Starting phenix.real_space_refine on Fri Oct 10 10:15:02 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wnw_37674/10_2025/8wnw_37674.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wnw_37674/10_2025/8wnw_37674.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8wnw_37674/10_2025/8wnw_37674.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wnw_37674/10_2025/8wnw_37674.map" model { file = "/net/cci-nas-00/data/ceres_data/8wnw_37674/10_2025/8wnw_37674.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wnw_37674/10_2025/8wnw_37674.cif" } resolution = 3.5 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: 5 Type Number sf(0) Gaussians Mg 2 5.21 5 S 6 5.16 5 C 909 2.51 5 N 220 2.21 5 O 263 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-2.0-5842/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 1400 Number of models: 1 Model: "" Number of chains: 2 Chain: "Q" Number of atoms: 1251 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1251 Classifications: {'peptide': 173} Link IDs: {'PTRANS': 9, 'TRANS': 163} Chain breaks: 1 Chain: "Q" Number of atoms: 149 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 149 Unusual residues: {'CLA': 2, 'LMG': 1} Classifications: {'undetermined': 3, 'water': 1} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 41 Unresolved non-hydrogen dihedrals: 28 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'CLA:plan-5': 1} Unresolved non-hydrogen planarities: 5 Time building chain proxies: 0.54, per 1000 atoms: 0.39 Number of scatterers: 1400 At special positions: 0 Unit cell: (57.2023, 68.6427, 59.2823, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 6 16.00 Mg 2 11.99 O 263 8.00 N 220 7.00 C 909 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.29 Conformation dependent library (CDL) restraints added in 49.6 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 338 Ramachandran restraints generated. 169 Oldfield, 0 Emsley, 169 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 320 Finding SS restraints... Secondary structure from input PDB file: 6 helices and 0 sheets defined 67.1% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.02 Creating SS restraints... Processing helix chain 'Q' and resid 91 through 110 Processing helix chain 'Q' and resid 110 through 124 removed outlier: 3.546A pdb=" N LEU Q 114 " --> pdb=" O LYS Q 110 " (cutoff:3.500A) Processing helix chain 'Q' and resid 130 through 159 removed outlier: 4.371A pdb=" N THR Q 143 " --> pdb=" O ALA Q 139 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N THR Q 144 " --> pdb=" O LEU Q 140 " (cutoff:3.500A) Processing helix chain 'Q' and resid 160 through 164 removed outlier: 3.724A pdb=" N GLY Q 164 " --> pdb=" O LYS Q 161 " (cutoff:3.500A) Processing helix chain 'Q' and resid 183 through 204 removed outlier: 3.843A pdb=" N VAL Q 187 " --> pdb=" O LEU Q 183 " (cutoff:3.500A) Processing helix chain 'Q' and resid 205 through 228 88 hydrogen bonds defined for protein. 261 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: 0.23 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.39: 506 1.39 - 1.56: 910 1.56 - 1.74: 0 1.74 - 1.92: 9 1.92 - 2.09: 8 Bond restraints: 1433 Sorted by residual: bond pdb=" C10 LMG Q 301 " pdb=" O7 LMG Q 301 " ideal model delta sigma weight residual 1.336 1.457 -0.121 2.00e-02 2.50e+03 3.64e+01 bond pdb=" C28 LMG Q 301 " pdb=" O8 LMG Q 301 " ideal model delta sigma weight residual 1.331 1.447 -0.116 2.00e-02 2.50e+03 3.38e+01 bond pdb=" N ASN Q 228 " pdb=" CA ASN Q 228 " ideal model delta sigma weight residual 1.458 1.491 -0.033 7.40e-03 1.83e+04 2.02e+01 bond pdb=" N VAL Q 187 " pdb=" CA VAL Q 187 " ideal model delta sigma weight residual 1.461 1.496 -0.035 1.19e-02 7.06e+03 8.71e+00 bond pdb=" C ASN Q 228 " pdb=" N PRO Q 229 " ideal model delta sigma weight residual 1.329 1.364 -0.034 1.18e-02 7.18e+03 8.49e+00 ... (remaining 1428 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.14: 1862 3.14 - 6.28: 93 6.28 - 9.43: 5 9.43 - 12.57: 1 12.57 - 15.71: 3 Bond angle restraints: 1964 Sorted by residual: angle pdb=" C TYR Q 141 " pdb=" CA TYR Q 141 " pdb=" CB TYR Q 141 " ideal model delta sigma weight residual 109.34 118.47 -9.13 1.55e+00 4.16e-01 3.47e+01 angle pdb=" NB CLA Q 302 " pdb="MG CLA Q 302 " pdb=" ND CLA Q 302 " ideal model delta sigma weight residual 176.90 161.19 15.71 3.00e+00 1.11e-01 2.74e+01 angle pdb=" NB CLA Q 303 " pdb="MG CLA Q 303 " pdb=" ND CLA Q 303 " ideal model delta sigma weight residual 176.90 162.26 14.64 3.00e+00 1.11e-01 2.38e+01 angle pdb=" N THR Q 143 " pdb=" CA THR Q 143 " pdb=" C THR Q 143 " ideal model delta sigma weight residual 111.07 105.96 5.11 1.07e+00 8.73e-01 2.28e+01 angle pdb=" CA PRO Q 85 " pdb=" C PRO Q 85 " pdb=" O PRO Q 85 " ideal model delta sigma weight residual 121.56 116.19 5.37 1.16e+00 7.43e-01 2.14e+01 ... (remaining 1959 not shown) Histogram of dihedral angle deviations from ideal: 0.01 - 14.54: 753 14.54 - 29.08: 68 29.08 - 43.62: 14 43.62 - 58.16: 12 58.16 - 72.69: 2 Dihedral angle restraints: 849 sinusoidal: 352 harmonic: 497 Sorted by residual: dihedral pdb=" C TYR Q 141 " pdb=" N TYR Q 141 " pdb=" CA TYR Q 141 " pdb=" CB TYR Q 141 " ideal model delta harmonic sigma weight residual -122.60 -135.36 12.76 0 2.50e+00 1.60e-01 2.60e+01 dihedral pdb=" C THR Q 98 " pdb=" N THR Q 98 " pdb=" CA THR Q 98 " pdb=" CB THR Q 98 " ideal model delta harmonic sigma weight residual -122.00 -132.91 10.91 0 2.50e+00 1.60e-01 1.90e+01 dihedral pdb=" N TYR Q 141 " pdb=" C TYR Q 141 " pdb=" CA TYR Q 141 " pdb=" CB TYR Q 141 " ideal model delta harmonic sigma weight residual 122.80 131.99 -9.19 0 2.50e+00 1.60e-01 1.35e+01 ... (remaining 846 not shown) Histogram of chiral volume deviations from ideal: 0.001 - 0.083: 123 0.083 - 0.166: 74 0.166 - 0.248: 18 0.248 - 0.331: 3 0.331 - 0.413: 1 Chirality restraints: 219 Sorted by residual: chirality pdb=" CA TYR Q 141 " pdb=" N TYR Q 141 " pdb=" C TYR Q 141 " pdb=" CB TYR Q 141 " both_signs ideal model delta sigma weight residual False 2.51 2.10 0.41 2.00e-01 2.50e+01 4.27e+00 chirality pdb=" CA THR Q 98 " pdb=" N THR Q 98 " pdb=" C THR Q 98 " pdb=" CB THR Q 98 " both_signs ideal model delta sigma weight residual False 2.53 2.21 0.31 2.00e-01 2.50e+01 2.42e+00 chirality pdb=" CA LEU Q 154 " pdb=" N LEU Q 154 " pdb=" C LEU Q 154 " pdb=" CB LEU Q 154 " both_signs ideal model delta sigma weight residual False 2.51 2.79 -0.28 2.00e-01 2.50e+01 1.91e+00 ... (remaining 216 not shown) Planarity restraints: 249 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" NB CLA Q 302 " 0.070 2.00e-02 2.50e+03 1.30e-01 2.11e+02 pdb=" ND CLA Q 302 " 0.067 2.00e-02 2.50e+03 pdb=" NA CLA Q 302 " 0.062 2.00e-02 2.50e+03 pdb=" NC CLA Q 302 " 0.060 2.00e-02 2.50e+03 pdb="MG CLA Q 302 " -0.259 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" NB CLA Q 303 " -0.073 2.00e-02 2.50e+03 1.19e-01 1.76e+02 pdb=" ND CLA Q 303 " -0.071 2.00e-02 2.50e+03 pdb=" NA CLA Q 303 " -0.048 2.00e-02 2.50e+03 pdb=" NC CLA Q 303 " -0.045 2.00e-02 2.50e+03 pdb="MG CLA Q 303 " 0.236 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1C CLA Q 302 " -0.036 2.00e-02 2.50e+03 2.26e-02 6.38e+00 pdb=" C2C CLA Q 302 " 0.024 2.00e-02 2.50e+03 pdb=" C4B CLA Q 302 " 0.021 2.00e-02 2.50e+03 pdb=" CHC CLA Q 302 " -0.015 2.00e-02 2.50e+03 pdb=" NC CLA Q 302 " 0.006 2.00e-02 2.50e+03 ... (remaining 246 not shown) Histogram of nonbonded interaction distances: 2.50 - 2.98: 659 2.98 - 3.46: 1475 3.46 - 3.94: 2366 3.94 - 4.42: 2477 4.42 - 4.90: 3990 Nonbonded interactions: 10967 Sorted by model distance: nonbonded pdb=" C1 CLA Q 302 " pdb=" O1A CLA Q 302 " model vdw 2.500 2.752 nonbonded pdb=" O ALA Q 139 " pdb=" OG1 THR Q 143 " model vdw 2.545 3.040 nonbonded pdb=" N PHE Q 171 " pdb=" O PHE Q 171 " model vdw 2.582 2.496 nonbonded pdb=" N THR Q 87 " pdb=" N GLN Q 88 " model vdw 2.583 2.560 nonbonded pdb=" N LYS Q 170 " pdb=" O LYS Q 170 " model vdw 2.603 2.496 ... (remaining 10962 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 2.940 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: 0.000 Process input model: 2.700 Find NCS groups from input model: 0.000 Set up NCS constraints: 0.000 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 6.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6563 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 : 0.025 0.795 1435 Z= 0.948 Angle : 1.766 15.709 1964 Z= 1.255 Chirality : 0.106 0.413 219 Planarity : 0.013 0.130 249 Dihedral : 13.585 72.693 529 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 2.31 % Allowed : 8.46 % Favored : 89.23 % Cbeta Deviations : 1.25 % 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 aren not related in a simple way. whole: 2.30 (0.65), residues: 169 helix: 2.58 (0.49), residues: 108 sheet: None (None), residues: 0 loop : -0.44 (0.79), residues: 61 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG Q 97 TYR 0.020 0.003 TYR Q 137 PHE 0.011 0.002 PHE Q 223 Details of bonding type rmsd covalent geometry : bond 0.01276 ( 1433) covalent geometry : angle 1.76557 ( 1964) hydrogen bonds : bond 0.16142 ( 88) hydrogen bonds : angle 6.17246 ( 261) Misc. bond : bond 0.57208 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 338 Ramachandran restraints generated. 169 Oldfield, 0 Emsley, 169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 338 Ramachandran restraints generated. 169 Oldfield, 0 Emsley, 169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 24 residues out of total 130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 21 time to evaluate : 0.026 Fit side-chains REVERT: Q 59 ASP cc_start: 0.8381 (m-30) cc_final: 0.7742 (m-30) REVERT: Q 61 LYS cc_start: 0.6348 (mmtt) cc_final: 0.5849 (tmtt) outliers start: 3 outliers final: 0 residues processed: 24 average time/residue: 0.0433 time to fit residues: 1.1622 Evaluate side-chains 13 residues out of total 130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 13 time to evaluate : 0.025 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 17 random chunks: chunk 12 optimal weight: 0.0070 chunk 13 optimal weight: 0.5980 chunk 1 optimal weight: 0.4980 chunk 8 optimal weight: 0.5980 chunk 16 optimal weight: 0.6980 chunk 15 optimal weight: 0.5980 chunk 9 optimal weight: 0.6980 chunk 11 optimal weight: 0.6980 chunk 6 optimal weight: 0.9990 chunk 4 optimal weight: 0.2980 chunk 3 optimal weight: 0.0870 overall best weight: 0.2976 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Q 234 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.167012 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.159811 restraints weight = 1902.365| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.160990 restraints weight = 1279.907| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.161800 restraints weight = 939.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.162004 restraints weight = 737.203| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.162897 restraints weight = 672.094| |-----------------------------------------------------------------------------| r_work (final): 0.3687 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7105 moved from start: 0.1771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.024 0.914 1435 Z= 0.294 Angle : 0.633 5.168 1964 Z= 0.325 Chirality : 0.041 0.169 219 Planarity : 0.005 0.041 249 Dihedral : 12.394 57.699 247 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 2.31 % Allowed : 9.23 % Favored : 88.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.62 (0.64), residues: 169 helix: 2.67 (0.47), residues: 108 sheet: None (None), residues: 0 loop : 0.02 (0.84), residues: 61 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG Q 155 TYR 0.009 0.002 TYR Q 137 PHE 0.008 0.002 PHE Q 233 Details of bonding type rmsd covalent geometry : bond 0.00356 ( 1433) covalent geometry : angle 0.63301 ( 1964) hydrogen bonds : bond 0.05023 ( 88) hydrogen bonds : angle 4.11785 ( 261) Misc. bond : bond 0.64690 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 338 Ramachandran restraints generated. 169 Oldfield, 0 Emsley, 169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 338 Ramachandran restraints generated. 169 Oldfield, 0 Emsley, 169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 21 residues out of total 130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 18 time to evaluate : 0.026 Fit side-chains REVERT: Q 59 ASP cc_start: 0.8173 (m-30) cc_final: 0.7798 (m-30) REVERT: Q 61 LYS cc_start: 0.6608 (mmtt) cc_final: 0.6252 (tmtt) outliers start: 3 outliers final: 3 residues processed: 20 average time/residue: 0.0335 time to fit residues: 0.7832 Evaluate side-chains 19 residues out of total 130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 16 time to evaluate : 0.026 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 62 THR Chi-restraints excluded: chain Q residue 231 ILE Chi-restraints excluded: chain Q residue 234 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 17 random chunks: chunk 1 optimal weight: 0.0670 chunk 15 optimal weight: 0.9990 chunk 2 optimal weight: 0.9980 chunk 11 optimal weight: 0.8980 chunk 9 optimal weight: 0.9980 chunk 4 optimal weight: 0.9990 chunk 14 optimal weight: 0.2980 chunk 7 optimal weight: 0.0980 chunk 16 optimal weight: 0.4980 chunk 5 optimal weight: 0.7980 chunk 12 optimal weight: 0.9980 overall best weight: 0.3518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Q 88 GLN ** Q 234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.151378 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.140633 restraints weight = 1995.894| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.142657 restraints weight = 1280.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.143861 restraints weight = 904.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.144300 restraints weight = 711.055| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.145441 restraints weight = 637.871| |-----------------------------------------------------------------------------| r_work (final): 0.3685 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7213 moved from start: 0.2381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.025 0.946 1435 Z= 0.311 Angle : 0.600 5.817 1964 Z= 0.311 Chirality : 0.041 0.158 219 Planarity : 0.005 0.039 249 Dihedral : 12.603 58.547 247 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 3.08 % Allowed : 12.31 % Favored : 84.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.59 (0.64), residues: 169 helix: 2.66 (0.47), residues: 107 sheet: None (None), residues: 0 loop : 0.02 (0.84), residues: 62 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG Q 136 TYR 0.009 0.001 TYR Q 137 PHE 0.008 0.002 PHE Q 233 Details of bonding type rmsd covalent geometry : bond 0.00413 ( 1433) covalent geometry : angle 0.59961 ( 1964) hydrogen bonds : bond 0.04330 ( 88) hydrogen bonds : angle 3.74975 ( 261) Misc. bond : bond 0.66937 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 338 Ramachandran restraints generated. 169 Oldfield, 0 Emsley, 169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 338 Ramachandran restraints generated. 169 Oldfield, 0 Emsley, 169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 20 residues out of total 130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 16 time to evaluate : 0.026 Fit side-chains REVERT: Q 59 ASP cc_start: 0.8202 (m-30) cc_final: 0.7839 (m-30) REVERT: Q 61 LYS cc_start: 0.6909 (mmtt) cc_final: 0.6424 (tmtt) REVERT: Q 158 ASN cc_start: 0.7482 (p0) cc_final: 0.7228 (p0) REVERT: Q 175 LEU cc_start: 0.7174 (OUTLIER) cc_final: 0.6840 (pp) outliers start: 4 outliers final: 2 residues processed: 19 average time/residue: 0.0247 time to fit residues: 0.5756 Evaluate side-chains 17 residues out of total 130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 14 time to evaluate : 0.025 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 62 THR Chi-restraints excluded: chain Q residue 175 LEU Chi-restraints excluded: chain Q residue 231 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 17 random chunks: chunk 12 optimal weight: 0.4980 chunk 16 optimal weight: 0.9990 chunk 6 optimal weight: 0.9990 chunk 15 optimal weight: 0.5980 chunk 3 optimal weight: 0.5980 chunk 4 optimal weight: 0.7980 chunk 2 optimal weight: 0.8980 chunk 0 optimal weight: 0.9990 chunk 7 optimal weight: 0.0970 chunk 14 optimal weight: 0.4980 chunk 8 optimal weight: 0.5980 overall best weight: 0.4578 ------------------------------------------------------------------------------- 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 = 0.3686 r_free = 0.3686 target = 0.145057 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.134437 restraints weight = 2055.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.136142 restraints weight = 1364.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.137282 restraints weight = 1005.351| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.137844 restraints weight = 799.241| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.138740 restraints weight = 702.189| |-----------------------------------------------------------------------------| r_work (final): 0.3581 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7345 moved from start: 0.3041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.013 0.450 1435 Z= 0.238 Angle : 0.627 4.854 1964 Z= 0.315 Chirality : 0.042 0.148 219 Planarity : 0.005 0.038 249 Dihedral : 12.803 56.038 247 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 5.38 % Allowed : 11.54 % Favored : 83.08 % 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 aren not related in a simple way. whole: 2.28 (0.66), residues: 169 helix: 2.38 (0.48), residues: 107 sheet: None (None), residues: 0 loop : -0.01 (0.87), residues: 62 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG Q 155 TYR 0.007 0.002 TYR Q 137 PHE 0.019 0.003 PHE Q 233 Details of bonding type rmsd covalent geometry : bond 0.00475 ( 1433) covalent geometry : angle 0.62729 ( 1964) hydrogen bonds : bond 0.04404 ( 88) hydrogen bonds : angle 3.67335 ( 261) Misc. bond : bond 0.31838 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 338 Ramachandran restraints generated. 169 Oldfield, 0 Emsley, 169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 338 Ramachandran restraints generated. 169 Oldfield, 0 Emsley, 169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 27 residues out of total 130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 20 time to evaluate : 0.028 Fit side-chains REVERT: Q 59 ASP cc_start: 0.8163 (m-30) cc_final: 0.7914 (m-30) REVERT: Q 61 LYS cc_start: 0.6934 (mmtt) cc_final: 0.6730 (tmtt) REVERT: Q 175 LEU cc_start: 0.7353 (OUTLIER) cc_final: 0.7037 (pp) REVERT: Q 211 LYS cc_start: 0.7570 (OUTLIER) cc_final: 0.7351 (tppt) outliers start: 7 outliers final: 5 residues processed: 25 average time/residue: 0.0319 time to fit residues: 0.9469 Evaluate side-chains 24 residues out of total 130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 17 time to evaluate : 0.026 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 62 THR Chi-restraints excluded: chain Q residue 123 THR Chi-restraints excluded: chain Q residue 175 LEU Chi-restraints excluded: chain Q residue 192 SER Chi-restraints excluded: chain Q residue 211 LYS Chi-restraints excluded: chain Q residue 231 ILE Chi-restraints excluded: chain Q residue 233 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 17 random chunks: chunk 9 optimal weight: 0.9980 chunk 7 optimal weight: 0.0970 chunk 2 optimal weight: 0.0770 chunk 4 optimal weight: 0.5980 chunk 12 optimal weight: 0.1980 chunk 11 optimal weight: 0.6980 chunk 16 optimal weight: 0.9980 chunk 0 optimal weight: 0.3980 chunk 8 optimal weight: 0.5980 chunk 6 optimal weight: 0.0870 chunk 5 optimal weight: 0.9990 overall best weight: 0.1714 ------------------------------------------------------------------------------- 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 = 0.3715 r_free = 0.3715 target = 0.145923 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.134986 restraints weight = 1974.390| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.137192 restraints weight = 1184.906| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.138607 restraints weight = 810.012| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 50)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.139780 restraints weight = 606.487| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.140455 restraints weight = 480.431| |-----------------------------------------------------------------------------| r_work (final): 0.3645 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7257 moved from start: 0.3284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.348 1435 Z= 0.151 Angle : 0.519 3.995 1964 Z= 0.266 Chirality : 0.040 0.194 219 Planarity : 0.004 0.039 249 Dihedral : 12.730 55.218 247 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 3.08 % Allowed : 15.38 % Favored : 81.54 % 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 aren not related in a simple way. whole: 2.58 (0.67), residues: 169 helix: 2.64 (0.49), residues: 107 sheet: None (None), residues: 0 loop : 0.04 (0.86), residues: 62 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG Q 131 TYR 0.016 0.002 TYR Q 133 PHE 0.009 0.001 PHE Q 233 Details of bonding type rmsd covalent geometry : bond 0.00255 ( 1433) covalent geometry : angle 0.51885 ( 1964) hydrogen bonds : bond 0.03746 ( 88) hydrogen bonds : angle 3.44647 ( 261) Misc. bond : bond 0.24579 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 338 Ramachandran restraints generated. 169 Oldfield, 0 Emsley, 169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 338 Ramachandran restraints generated. 169 Oldfield, 0 Emsley, 169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 20 residues out of total 130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 16 time to evaluate : 0.051 Fit side-chains REVERT: Q 59 ASP cc_start: 0.8142 (m-30) cc_final: 0.7835 (m-30) REVERT: Q 61 LYS cc_start: 0.6878 (mmtt) cc_final: 0.6525 (tmtt) REVERT: Q 175 LEU cc_start: 0.7232 (OUTLIER) cc_final: 0.6956 (pp) outliers start: 4 outliers final: 2 residues processed: 20 average time/residue: 0.0387 time to fit residues: 0.9693 Evaluate side-chains 18 residues out of total 130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 15 time to evaluate : 0.050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 175 LEU Chi-restraints excluded: chain Q residue 231 ILE Chi-restraints excluded: chain Q residue 233 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 17 random chunks: chunk 3 optimal weight: 0.6980 chunk 10 optimal weight: 0.5980 chunk 2 optimal weight: 0.5980 chunk 4 optimal weight: 0.5980 chunk 12 optimal weight: 0.1980 chunk 14 optimal weight: 0.2980 chunk 8 optimal weight: 0.3980 chunk 11 optimal weight: 0.5980 chunk 7 optimal weight: 0.0870 chunk 5 optimal weight: 0.5980 chunk 15 optimal weight: 0.7980 overall best weight: 0.3158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Q 151 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.146294 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.136349 restraints weight = 2028.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.137905 restraints weight = 1340.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.139122 restraints weight = 993.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.139794 restraints weight = 785.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 18)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.139917 restraints weight = 672.523| |-----------------------------------------------------------------------------| r_work (final): 0.3640 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7300 moved from start: 0.3563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.251 1435 Z= 0.169 Angle : 0.544 3.846 1964 Z= 0.276 Chirality : 0.039 0.133 219 Planarity : 0.004 0.038 249 Dihedral : 12.744 55.373 247 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 6.15 % Allowed : 13.08 % 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 aren not related in a simple way. whole: 2.44 (0.66), residues: 169 helix: 2.52 (0.49), residues: 107 sheet: None (None), residues: 0 loop : 0.04 (0.84), residues: 62 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG Q 131 TYR 0.008 0.001 TYR Q 133 PHE 0.009 0.002 PHE Q 233 Details of bonding type rmsd covalent geometry : bond 0.00358 ( 1433) covalent geometry : angle 0.54350 ( 1964) hydrogen bonds : bond 0.03897 ( 88) hydrogen bonds : angle 3.42933 ( 261) Misc. bond : bond 0.17807 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 338 Ramachandran restraints generated. 169 Oldfield, 0 Emsley, 169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 338 Ramachandran restraints generated. 169 Oldfield, 0 Emsley, 169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 25 residues out of total 130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 17 time to evaluate : 0.060 Fit side-chains REVERT: Q 61 LYS cc_start: 0.6891 (mmtt) cc_final: 0.6633 (tmtt) REVERT: Q 175 LEU cc_start: 0.7064 (OUTLIER) cc_final: 0.6863 (pp) outliers start: 8 outliers final: 5 residues processed: 23 average time/residue: 0.0381 time to fit residues: 1.1044 Evaluate side-chains 26 residues out of total 130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 20 time to evaluate : 0.049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 62 THR Chi-restraints excluded: chain Q residue 123 THR Chi-restraints excluded: chain Q residue 175 LEU Chi-restraints excluded: chain Q residue 192 SER Chi-restraints excluded: chain Q residue 197 VAL Chi-restraints excluded: chain Q residue 231 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 17 random chunks: chunk 10 optimal weight: 0.9980 chunk 13 optimal weight: 0.9990 chunk 5 optimal weight: 0.9990 chunk 14 optimal weight: 0.9990 chunk 4 optimal weight: 0.3980 chunk 11 optimal weight: 0.9980 chunk 3 optimal weight: 0.1980 chunk 0 optimal weight: 0.9990 chunk 6 optimal weight: 0.1980 chunk 9 optimal weight: 0.1980 chunk 1 optimal weight: 0.0040 overall best weight: 0.1992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Q 151 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.144572 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.133916 restraints weight = 1998.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.135962 restraints weight = 1210.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.137469 restraints weight = 838.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.138461 restraints weight = 628.562| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.139125 restraints weight = 502.883| |-----------------------------------------------------------------------------| r_work (final): 0.3609 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7267 moved from start: 0.3748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.218 1435 Z= 0.131 Angle : 0.489 3.596 1964 Z= 0.254 Chirality : 0.037 0.119 219 Planarity : 0.004 0.038 249 Dihedral : 12.726 56.169 247 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 6.92 % Allowed : 11.54 % Favored : 81.54 % 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 aren not related in a simple way. whole: 2.65 (0.66), residues: 169 helix: 2.68 (0.49), residues: 107 sheet: None (None), residues: 0 loop : 0.11 (0.83), residues: 62 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG Q 155 TYR 0.008 0.001 TYR Q 133 PHE 0.007 0.001 PHE Q 233 Details of bonding type rmsd covalent geometry : bond 0.00262 ( 1433) covalent geometry : angle 0.48900 ( 1964) hydrogen bonds : bond 0.03568 ( 88) hydrogen bonds : angle 3.40476 ( 261) Misc. bond : bond 0.15459 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 338 Ramachandran restraints generated. 169 Oldfield, 0 Emsley, 169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 338 Ramachandran restraints generated. 169 Oldfield, 0 Emsley, 169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 23 residues out of total 130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 14 time to evaluate : 0.074 Fit side-chains REVERT: Q 61 LYS cc_start: 0.6819 (mmtt) cc_final: 0.6483 (tmtt) REVERT: Q 173 GLU cc_start: 0.6968 (OUTLIER) cc_final: 0.6127 (mt-10) outliers start: 9 outliers final: 5 residues processed: 22 average time/residue: 0.0376 time to fit residues: 1.0299 Evaluate side-chains 21 residues out of total 130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 15 time to evaluate : 0.045 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 62 THR Chi-restraints excluded: chain Q residue 74 LEU Chi-restraints excluded: chain Q residue 91 SER Chi-restraints excluded: chain Q residue 173 GLU Chi-restraints excluded: chain Q residue 183 LEU Chi-restraints excluded: chain Q residue 197 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 17 random chunks: chunk 5 optimal weight: 0.4980 chunk 4 optimal weight: 0.5980 chunk 1 optimal weight: 0.1980 chunk 7 optimal weight: 0.1980 chunk 3 optimal weight: 0.7980 chunk 0 optimal weight: 0.0970 chunk 2 optimal weight: 0.9990 chunk 6 optimal weight: 0.2980 chunk 10 optimal weight: 0.4980 chunk 13 optimal weight: 0.4980 chunk 16 optimal weight: 0.0980 overall best weight: 0.1778 ------------------------------------------------------------------------------- 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 = 0.145358 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.134672 restraints weight = 2013.388| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.136702 restraints weight = 1233.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.138215 restraints weight = 860.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.139166 restraints weight = 644.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.139956 restraints weight = 520.693| |-----------------------------------------------------------------------------| r_work (final): 0.3593 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7252 moved from start: 0.3870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.174 1435 Z= 0.123 Angle : 0.486 3.745 1964 Z= 0.252 Chirality : 0.036 0.107 219 Planarity : 0.004 0.038 249 Dihedral : 12.740 56.392 247 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 4.62 % Allowed : 14.62 % 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 aren not related in a simple way. whole: 2.62 (0.66), residues: 169 helix: 2.67 (0.49), residues: 107 sheet: None (None), residues: 0 loop : 0.08 (0.82), residues: 62 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG Q 155 TYR 0.009 0.001 TYR Q 133 PHE 0.007 0.001 PHE Q 233 Details of bonding type rmsd covalent geometry : bond 0.00249 ( 1433) covalent geometry : angle 0.48630 ( 1964) hydrogen bonds : bond 0.03475 ( 88) hydrogen bonds : angle 3.37179 ( 261) Misc. bond : bond 0.12330 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 338 Ramachandran restraints generated. 169 Oldfield, 0 Emsley, 169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 338 Ramachandran restraints generated. 169 Oldfield, 0 Emsley, 169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 21 residues out of total 130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 15 time to evaluate : 0.062 Fit side-chains REVERT: Q 61 LYS cc_start: 0.6841 (mmtt) cc_final: 0.6485 (tmtt) outliers start: 6 outliers final: 3 residues processed: 21 average time/residue: 0.0447 time to fit residues: 1.1185 Evaluate side-chains 18 residues out of total 130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 15 time to evaluate : 0.050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 74 LEU Chi-restraints excluded: chain Q residue 91 SER Chi-restraints excluded: chain Q residue 197 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 17 random chunks: chunk 1 optimal weight: 0.0050 chunk 16 optimal weight: 0.0060 chunk 8 optimal weight: 0.9980 chunk 9 optimal weight: 0.2980 chunk 3 optimal weight: 0.2980 chunk 0 optimal weight: 0.0980 chunk 15 optimal weight: 0.5980 chunk 13 optimal weight: 0.0980 chunk 10 optimal weight: 0.7980 chunk 2 optimal weight: 0.4980 chunk 7 optimal weight: 0.0970 overall best weight: 0.0608 ------------------------------------------------------------------------------- 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 = 0.3747 r_free = 0.3747 target = 0.150899 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.141826 restraints weight = 1950.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.143275 restraints weight = 1357.401| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.144222 restraints weight = 1023.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.145098 restraints weight = 832.065| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.145556 restraints weight = 702.541| |-----------------------------------------------------------------------------| r_work (final): 0.3682 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7199 moved from start: 0.4044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.187 1435 Z= 0.111 Angle : 0.465 3.845 1964 Z= 0.245 Chirality : 0.035 0.102 219 Planarity : 0.004 0.040 249 Dihedral : 12.711 58.808 247 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 3.85 % Allowed : 14.62 % Favored : 81.54 % 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 aren not related in a simple way. whole: 2.62 (0.66), residues: 169 helix: 2.70 (0.50), residues: 108 sheet: None (None), residues: 0 loop : -0.03 (0.82), residues: 61 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG Q 97 TYR 0.008 0.001 TYR Q 186 PHE 0.005 0.001 PHE Q 233 Details of bonding type rmsd covalent geometry : bond 0.00201 ( 1433) covalent geometry : angle 0.46453 ( 1964) hydrogen bonds : bond 0.03164 ( 88) hydrogen bonds : angle 3.36485 ( 261) Misc. bond : bond 0.13198 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 338 Ramachandran restraints generated. 169 Oldfield, 0 Emsley, 169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 338 Ramachandran restraints generated. 169 Oldfield, 0 Emsley, 169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 20 residues out of total 130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 15 time to evaluate : 0.059 Fit side-chains REVERT: Q 61 LYS cc_start: 0.6919 (mmtt) cc_final: 0.6651 (tmtt) outliers start: 5 outliers final: 5 residues processed: 20 average time/residue: 0.0505 time to fit residues: 1.2184 Evaluate side-chains 20 residues out of total 130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 15 time to evaluate : 0.055 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 74 LEU Chi-restraints excluded: chain Q residue 91 SER Chi-restraints excluded: chain Q residue 183 LEU Chi-restraints excluded: chain Q residue 192 SER Chi-restraints excluded: chain Q residue 197 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 17 random chunks: chunk 0 optimal weight: 0.9990 chunk 2 optimal weight: 0.6980 chunk 9 optimal weight: 0.4980 chunk 8 optimal weight: 0.3980 chunk 10 optimal weight: 0.3980 chunk 13 optimal weight: 0.0980 chunk 4 optimal weight: 0.2980 chunk 16 optimal weight: 0.0060 chunk 3 optimal weight: 0.1980 chunk 14 optimal weight: 0.3980 chunk 11 optimal weight: 0.6980 overall best weight: 0.1996 ------------------------------------------------------------------------------- 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 = 0.3720 r_free = 0.3720 target = 0.147902 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.138653 restraints weight = 2003.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.140069 restraints weight = 1410.434| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.141171 restraints weight = 1067.251| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.142041 restraints weight = 850.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.142506 restraints weight = 722.431| |-----------------------------------------------------------------------------| r_work (final): 0.3652 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7256 moved from start: 0.4036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.135 1435 Z= 0.121 Angle : 0.492 4.500 1964 Z= 0.254 Chirality : 0.036 0.107 219 Planarity : 0.004 0.037 249 Dihedral : 12.690 57.638 247 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 4.62 % Allowed : 13.85 % Favored : 81.54 % 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 aren not related in a simple way. whole: 2.62 (0.66), residues: 169 helix: 2.72 (0.50), residues: 108 sheet: None (None), residues: 0 loop : -0.09 (0.81), residues: 61 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG Q 155 TYR 0.009 0.001 TYR Q 133 PHE 0.005 0.001 PHE Q 233 Details of bonding type rmsd covalent geometry : bond 0.00262 ( 1433) covalent geometry : angle 0.49216 ( 1964) hydrogen bonds : bond 0.03298 ( 88) hydrogen bonds : angle 3.37819 ( 261) Misc. bond : bond 0.09579 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 338 Ramachandran restraints generated. 169 Oldfield, 0 Emsley, 169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 338 Ramachandran restraints generated. 169 Oldfield, 0 Emsley, 169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 20 residues out of total 130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 14 time to evaluate : 0.055 Fit side-chains REVERT: Q 61 LYS cc_start: 0.6895 (mmtt) cc_final: 0.6594 (tmtt) outliers start: 6 outliers final: 6 residues processed: 20 average time/residue: 0.0407 time to fit residues: 1.0361 Evaluate side-chains 22 residues out of total 130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 16 time to evaluate : 0.050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 74 LEU Chi-restraints excluded: chain Q residue 91 SER Chi-restraints excluded: chain Q residue 123 THR Chi-restraints excluded: chain Q residue 183 LEU Chi-restraints excluded: chain Q residue 192 SER Chi-restraints excluded: chain Q residue 197 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 17 random chunks: chunk 6 optimal weight: 0.7980 chunk 10 optimal weight: 0.7980 chunk 9 optimal weight: 0.4980 chunk 14 optimal weight: 0.0980 chunk 4 optimal weight: 0.0970 chunk 5 optimal weight: 0.6980 chunk 3 optimal weight: 0.4980 chunk 16 optimal weight: 0.0470 chunk 2 optimal weight: 0.5980 chunk 12 optimal weight: 0.0770 chunk 13 optimal weight: 0.5980 overall best weight: 0.1634 ------------------------------------------------------------------------------- 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 = 0.3700 r_free = 0.3700 target = 0.146625 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.136482 restraints weight = 2037.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.138229 restraints weight = 1352.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.139467 restraints weight = 985.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.140223 restraints weight = 788.192| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.140876 restraints weight = 653.312| |-----------------------------------------------------------------------------| r_work (final): 0.3630 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7194 moved from start: 0.4070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.138 1435 Z= 0.114 Angle : 0.488 4.722 1964 Z= 0.253 Chirality : 0.035 0.108 219 Planarity : 0.004 0.037 249 Dihedral : 12.674 58.051 247 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 3.85 % Allowed : 15.38 % 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 aren not related in a simple way. whole: 2.65 (0.66), residues: 169 helix: 2.74 (0.49), residues: 108 sheet: None (None), residues: 0 loop : -0.06 (0.81), residues: 61 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG Q 155 TYR 0.009 0.001 TYR Q 133 PHE 0.005 0.001 PHE Q 233 Details of bonding type rmsd covalent geometry : bond 0.00238 ( 1433) covalent geometry : angle 0.48805 ( 1964) hydrogen bonds : bond 0.03252 ( 88) hydrogen bonds : angle 3.37757 ( 261) Misc. bond : bond 0.09793 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 521.93 seconds wall clock time: 9 minutes 58.59 seconds (598.59 seconds total)