chunk 9 optimal weight: 0.0470 chunk 14 optimal weight: 9.9990 chunk 15 optimal weight: 0.0670 chunk 0 optimal weight: 10.0000 chunk 3 optimal weight: 4.9990 chunk 5 optimal weight: 5.9990 chunk 1 optimal weight: 10.0000 chunk 7 optimal weight: 2.9990 chunk 13 optimal weight: 6.9990 overall best weight: 2.8222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: AA 13 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4359 r_free = 0.4359 target = 0.151790 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4116 r_free = 0.4116 target = 0.124579 restraints weight = 1658.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4134 r_free = 0.4134 target = 0.126577 restraints weight = 1020.809| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4144 r_free = 0.4144 target = 0.128040 restraints weight = 783.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4150 r_free = 0.4150 target = 0.128662 restraints weight = 672.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.4150 r_free = 0.4150 target = 0.128662 restraints weight = 621.507| |-----------------------------------------------------------------------------| r_work (final): 0.4156 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.5947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 1446 Z= 0.193 Angle : 0.596 6.063 1956 Z= 0.311 Chirality : 0.049 0.161 258 Planarity : 0.002 0.010 222 Dihedral : 3.182 10.444 192 Min Nonbonded Distance : 2.644 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.00 % Favored : 85.00 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: -2.86 (0.58), residues: 180 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.17 (0.44), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.014 0.003 TYRAE 20 TRP 0.007 0.001 TRPAB 19 Details of bonding type rmsd covalent geometry : bond 0.00442 ( 1446) covalent geometry : angle 0.59629 ( 1956) hydrogen bonds : bond 0.02305 ( 17) hydrogen bonds : angle 4.32505 ( 51) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 458.15 seconds wall clock time: 8 minutes 53.47 seconds (533.47 seconds total)