Starting phenix.real_space_refine on Tue Feb 3 12:19:43 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9iyj_60998/02_2026/9iyj_60998.cif Found real_map, /net/cci-nas-00/data/ceres_data/9iyj_60998/02_2026/9iyj_60998.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.92 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9iyj_60998/02_2026/9iyj_60998.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9iyj_60998/02_2026/9iyj_60998.map" model { file = "/net/cci-nas-00/data/ceres_data/9iyj_60998/02_2026/9iyj_60998.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9iyj_60998/02_2026/9iyj_60998.cif" } resolution = 2.92 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= 0.001 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 6 5.16 5 C 747 2.51 5 N 228 2.21 5 O 264 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model 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: 1245 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 415 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 415 Classifications: {'peptide': 59} Link IDs: {'TRANS': 58} Restraints were copied for chains: B, C Time building chain proxies: 0.27, per 1000 atoms: 0.22 Number of scatterers: 1245 At special positions: 0 Unit cell: (59.64, 69.72, 42, 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 6 16.00 O 264 8.00 N 228 7.00 C 747 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: 0.05 Conformation dependent library (CDL) restraints added in 34.5 milliseconds 342 Ramachandran restraints generated. 171 Oldfield, 0 Emsley, 171 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 300 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 6 sheets defined 0.0% alpha, 28.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.09 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 96 through 98 removed outlier: 6.686A pdb=" N ASP A 96 " --> pdb=" O VAL B 97 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N ASP B 96 " --> pdb=" O VAL C 97 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 103 through 105 removed outlier: 6.153A pdb=" N VAL A 103 " --> pdb=" O ILE B 104 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N VAL B 103 " --> pdb=" O ILE C 104 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 110 through 113 removed outlier: 6.485A pdb=" N HIS A 110 " --> pdb=" O CYS B 111 " (cutoff:3.500A) removed outlier: 8.066A pdb=" N ILE B 113 " --> pdb=" O HIS A 110 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N ILE A 112 " --> pdb=" O ILE B 113 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N HIS B 110 " --> pdb=" O CYS C 111 " (cutoff:3.500A) removed outlier: 8.143A pdb=" N ILE C 113 " --> pdb=" O HIS B 110 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N ILE B 112 " --> pdb=" O ILE C 113 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 116 through 117 Processing sheet with id=AA5, first strand: chain 'A' and resid 122 through 125 removed outlier: 7.103A pdb=" N ASP A 125 " --> pdb=" O ASP B 124 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N ASP B 125 " --> pdb=" O ASP C 124 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 142 through 148 removed outlier: 6.363A pdb=" N ARG A 143 " --> pdb=" O LEU B 144 " (cutoff:3.500A) removed outlier: 7.745A pdb=" N CYS B 146 " --> pdb=" O ARG A 143 " (cutoff:3.500A) removed outlier: 7.636A pdb=" N ALA A 145 " --> pdb=" O CYS B 146 " (cutoff:3.500A) removed outlier: 7.580A pdb=" N VAL B 148 " --> pdb=" O ALA A 145 " (cutoff:3.500A) removed outlier: 8.941A pdb=" N GLY A 147 " --> pdb=" O VAL B 148 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N ARG B 143 " --> pdb=" O LEU C 144 " (cutoff:3.500A) removed outlier: 7.743A pdb=" N CYS C 146 " --> pdb=" O ARG B 143 " (cutoff:3.500A) removed outlier: 7.586A pdb=" N ALA B 145 " --> pdb=" O CYS C 146 " (cutoff:3.500A) removed outlier: 7.507A pdb=" N VAL C 148 " --> pdb=" O ALA B 145 " (cutoff:3.500A) removed outlier: 8.870A pdb=" N GLY B 147 " --> pdb=" O VAL C 148 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 6 hydrogen bonds defined for protein. 18 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: 0.10 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 - 1.33: 450 1.33 - 1.45: 69 1.45 - 1.56: 723 1.56 - 1.67: 0 1.67 - 1.79: 6 Bond restraints: 1248 Sorted by residual: bond pdb=" CB VAL C 97 " pdb=" CG2 VAL C 97 " ideal model delta sigma weight residual 1.521 1.473 0.048 3.30e-02 9.18e+02 2.13e+00 bond pdb=" CB VAL A 97 " pdb=" CG2 VAL A 97 " ideal model delta sigma weight residual 1.521 1.473 0.048 3.30e-02 9.18e+02 2.13e+00 bond pdb=" CB VAL B 97 " pdb=" CG2 VAL B 97 " ideal model delta sigma weight residual 1.521 1.474 0.047 3.30e-02 9.18e+02 2.07e+00 bond pdb=" CA LYS A 122 " pdb=" CB LYS A 122 " ideal model delta sigma weight residual 1.532 1.510 0.022 1.58e-02 4.01e+03 1.89e+00 bond pdb=" CA LYS B 122 " pdb=" CB LYS B 122 " ideal model delta sigma weight residual 1.532 1.511 0.021 1.58e-02 4.01e+03 1.77e+00 ... (remaining 1243 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.05: 1341 1.05 - 2.10: 250 2.10 - 3.15: 62 3.15 - 4.20: 21 4.20 - 5.25: 3 Bond angle restraints: 1677 Sorted by residual: angle pdb=" C LEU A 126 " pdb=" N GLY A 127 " pdb=" CA GLY A 127 " ideal model delta sigma weight residual 122.73 119.91 2.82 9.30e-01 1.16e+00 9.19e+00 angle pdb=" C LEU B 126 " pdb=" N GLY B 127 " pdb=" CA GLY B 127 " ideal model delta sigma weight residual 122.73 119.93 2.80 9.30e-01 1.16e+00 9.06e+00 angle pdb=" C LEU C 126 " pdb=" N GLY C 127 " pdb=" CA GLY C 127 " ideal model delta sigma weight residual 122.73 119.95 2.78 9.30e-01 1.16e+00 8.94e+00 angle pdb=" N GLY B 147 " pdb=" CA GLY B 147 " pdb=" C GLY B 147 " ideal model delta sigma weight residual 111.42 115.33 -3.91 1.42e+00 4.96e-01 7.58e+00 angle pdb=" N GLY C 147 " pdb=" CA GLY C 147 " pdb=" C GLY C 147 " ideal model delta sigma weight residual 111.42 115.29 -3.87 1.42e+00 4.96e-01 7.44e+00 ... (remaining 1672 not shown) Histogram of dihedral angle deviations from ideal: 0.01 - 8.39: 594 8.39 - 16.77: 96 16.77 - 25.15: 30 25.15 - 33.53: 9 33.53 - 41.91: 18 Dihedral angle restraints: 747 sinusoidal: 273 harmonic: 474 Sorted by residual: dihedral pdb=" CA ILE A 99 " pdb=" C ILE A 99 " pdb=" N GLU A 100 " pdb=" CA GLU A 100 " ideal model delta harmonic sigma weight residual 180.00 -163.63 -16.37 0 5.00e+00 4.00e-02 1.07e+01 dihedral pdb=" CA ILE B 99 " pdb=" C ILE B 99 " pdb=" N GLU B 100 " pdb=" CA GLU B 100 " ideal model delta harmonic sigma weight residual 180.00 -163.63 -16.37 0 5.00e+00 4.00e-02 1.07e+01 dihedral pdb=" CA ILE C 99 " pdb=" C ILE C 99 " pdb=" N GLU C 100 " pdb=" CA GLU C 100 " ideal model delta harmonic sigma weight residual -180.00 -163.65 -16.35 0 5.00e+00 4.00e-02 1.07e+01 ... (remaining 744 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 111 0.040 - 0.080: 46 0.080 - 0.120: 38 0.120 - 0.160: 6 0.160 - 0.199: 3 Chirality restraints: 204 Sorted by residual: chirality pdb=" CB ILE A 151 " pdb=" CA ILE A 151 " pdb=" CG1 ILE A 151 " pdb=" CG2 ILE A 151 " both_signs ideal model delta sigma weight residual False 2.64 2.45 0.20 2.00e-01 2.50e+01 9.94e-01 chirality pdb=" CB ILE B 151 " pdb=" CA ILE B 151 " pdb=" CG1 ILE B 151 " pdb=" CG2 ILE B 151 " both_signs ideal model delta sigma weight residual False 2.64 2.45 0.20 2.00e-01 2.50e+01 9.89e-01 chirality pdb=" CB ILE C 151 " pdb=" CA ILE C 151 " pdb=" CG1 ILE C 151 " pdb=" CG2 ILE C 151 " both_signs ideal model delta sigma weight residual False 2.64 2.45 0.20 2.00e-01 2.50e+01 9.55e-01 ... (remaining 201 not shown) Planarity restraints: 222 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB HIS A 110 " 0.010 2.00e-02 2.50e+03 1.00e-02 1.51e+00 pdb=" CG HIS A 110 " -0.021 2.00e-02 2.50e+03 pdb=" ND1 HIS A 110 " 0.005 2.00e-02 2.50e+03 pdb=" CD2 HIS A 110 " 0.003 2.00e-02 2.50e+03 pdb=" CE1 HIS A 110 " -0.001 2.00e-02 2.50e+03 pdb=" NE2 HIS A 110 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS B 110 " 0.010 2.00e-02 2.50e+03 9.98e-03 1.49e+00 pdb=" CG HIS B 110 " -0.021 2.00e-02 2.50e+03 pdb=" ND1 HIS B 110 " 0.005 2.00e-02 2.50e+03 pdb=" CD2 HIS B 110 " 0.003 2.00e-02 2.50e+03 pdb=" CE1 HIS B 110 " -0.000 2.00e-02 2.50e+03 pdb=" NE2 HIS B 110 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS C 110 " 0.009 2.00e-02 2.50e+03 9.68e-03 1.41e+00 pdb=" CG HIS C 110 " -0.021 2.00e-02 2.50e+03 pdb=" ND1 HIS C 110 " 0.004 2.00e-02 2.50e+03 pdb=" CD2 HIS C 110 " 0.003 2.00e-02 2.50e+03 pdb=" CE1 HIS C 110 " -0.000 2.00e-02 2.50e+03 pdb=" NE2 HIS C 110 " 0.004 2.00e-02 2.50e+03 ... (remaining 219 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 148 2.74 - 3.28: 1116 3.28 - 3.82: 1857 3.82 - 4.36: 1966 4.36 - 4.90: 3960 Nonbonded interactions: 9047 Sorted by model distance: nonbonded pdb=" OD1 ASP A 109 " pdb=" N ASP B 109 " model vdw 2.198 3.120 nonbonded pdb=" OD1 ASP B 109 " pdb=" N ASP C 109 " model vdw 2.212 3.120 nonbonded pdb=" N ALA B 95 " pdb=" O ALA C 95 " model vdw 2.353 3.120 nonbonded pdb=" N ALA A 95 " pdb=" O ALA B 95 " model vdw 2.447 3.120 nonbonded pdb=" OD2 ASP B 125 " pdb=" NZ LYS B 128 " model vdw 2.507 3.120 ... (remaining 9042 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.380 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.020 Check model and map are aligned: 0.000 Set scattering table: 0.010 Process input model: 2.250 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:4.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8502 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 0.048 1248 Z= 0.498 Angle : 0.963 5.253 1677 Z= 0.575 Chirality : 0.061 0.199 204 Planarity : 0.003 0.010 222 Dihedral : 12.354 41.907 447 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 16.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.04 % Favored : 85.96 % Rotamer: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.63 (0.41), residues: 171 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.28 (0.31), residues: 171 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 115 HIS 0.011 0.004 HIS A 110 Details of bonding type rmsd covalent geometry : bond 0.01091 ( 1248) covalent geometry : angle 0.96350 ( 1677) hydrogen bonds : bond 0.23320 ( 6) hydrogen bonds : angle 9.05127 ( 18) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 342 Ramachandran restraints generated. 171 Oldfield, 0 Emsley, 171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 342 Ramachandran restraints generated. 171 Oldfield, 0 Emsley, 171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 58 time to evaluate : 0.030 Fit side-chains REVERT: A 96 ASP cc_start: 0.7096 (t0) cc_final: 0.6613 (t70) REVERT: A 98 SER cc_start: 0.7902 (p) cc_final: 0.7123 (t) REVERT: A 115 ARG cc_start: 0.8421 (ttt90) cc_final: 0.7403 (pmt170) REVERT: A 131 ASN cc_start: 0.8728 (t0) cc_final: 0.7937 (t0) REVERT: A 132 GLU cc_start: 0.8236 (tt0) cc_final: 0.7828 (tt0) REVERT: A 136 LYS cc_start: 0.8819 (tttt) cc_final: 0.7133 (pptt) REVERT: B 99 ILE cc_start: 0.8082 (mt) cc_final: 0.6842 (mm) REVERT: B 115 ARG cc_start: 0.8474 (ttt90) cc_final: 0.8185 (ttt-90) REVERT: B 131 ASN cc_start: 0.8553 (t0) cc_final: 0.7972 (t0) REVERT: B 132 GLU cc_start: 0.8176 (tt0) cc_final: 0.7912 (tt0) REVERT: B 143 ARG cc_start: 0.8376 (tpt-90) cc_final: 0.8033 (ttt90) REVERT: C 131 ASN cc_start: 0.8594 (t0) cc_final: 0.8099 (t0) REVERT: C 133 GLU cc_start: 0.8022 (mm-30) cc_final: 0.7803 (mp0) outliers start: 0 outliers final: 0 residues processed: 58 average time/residue: 0.2720 time to fit residues: 16.0259 Evaluate side-chains 43 residues out of total 135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 43 time to evaluate : 0.029 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 15 random chunks: chunk 13 optimal weight: 0.8980 chunk 6 optimal weight: 4.9990 chunk 12 optimal weight: 1.9990 chunk 14 optimal weight: 0.0370 chunk 0 optimal weight: 0.5980 chunk 4 optimal weight: 3.9990 chunk 8 optimal weight: 2.9990 chunk 7 optimal weight: 2.9990 chunk 5 optimal weight: 0.8980 chunk 9 optimal weight: 2.9990 chunk 3 optimal weight: 4.9990 overall best weight: 0.8860 ------------------------------------------------------------------------------- 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 = 0.3743 r_free = 0.3743 target = 0.099560 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.085906 restraints weight = 2393.356| |-----------------------------------------------------------------------------| r_work (start): 0.3589 rms_B_bonded: 3.03 r_work: 0.3478 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3378 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3378 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8653 moved from start: 0.2537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.016 1248 Z= 0.141 Angle : 0.681 7.411 1677 Z= 0.326 Chirality : 0.049 0.129 204 Planarity : 0.002 0.015 222 Dihedral : 4.327 11.596 180 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.45 % Favored : 86.55 % Rotamer: Outliers : 3.70 % Allowed : 18.52 % Favored : 77.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.98 (0.45), residues: 171 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.79 (0.35), residues: 171 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 143 HIS 0.003 0.001 HIS C 110 Details of bonding type rmsd covalent geometry : bond 0.00301 ( 1248) covalent geometry : angle 0.68073 ( 1677) hydrogen bonds : bond 0.03000 ( 6) hydrogen bonds : angle 4.88768 ( 18) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 342 Ramachandran restraints generated. 171 Oldfield, 0 Emsley, 171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 342 Ramachandran restraints generated. 171 Oldfield, 0 Emsley, 171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 41 time to evaluate : 0.051 Fit side-chains REVERT: A 96 ASP cc_start: 0.7415 (t0) cc_final: 0.6713 (p0) REVERT: A 115 ARG cc_start: 0.8838 (ttt90) cc_final: 0.7494 (pmt170) REVERT: A 131 ASN cc_start: 0.8419 (t0) cc_final: 0.8065 (t0) REVERT: A 132 GLU cc_start: 0.8554 (tt0) cc_final: 0.8257 (tt0) REVERT: A 133 GLU cc_start: 0.8053 (mp0) cc_final: 0.7523 (mp0) REVERT: B 115 ARG cc_start: 0.8803 (ttt90) cc_final: 0.8342 (ttt-90) REVERT: B 131 ASN cc_start: 0.8237 (t0) cc_final: 0.7862 (t0) REVERT: B 132 GLU cc_start: 0.8455 (tt0) cc_final: 0.8174 (tt0) REVERT: C 115 ARG cc_start: 0.8926 (ttt90) cc_final: 0.7104 (tpm170) REVERT: C 131 ASN cc_start: 0.8700 (t0) cc_final: 0.8372 (t0) REVERT: C 133 GLU cc_start: 0.8547 (mm-30) cc_final: 0.7876 (mp0) outliers start: 5 outliers final: 0 residues processed: 43 average time/residue: 0.6236 time to fit residues: 27.1117 Evaluate side-chains 36 residues out of total 135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 36 time to evaluate : 0.062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 15 random chunks: chunk 12 optimal weight: 0.9990 chunk 3 optimal weight: 4.9990 chunk 14 optimal weight: 5.9990 chunk 7 optimal weight: 1.9990 chunk 9 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 chunk 2 optimal weight: 2.9990 chunk 13 optimal weight: 0.0970 chunk 6 optimal weight: 0.9990 chunk 5 optimal weight: 0.6980 chunk 10 optimal weight: 0.6980 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 101 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.100618 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.086877 restraints weight = 2409.749| |-----------------------------------------------------------------------------| r_work (start): 0.3606 rms_B_bonded: 3.01 r_work: 0.3496 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3401 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3401 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8640 moved from start: 0.3098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 1248 Z= 0.125 Angle : 0.639 6.413 1677 Z= 0.312 Chirality : 0.049 0.127 204 Planarity : 0.002 0.017 222 Dihedral : 3.902 10.998 180 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.04 % Favored : 85.96 % Rotamer: Outliers : 2.22 % Allowed : 20.74 % Favored : 77.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -4.53 (0.48), residues: 171 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.45 (0.37), residues: 171 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 143 HIS 0.001 0.000 HIS A 110 Details of bonding type rmsd covalent geometry : bond 0.00272 ( 1248) covalent geometry : angle 0.63923 ( 1677) hydrogen bonds : bond 0.02084 ( 6) hydrogen bonds : angle 4.66914 ( 18) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 342 Ramachandran restraints generated. 171 Oldfield, 0 Emsley, 171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 342 Ramachandran restraints generated. 171 Oldfield, 0 Emsley, 171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 37 time to evaluate : 0.053 Fit side-chains REVERT: A 96 ASP cc_start: 0.7414 (t0) cc_final: 0.6641 (p0) REVERT: A 115 ARG cc_start: 0.8794 (ttt90) cc_final: 0.7398 (pmt170) REVERT: A 131 ASN cc_start: 0.8508 (t0) cc_final: 0.8207 (t0) REVERT: A 132 GLU cc_start: 0.8557 (tt0) cc_final: 0.8275 (tt0) REVERT: A 133 GLU cc_start: 0.8106 (mp0) cc_final: 0.7507 (mp0) REVERT: B 115 ARG cc_start: 0.8768 (ttt90) cc_final: 0.8283 (ttt-90) REVERT: B 131 ASN cc_start: 0.8228 (t0) cc_final: 0.7891 (t0) REVERT: B 132 GLU cc_start: 0.8474 (tt0) cc_final: 0.8204 (tt0) REVERT: C 115 ARG cc_start: 0.8909 (ttt90) cc_final: 0.7132 (tpm170) REVERT: C 131 ASN cc_start: 0.8760 (t0) cc_final: 0.8479 (t0) REVERT: C 133 GLU cc_start: 0.8543 (mm-30) cc_final: 0.7873 (mp0) outliers start: 3 outliers final: 0 residues processed: 38 average time/residue: 0.6152 time to fit residues: 23.6593 Evaluate side-chains 33 residues out of total 135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 33 time to evaluate : 0.052 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 15 random chunks: chunk 1 optimal weight: 2.9990 chunk 2 optimal weight: 3.9990 chunk 3 optimal weight: 0.0070 chunk 12 optimal weight: 2.9990 chunk 14 optimal weight: 0.8980 chunk 6 optimal weight: 2.9990 chunk 7 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 8 optimal weight: 3.9990 chunk 5 optimal weight: 4.9990 chunk 0 optimal weight: 0.9980 overall best weight: 1.3802 ------------------------------------------------------------------------------- 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 = 0.3674 r_free = 0.3674 target = 0.094689 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.080942 restraints weight = 2433.366| |-----------------------------------------------------------------------------| r_work (start): 0.3495 rms_B_bonded: 3.06 r_work: 0.3378 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3279 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3279 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8673 moved from start: 0.3092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 1248 Z= 0.199 Angle : 0.669 6.500 1677 Z= 0.339 Chirality : 0.050 0.136 204 Planarity : 0.002 0.012 222 Dihedral : 4.440 12.542 180 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.04 % Favored : 85.96 % Rotamer: Outliers : 3.70 % Allowed : 17.78 % Favored : 78.52 % 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: -4.35 (0.50), residues: 171 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.31 (0.38), residues: 171 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG A 143 HIS 0.002 0.001 HIS B 110 Details of bonding type rmsd covalent geometry : bond 0.00441 ( 1248) covalent geometry : angle 0.66917 ( 1677) hydrogen bonds : bond 0.01983 ( 6) hydrogen bonds : angle 4.77321 ( 18) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 342 Ramachandran restraints generated. 171 Oldfield, 0 Emsley, 171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 342 Ramachandran restraints generated. 171 Oldfield, 0 Emsley, 171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 38 time to evaluate : 0.052 Fit side-chains REVERT: A 96 ASP cc_start: 0.7490 (t0) cc_final: 0.6563 (p0) REVERT: A 100 GLU cc_start: 0.7752 (mp0) cc_final: 0.7316 (mp0) REVERT: A 121 GLU cc_start: 0.8887 (mt-10) cc_final: 0.8547 (mt-10) REVERT: A 131 ASN cc_start: 0.8632 (t0) cc_final: 0.8422 (t0) REVERT: A 132 GLU cc_start: 0.8557 (tt0) cc_final: 0.8284 (tt0) REVERT: A 133 GLU cc_start: 0.8166 (mp0) cc_final: 0.7561 (mp0) REVERT: B 115 ARG cc_start: 0.8765 (ttt90) cc_final: 0.8373 (ttt-90) REVERT: B 125 ASP cc_start: 0.8452 (t0) cc_final: 0.7958 (t0) REVERT: C 99 ILE cc_start: 0.8798 (OUTLIER) cc_final: 0.8588 (mp) REVERT: C 125 ASP cc_start: 0.8604 (t0) cc_final: 0.8271 (t0) REVERT: C 131 ASN cc_start: 0.8842 (t0) cc_final: 0.8563 (t0) REVERT: C 133 GLU cc_start: 0.8522 (mm-30) cc_final: 0.7873 (mp0) outliers start: 5 outliers final: 0 residues processed: 40 average time/residue: 0.5102 time to fit residues: 20.6877 Evaluate side-chains 37 residues out of total 135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 36 time to evaluate : 0.048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 99 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 15 random chunks: chunk 3 optimal weight: 4.9990 chunk 13 optimal weight: 3.9990 chunk 8 optimal weight: 4.9990 chunk 7 optimal weight: 1.9990 chunk 5 optimal weight: 4.9990 chunk 0 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 4 optimal weight: 4.9990 chunk 6 optimal weight: 2.9990 chunk 9 optimal weight: 0.0870 chunk 2 optimal weight: 3.9990 overall best weight: 1.8166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 101 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.092284 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.078610 restraints weight = 2336.474| |-----------------------------------------------------------------------------| r_work (start): 0.3453 rms_B_bonded: 2.97 r_work: 0.3338 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3240 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3240 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8697 moved from start: 0.3234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.026 1248 Z= 0.250 Angle : 0.688 6.918 1677 Z= 0.349 Chirality : 0.051 0.140 204 Planarity : 0.003 0.014 222 Dihedral : 4.767 13.265 180 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.20 % Favored : 84.80 % Rotamer: Outliers : 3.70 % Allowed : 20.00 % Favored : 76.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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 (0.51), residues: 171 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.32 (0.39), residues: 171 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG C 115 HIS 0.001 0.001 HIS B 110 Details of bonding type rmsd covalent geometry : bond 0.00553 ( 1248) covalent geometry : angle 0.68764 ( 1677) hydrogen bonds : bond 0.02172 ( 6) hydrogen bonds : angle 4.76628 ( 18) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 342 Ramachandran restraints generated. 171 Oldfield, 0 Emsley, 171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 342 Ramachandran restraints generated. 171 Oldfield, 0 Emsley, 171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 37 time to evaluate : 0.050 Fit side-chains REVERT: A 96 ASP cc_start: 0.7511 (t0) cc_final: 0.6525 (p0) REVERT: A 100 GLU cc_start: 0.7869 (mp0) cc_final: 0.7495 (mp0) REVERT: A 121 GLU cc_start: 0.8957 (mt-10) cc_final: 0.8599 (mt-10) REVERT: A 131 ASN cc_start: 0.8755 (t0) cc_final: 0.8388 (t0) REVERT: A 132 GLU cc_start: 0.8498 (tt0) cc_final: 0.8083 (tt0) REVERT: A 133 GLU cc_start: 0.8162 (mp0) cc_final: 0.7347 (mp0) REVERT: B 115 ARG cc_start: 0.8744 (ttt90) cc_final: 0.8345 (ttt-90) REVERT: B 125 ASP cc_start: 0.8471 (t0) cc_final: 0.7972 (t0) REVERT: B 151 ILE cc_start: 0.8847 (OUTLIER) cc_final: 0.8554 (mt) REVERT: C 99 ILE cc_start: 0.8804 (OUTLIER) cc_final: 0.8583 (mm) REVERT: C 125 ASP cc_start: 0.8630 (t0) cc_final: 0.8267 (t0) REVERT: C 131 ASN cc_start: 0.8974 (t0) cc_final: 0.8746 (t0) REVERT: C 133 GLU cc_start: 0.8521 (mm-30) cc_final: 0.7901 (mp0) outliers start: 5 outliers final: 0 residues processed: 39 average time/residue: 0.4836 time to fit residues: 19.1387 Evaluate side-chains 38 residues out of total 135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 36 time to evaluate : 0.049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain C residue 99 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 15 random chunks: chunk 7 optimal weight: 0.8980 chunk 14 optimal weight: 3.9990 chunk 8 optimal weight: 4.9990 chunk 11 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 4 optimal weight: 4.9990 chunk 13 optimal weight: 0.7980 chunk 6 optimal weight: 0.6980 chunk 3 optimal weight: 5.9990 chunk 12 optimal weight: 1.9990 chunk 9 optimal weight: 0.8980 overall best weight: 1.0582 ------------------------------------------------------------------------------- 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 = 0.3697 r_free = 0.3697 target = 0.095609 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.081739 restraints weight = 2371.374| |-----------------------------------------------------------------------------| r_work (start): 0.3514 rms_B_bonded: 3.05 r_work: 0.3399 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3302 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3302 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8678 moved from start: 0.3405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 1248 Z= 0.155 Angle : 0.623 7.017 1677 Z= 0.303 Chirality : 0.049 0.133 204 Planarity : 0.002 0.014 222 Dihedral : 4.315 12.992 180 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.04 % Favored : 85.96 % Rotamer: Outliers : 2.96 % Allowed : 22.22 % Favored : 74.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.23 (0.52), residues: 171 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.21 (0.39), residues: 171 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG C 115 HIS 0.001 0.000 HIS A 120 Details of bonding type rmsd covalent geometry : bond 0.00338 ( 1248) covalent geometry : angle 0.62291 ( 1677) hydrogen bonds : bond 0.01793 ( 6) hydrogen bonds : angle 4.74957 ( 18) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 342 Ramachandran restraints generated. 171 Oldfield, 0 Emsley, 171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 342 Ramachandran restraints generated. 171 Oldfield, 0 Emsley, 171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 37 time to evaluate : 0.051 Fit side-chains REVERT: A 96 ASP cc_start: 0.7514 (t0) cc_final: 0.7010 (t70) REVERT: A 100 GLU cc_start: 0.7900 (mp0) cc_final: 0.7513 (mp0) REVERT: A 115 ARG cc_start: 0.8779 (ttt90) cc_final: 0.7442 (pmt170) REVERT: A 121 GLU cc_start: 0.8925 (mt-10) cc_final: 0.8440 (mt-10) REVERT: A 131 ASN cc_start: 0.8807 (t0) cc_final: 0.8370 (t0) REVERT: A 132 GLU cc_start: 0.8500 (tt0) cc_final: 0.8048 (tt0) REVERT: A 133 GLU cc_start: 0.8183 (mp0) cc_final: 0.7335 (mp0) REVERT: B 125 ASP cc_start: 0.8481 (t0) cc_final: 0.7983 (t0) REVERT: C 125 ASP cc_start: 0.8627 (t0) cc_final: 0.8286 (t0) REVERT: C 131 ASN cc_start: 0.8940 (t0) cc_final: 0.8678 (t0) REVERT: C 133 GLU cc_start: 0.8477 (mm-30) cc_final: 0.7878 (mp0) outliers start: 4 outliers final: 0 residues processed: 39 average time/residue: 0.5834 time to fit residues: 23.0393 Evaluate side-chains 35 residues out of total 135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 35 time to evaluate : 0.084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 15 random chunks: chunk 0 optimal weight: 3.9990 chunk 14 optimal weight: 5.9990 chunk 8 optimal weight: 5.9990 chunk 6 optimal weight: 2.9990 chunk 1 optimal weight: 4.9990 chunk 4 optimal weight: 4.9990 chunk 12 optimal weight: 2.9990 chunk 11 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 10 optimal weight: 0.6980 chunk 9 optimal weight: 0.8980 overall best weight: 2.1186 ------------------------------------------------------------------------------- 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 = 0.3625 r_free = 0.3625 target = 0.090995 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.077288 restraints weight = 2375.110| |-----------------------------------------------------------------------------| r_work (start): 0.3432 rms_B_bonded: 2.99 r_work: 0.3314 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3216 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3216 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8716 moved from start: 0.3417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.030 1248 Z= 0.289 Angle : 0.740 7.766 1677 Z= 0.369 Chirality : 0.052 0.141 204 Planarity : 0.003 0.020 222 Dihedral : 4.802 13.655 180 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.37 % Favored : 83.63 % Rotamer: Outliers : 3.70 % Allowed : 23.70 % Favored : 72.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.36 (0.52), residues: 171 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.32 (0.39), residues: 171 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 143 HIS 0.001 0.000 HIS A 110 Details of bonding type rmsd covalent geometry : bond 0.00636 ( 1248) covalent geometry : angle 0.74038 ( 1677) hydrogen bonds : bond 0.02290 ( 6) hydrogen bonds : angle 4.69360 ( 18) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 342 Ramachandran restraints generated. 171 Oldfield, 0 Emsley, 171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 342 Ramachandran restraints generated. 171 Oldfield, 0 Emsley, 171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 35 time to evaluate : 0.051 Fit side-chains REVERT: A 96 ASP cc_start: 0.7308 (t0) cc_final: 0.6296 (p0) REVERT: A 100 GLU cc_start: 0.7960 (mp0) cc_final: 0.7517 (mp0) REVERT: A 121 GLU cc_start: 0.9016 (mt-10) cc_final: 0.8656 (mt-10) REVERT: A 131 ASN cc_start: 0.8852 (t0) cc_final: 0.8434 (t0) REVERT: A 132 GLU cc_start: 0.8464 (tt0) cc_final: 0.7992 (tt0) REVERT: A 133 GLU cc_start: 0.8198 (mp0) cc_final: 0.7355 (mp0) REVERT: B 125 ASP cc_start: 0.8512 (t0) cc_final: 0.7971 (t0) REVERT: B 151 ILE cc_start: 0.8915 (OUTLIER) cc_final: 0.8428 (mt) REVERT: C 99 ILE cc_start: 0.8912 (OUTLIER) cc_final: 0.8668 (mm) REVERT: C 125 ASP cc_start: 0.8638 (t0) cc_final: 0.8261 (t0) REVERT: C 133 GLU cc_start: 0.8548 (mm-30) cc_final: 0.7948 (mp0) outliers start: 5 outliers final: 0 residues processed: 36 average time/residue: 0.3574 time to fit residues: 13.0734 Evaluate side-chains 34 residues out of total 135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 32 time to evaluate : 0.029 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain C residue 99 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 15 random chunks: chunk 9 optimal weight: 6.9990 chunk 11 optimal weight: 0.9990 chunk 7 optimal weight: 0.9990 chunk 0 optimal weight: 3.9990 chunk 12 optimal weight: 2.9990 chunk 3 optimal weight: 5.9990 chunk 8 optimal weight: 0.9990 chunk 6 optimal weight: 0.8980 chunk 10 optimal weight: 0.8980 chunk 1 optimal weight: 3.9990 chunk 13 optimal weight: 0.9980 overall best weight: 0.9584 ------------------------------------------------------------------------------- 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 = 0.3695 r_free = 0.3695 target = 0.095190 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.081219 restraints weight = 2411.791| |-----------------------------------------------------------------------------| r_work (start): 0.3511 rms_B_bonded: 3.09 r_work: 0.3397 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3298 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3298 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8675 moved from start: 0.3662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 1248 Z= 0.150 Angle : 0.680 7.191 1677 Z= 0.324 Chirality : 0.050 0.134 204 Planarity : 0.002 0.015 222 Dihedral : 4.314 13.380 180 Min Nonbonded Distance : 2.646 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.04 % Favored : 85.96 % Rotamer: Outliers : 3.70 % Allowed : 23.70 % Favored : 72.59 % 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: -4.24 (0.53), residues: 171 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.22 (0.40), residues: 171 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG C 115 HIS 0.001 0.000 HIS C 110 Details of bonding type rmsd covalent geometry : bond 0.00330 ( 1248) covalent geometry : angle 0.67969 ( 1677) hydrogen bonds : bond 0.01621 ( 6) hydrogen bonds : angle 4.73371 ( 18) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 342 Ramachandran restraints generated. 171 Oldfield, 0 Emsley, 171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 342 Ramachandran restraints generated. 171 Oldfield, 0 Emsley, 171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 32 time to evaluate : 0.032 Fit side-chains REVERT: A 96 ASP cc_start: 0.7338 (t0) cc_final: 0.6270 (p0) REVERT: A 100 GLU cc_start: 0.7911 (mp0) cc_final: 0.7465 (mp0) REVERT: A 115 ARG cc_start: 0.8777 (ttt90) cc_final: 0.7428 (pmt170) REVERT: A 121 GLU cc_start: 0.8941 (mt-10) cc_final: 0.8436 (mt-10) REVERT: A 131 ASN cc_start: 0.8843 (t0) cc_final: 0.8383 (t0) REVERT: A 132 GLU cc_start: 0.8446 (tt0) cc_final: 0.7930 (tt0) REVERT: A 133 GLU cc_start: 0.8189 (mp0) cc_final: 0.7316 (mp0) REVERT: B 121 GLU cc_start: 0.8999 (OUTLIER) cc_final: 0.8777 (mt-10) REVERT: B 125 ASP cc_start: 0.8478 (t0) cc_final: 0.7971 (t0) REVERT: B 151 ILE cc_start: 0.8946 (OUTLIER) cc_final: 0.8426 (mt) REVERT: C 125 ASP cc_start: 0.8620 (t0) cc_final: 0.8287 (t0) REVERT: C 133 GLU cc_start: 0.8504 (mm-30) cc_final: 0.7939 (mp0) outliers start: 5 outliers final: 0 residues processed: 35 average time/residue: 0.4904 time to fit residues: 17.3769 Evaluate side-chains 34 residues out of total 135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 32 time to evaluate : 0.029 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 121 GLU Chi-restraints excluded: chain B residue 151 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 15 random chunks: chunk 4 optimal weight: 3.9990 chunk 13 optimal weight: 4.9990 chunk 9 optimal weight: 0.9980 chunk 1 optimal weight: 0.7980 chunk 10 optimal weight: 0.0060 chunk 2 optimal weight: 4.9990 chunk 8 optimal weight: 3.9990 chunk 12 optimal weight: 4.9990 chunk 11 optimal weight: 1.9990 chunk 6 optimal weight: 3.9990 chunk 14 optimal weight: 3.9990 overall best weight: 1.5600 ------------------------------------------------------------------------------- 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 = 0.3646 r_free = 0.3646 target = 0.092621 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.078662 restraints weight = 2357.828| |-----------------------------------------------------------------------------| r_work (start): 0.3462 rms_B_bonded: 3.03 r_work: 0.3345 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3248 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3248 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8706 moved from start: 0.3647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.027 1248 Z= 0.221 Angle : 0.710 7.401 1677 Z= 0.350 Chirality : 0.051 0.147 204 Planarity : 0.003 0.015 222 Dihedral : 4.518 12.999 180 Min Nonbonded Distance : 2.622 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.37 % Favored : 83.63 % Rotamer: Outliers : 1.48 % Allowed : 27.41 % Favored : 71.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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 (0.53), residues: 171 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.24 (0.40), residues: 171 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG B 143 HIS 0.001 0.000 HIS A 120 Details of bonding type rmsd covalent geometry : bond 0.00493 ( 1248) covalent geometry : angle 0.70982 ( 1677) hydrogen bonds : bond 0.02523 ( 6) hydrogen bonds : angle 4.97596 ( 18) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 342 Ramachandran restraints generated. 171 Oldfield, 0 Emsley, 171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 342 Ramachandran restraints generated. 171 Oldfield, 0 Emsley, 171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 32 time to evaluate : 0.031 Fit side-chains REVERT: A 96 ASP cc_start: 0.7217 (t0) cc_final: 0.6213 (p0) REVERT: A 100 GLU cc_start: 0.7938 (mp0) cc_final: 0.7487 (mp0) REVERT: A 121 GLU cc_start: 0.9007 (mt-10) cc_final: 0.8583 (mt-10) REVERT: A 131 ASN cc_start: 0.8896 (t0) cc_final: 0.8445 (t0) REVERT: A 132 GLU cc_start: 0.8440 (tt0) cc_final: 0.7944 (tt0) REVERT: A 133 GLU cc_start: 0.8224 (mp0) cc_final: 0.7357 (mp0) REVERT: B 121 GLU cc_start: 0.8998 (OUTLIER) cc_final: 0.8755 (mt-10) REVERT: B 125 ASP cc_start: 0.8501 (t0) cc_final: 0.7981 (t0) REVERT: B 151 ILE cc_start: 0.8920 (OUTLIER) cc_final: 0.8449 (mt) REVERT: C 125 ASP cc_start: 0.8624 (t0) cc_final: 0.8288 (t0) REVERT: C 133 GLU cc_start: 0.8526 (mm-30) cc_final: 0.8032 (mp0) outliers start: 2 outliers final: 1 residues processed: 32 average time/residue: 0.3243 time to fit residues: 10.5302 Evaluate side-chains 35 residues out of total 135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 32 time to evaluate : 0.029 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 121 GLU Chi-restraints excluded: chain B residue 133 GLU Chi-restraints excluded: chain B residue 151 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 15 random chunks: chunk 11 optimal weight: 1.9990 chunk 4 optimal weight: 2.9990 chunk 2 optimal weight: 3.9990 chunk 5 optimal weight: 4.9990 chunk 12 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 9 optimal weight: 0.8980 chunk 14 optimal weight: 2.9990 chunk 3 optimal weight: 3.9990 chunk 0 optimal weight: 1.9990 chunk 6 optimal weight: 3.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- 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 = 0.3636 r_free = 0.3636 target = 0.091980 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.077951 restraints weight = 2432.034| |-----------------------------------------------------------------------------| r_work (start): 0.3444 rms_B_bonded: 3.05 r_work: 0.3328 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3229 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3229 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8711 moved from start: 0.3635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.033 1248 Z= 0.274 Angle : 0.729 6.790 1677 Z= 0.375 Chirality : 0.053 0.164 204 Planarity : 0.003 0.017 222 Dihedral : 4.722 13.151 180 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.04 % Favored : 85.96 % Rotamer: Outliers : 2.96 % Allowed : 25.93 % Favored : 71.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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 (0.53), residues: 171 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.24 (0.41), residues: 171 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG B 143 HIS 0.001 0.000 HIS A 110 Details of bonding type rmsd covalent geometry : bond 0.00611 ( 1248) covalent geometry : angle 0.72858 ( 1677) hydrogen bonds : bond 0.03202 ( 6) hydrogen bonds : angle 5.35566 ( 18) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 342 Ramachandran restraints generated. 171 Oldfield, 0 Emsley, 171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 342 Ramachandran restraints generated. 171 Oldfield, 0 Emsley, 171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 32 time to evaluate : 0.031 Fit side-chains REVERT: A 96 ASP cc_start: 0.7226 (t0) cc_final: 0.6172 (p0) REVERT: A 100 GLU cc_start: 0.7943 (mp0) cc_final: 0.7490 (mp0) REVERT: A 121 GLU cc_start: 0.9027 (mt-10) cc_final: 0.8765 (mt-10) REVERT: A 131 ASN cc_start: 0.8906 (t0) cc_final: 0.8485 (t0) REVERT: A 132 GLU cc_start: 0.8407 (tt0) cc_final: 0.7963 (tt0) REVERT: A 133 GLU cc_start: 0.8159 (mp0) cc_final: 0.7337 (mp0) REVERT: B 125 ASP cc_start: 0.8522 (t0) cc_final: 0.7965 (t0) REVERT: B 151 ILE cc_start: 0.8956 (OUTLIER) cc_final: 0.8491 (mt) REVERT: C 99 ILE cc_start: 0.8915 (OUTLIER) cc_final: 0.8682 (mm) REVERT: C 125 ASP cc_start: 0.8646 (t0) cc_final: 0.8286 (t0) REVERT: C 133 GLU cc_start: 0.8516 (mm-30) cc_final: 0.8007 (mp0) outliers start: 4 outliers final: 0 residues processed: 33 average time/residue: 0.3618 time to fit residues: 12.1413 Evaluate side-chains 33 residues out of total 135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 31 time to evaluate : 0.046 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain C residue 99 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 15 random chunks: chunk 1 optimal weight: 0.9980 chunk 12 optimal weight: 4.9990 chunk 2 optimal weight: 4.9990 chunk 9 optimal weight: 6.9990 chunk 13 optimal weight: 0.7980 chunk 5 optimal weight: 2.9990 chunk 4 optimal weight: 0.7980 chunk 8 optimal weight: 2.9990 chunk 7 optimal weight: 3.9990 chunk 10 optimal weight: 0.6980 chunk 11 optimal weight: 0.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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 = 0.3706 r_free = 0.3706 target = 0.096132 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.082019 restraints weight = 2406.853| |-----------------------------------------------------------------------------| r_work (start): 0.3522 rms_B_bonded: 3.10 r_work: 0.3409 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3312 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3312 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8676 moved from start: 0.3842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 1248 Z= 0.142 Angle : 0.647 6.746 1677 Z= 0.321 Chirality : 0.049 0.133 204 Planarity : 0.002 0.015 222 Dihedral : 4.114 12.806 180 Min Nonbonded Distance : 2.634 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.04 % Favored : 85.96 % Rotamer: Outliers : 1.48 % Allowed : 26.67 % Favored : 71.85 % 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 (0.55), residues: 171 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.12 (0.42), residues: 171 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG C 115 HIS 0.002 0.000 HIS C 110 Details of bonding type rmsd covalent geometry : bond 0.00317 ( 1248) covalent geometry : angle 0.64698 ( 1677) hydrogen bonds : bond 0.02301 ( 6) hydrogen bonds : angle 4.95852 ( 18) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 807.22 seconds wall clock time: 14 minutes 33.55 seconds (873.55 seconds total)