Starting phenix.real_space_refine on Fri May 9 12:42:54 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wnw_37674/05_2025/8wnw_37674.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wnw_37674/05_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_37674/05_2025/8wnw_37674.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wnw_37674/05_2025/8wnw_37674.map" model { file = "/net/cci-nas-00/data/ceres_data/8wnw_37674/05_2025/8wnw_37674.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wnw_37674/05_2025/8wnw_37674.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 3.16, per 1000 atoms: 2.26 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: 0.58 Conformation dependent library (CDL) restraints added in 167.3 milliseconds 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: 0.14 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: 0.35 Time building geometry restraints manager: 0.61 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: 2.380 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: 0.010 Extract box with map and model: 0.050 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 11.360 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.000 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.690 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 PHE 0.011 0.002 PHE Q 223 TYR 0.020 0.003 TYR Q 137 ARG 0.003 0.001 ARG Q 97 Details of bonding type rmsd hydrogen bonds : bond 0.16142 ( 88) hydrogen bonds : angle 6.17246 ( 261) covalent geometry : bond 0.01276 ( 1433) covalent geometry : angle 1.76557 ( 1964) 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 : 0.158 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: 0.1737 time to fit residues: 4.6489 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 : 0.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 17 random chunks: chunk 14 optimal weight: 0.0870 chunk 12 optimal weight: 0.0070 chunk 7 optimal weight: 0.1980 chunk 4 optimal weight: 0.2980 chunk 8 optimal weight: 0.3980 chunk 6 optimal weight: 0.5980 chunk 13 optimal weight: 0.2980 chunk 5 optimal weight: 0.6980 chunk 9 optimal weight: 0.1980 chunk 15 optimal weight: 0.7980 chunk 10 optimal weight: 0.8980 overall best weight: 0.1576 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Q 151 GLN Q 234 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.152693 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.141736 restraints weight = 1951.743| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.143743 restraints weight = 1191.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.145132 restraints weight = 821.826| |-----------------------------------------------------------------------------| r_work (final): 0.3688 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6992 moved from start: 0.1782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.024 0.916 1435 Z= 0.277 Angle : 0.599 4.829 1964 Z= 0.312 Chirality : 0.040 0.185 219 Planarity : 0.005 0.042 249 Dihedral : 12.384 57.128 247 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 8.09 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.83 (0.65), residues: 169 helix: 2.85 (0.47), residues: 108 sheet: None (None), residues: 0 loop : 0.08 (0.85), residues: 61 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.010 0.002 PHE Q 233 TYR 0.008 0.002 TYR Q 137 ARG 0.001 0.000 ARG Q 155 Details of bonding type rmsd hydrogen bonds : bond 0.04729 ( 88) hydrogen bonds : angle 4.08069 ( 261) covalent geometry : bond 0.00276 ( 1433) covalent geometry : angle 0.59920 ( 1964) Misc. bond : bond 0.64752 ( 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 20 residues out of total 130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 17 time to evaluate : 0.148 Fit side-chains REVERT: Q 59 ASP cc_start: 0.8302 (m-30) cc_final: 0.7826 (m-30) REVERT: Q 61 LYS cc_start: 0.6542 (mmtt) cc_final: 0.6095 (tmtt) outliers start: 3 outliers final: 3 residues processed: 19 average time/residue: 0.1249 time to fit residues: 2.8392 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 : 0.141 ------------------------------------------------------------------------------- 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 3 optimal weight: 0.7980 chunk 12 optimal weight: 0.1980 chunk 6 optimal weight: 0.9980 chunk 0 optimal weight: 0.9990 chunk 2 optimal weight: 0.0470 chunk 15 optimal weight: 0.5980 chunk 9 optimal weight: 0.5980 chunk 1 optimal weight: 2.9990 chunk 5 optimal weight: 0.7980 chunk 8 optimal weight: 0.5980 chunk 7 optimal weight: 0.0870 overall best weight: 0.3056 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Q 88 GLN Q 151 GLN ** Q 234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.147064 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.136059 restraints weight = 1933.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.137801 restraints weight = 1244.291| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.139275 restraints weight = 905.869| |-----------------------------------------------------------------------------| r_work (final): 0.3614 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7184 moved from start: 0.2257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.027 1.011 1435 Z= 0.318 Angle : 0.569 5.056 1964 Z= 0.296 Chirality : 0.040 0.145 219 Planarity : 0.005 0.038 249 Dihedral : 12.550 59.300 247 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.59 % Favored : 99.41 % Rotamer: Outliers : 2.31 % Allowed : 12.31 % Favored : 85.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.74 (0.65), residues: 169 helix: 2.76 (0.48), residues: 108 sheet: None (None), residues: 0 loop : 0.08 (0.85), residues: 61 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.011 0.002 PHE Q 171 TYR 0.009 0.001 TYR Q 137 ARG 0.001 0.000 ARG Q 155 Details of bonding type rmsd hydrogen bonds : bond 0.04257 ( 88) hydrogen bonds : angle 3.72540 ( 261) covalent geometry : bond 0.00372 ( 1433) covalent geometry : angle 0.56913 ( 1964) Misc. bond : bond 0.71526 ( 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 21 residues out of total 130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 18 time to evaluate : 0.140 Fit side-chains REVERT: Q 59 ASP cc_start: 0.8211 (m-30) cc_final: 0.7831 (m-30) REVERT: Q 61 LYS cc_start: 0.6738 (mmtt) cc_final: 0.6266 (tmtt) REVERT: Q 158 ASN cc_start: 0.7476 (p0) cc_final: 0.7234 (p0) REVERT: Q 175 LEU cc_start: 0.7104 (OUTLIER) cc_final: 0.6806 (pp) outliers start: 3 outliers final: 2 residues processed: 20 average time/residue: 0.0929 time to fit residues: 2.3136 Evaluate side-chains 20 residues out of total 130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 17 time to evaluate : 0.138 ------------------------------------------------------------------------------- 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 5 optimal weight: 0.6980 chunk 11 optimal weight: 0.9990 chunk 9 optimal weight: 0.5980 chunk 15 optimal weight: 0.5980 chunk 4 optimal weight: 0.7980 chunk 2 optimal weight: 0.9990 chunk 6 optimal weight: 0.6980 chunk 13 optimal weight: 0.4980 chunk 0 optimal weight: 0.9980 chunk 12 optimal weight: 0.7980 chunk 1 optimal weight: 0.9980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Q 234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.137976 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.126868 restraints weight = 2058.379| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.128638 restraints weight = 1373.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.129856 restraints weight = 1019.340| |-----------------------------------------------------------------------------| r_work (final): 0.3499 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7352 moved from start: 0.3017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.013 0.422 1435 Z= 0.283 Angle : 0.714 5.141 1964 Z= 0.355 Chirality : 0.045 0.171 219 Planarity : 0.005 0.037 249 Dihedral : 12.919 56.911 247 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 4.62 % Allowed : 11.54 % Favored : 83.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.01 (0.64), residues: 169 helix: 2.16 (0.47), residues: 107 sheet: None (None), residues: 0 loop : -0.10 (0.86), residues: 62 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.021 0.003 PHE Q 233 TYR 0.009 0.002 TYR Q 137 ARG 0.002 0.001 ARG Q 155 Details of bonding type rmsd hydrogen bonds : bond 0.04856 ( 88) hydrogen bonds : angle 3.80893 ( 261) covalent geometry : bond 0.00605 ( 1433) covalent geometry : angle 0.71391 ( 1964) Misc. bond : bond 0.29906 ( 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 26 residues out of total 130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 20 time to evaluate : 0.137 Fit side-chains REVERT: Q 61 LYS cc_start: 0.6875 (mmtt) cc_final: 0.6540 (tmtt) REVERT: Q 175 LEU cc_start: 0.7239 (OUTLIER) cc_final: 0.6906 (pp) outliers start: 6 outliers final: 5 residues processed: 25 average time/residue: 0.1028 time to fit residues: 3.0728 Evaluate side-chains 23 residues out of total 130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 17 time to evaluate : 0.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 62 THR Chi-restraints excluded: chain Q residue 171 PHE Chi-restraints excluded: chain Q residue 175 LEU Chi-restraints excluded: chain Q residue 192 SER 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 7 optimal weight: 0.2980 chunk 4 optimal weight: 0.8980 chunk 14 optimal weight: 0.8980 chunk 16 optimal weight: 0.0980 chunk 2 optimal weight: 0.9980 chunk 8 optimal weight: 0.6980 chunk 13 optimal weight: 0.8980 chunk 9 optimal weight: 0.5980 chunk 11 optimal weight: 0.6980 chunk 6 optimal weight: 0.7980 chunk 12 optimal weight: 0.0470 overall best weight: 0.3478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Q 88 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.141643 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.130748 restraints weight = 2010.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.132883 restraints weight = 1217.145| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.134419 restraints weight = 837.152| |-----------------------------------------------------------------------------| r_work (final): 0.3558 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7334 moved from start: 0.3363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.322 1435 Z= 0.182 Angle : 0.576 4.166 1964 Z= 0.291 Chirality : 0.042 0.171 219 Planarity : 0.005 0.038 249 Dihedral : 12.846 56.134 247 Min Nonbonded Distance : 2.465 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.35 (0.67), residues: 169 helix: 2.39 (0.49), residues: 107 sheet: None (None), residues: 0 loop : 0.10 (0.90), residues: 62 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.012 0.002 PHE Q 233 TYR 0.017 0.002 TYR Q 133 ARG 0.001 0.000 ARG Q 155 Details of bonding type rmsd hydrogen bonds : bond 0.04062 ( 88) hydrogen bonds : angle 3.55431 ( 261) covalent geometry : bond 0.00371 ( 1433) covalent geometry : angle 0.57588 ( 1964) Misc. bond : bond 0.22792 ( 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 27 residues out of total 130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 19 time to evaluate : 0.160 Fit side-chains REVERT: Q 61 LYS cc_start: 0.6891 (mmtt) cc_final: 0.6663 (tmtt) REVERT: Q 175 LEU cc_start: 0.7313 (OUTLIER) cc_final: 0.7054 (pp) outliers start: 8 outliers final: 4 residues processed: 25 average time/residue: 0.1109 time to fit residues: 3.3192 Evaluate side-chains 24 residues out of total 130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 19 time to evaluate : 0.128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 62 THR Chi-restraints excluded: chain Q residue 171 PHE 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 2 optimal weight: 0.3980 chunk 4 optimal weight: 0.9990 chunk 15 optimal weight: 0.8980 chunk 12 optimal weight: 0.4980 chunk 14 optimal weight: 0.2980 chunk 11 optimal weight: 0.2980 chunk 5 optimal weight: 0.0670 chunk 16 optimal weight: 0.6980 chunk 3 optimal weight: 0.0970 chunk 13 optimal weight: 0.5980 chunk 10 optimal weight: 0.7980 overall best weight: 0.2316 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Q 88 GLN Q 151 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.142584 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.132114 restraints weight = 1978.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.133942 restraints weight = 1316.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.135300 restraints weight = 965.627| |-----------------------------------------------------------------------------| r_work (final): 0.3564 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7333 moved from start: 0.3582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.251 1435 Z= 0.152 Angle : 0.537 3.676 1964 Z= 0.274 Chirality : 0.038 0.126 219 Planarity : 0.004 0.039 249 Dihedral : 12.809 55.119 247 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 5.38 % Allowed : 13.08 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.36 (0.67), residues: 169 helix: 2.52 (0.49), residues: 107 sheet: None (None), residues: 0 loop : -0.15 (0.86), residues: 62 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.011 0.002 PHE Q 171 TYR 0.008 0.001 TYR Q 186 ARG 0.000 0.000 ARG Q 155 Details of bonding type rmsd hydrogen bonds : bond 0.03846 ( 88) hydrogen bonds : angle 3.48028 ( 261) covalent geometry : bond 0.00312 ( 1433) covalent geometry : angle 0.53667 ( 1964) Misc. bond : bond 0.17792 ( 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 26 residues out of total 130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 19 time to evaluate : 0.134 Fit side-chains REVERT: Q 61 LYS cc_start: 0.6900 (mmtt) cc_final: 0.6612 (tmtt) REVERT: Q 175 LEU cc_start: 0.7279 (OUTLIER) cc_final: 0.6986 (pp) REVERT: Q 188 ASP cc_start: 0.6711 (m-30) cc_final: 0.6482 (m-30) outliers start: 7 outliers final: 3 residues processed: 24 average time/residue: 0.0852 time to fit residues: 2.5260 Evaluate side-chains 23 residues out of total 130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 19 time to evaluate : 0.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 62 THR Chi-restraints excluded: chain Q residue 171 PHE Chi-restraints excluded: chain Q residue 175 LEU Chi-restraints excluded: chain Q residue 197 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 17 random chunks: chunk 9 optimal weight: 0.9990 chunk 4 optimal weight: 0.3980 chunk 2 optimal weight: 0.9980 chunk 7 optimal weight: 0.2980 chunk 11 optimal weight: 0.6980 chunk 8 optimal weight: 0.6980 chunk 6 optimal weight: 0.3980 chunk 16 optimal weight: 0.6980 chunk 3 optimal weight: 0.5980 chunk 13 optimal weight: 0.7980 chunk 0 optimal weight: 0.6980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Q 88 GLN Q 151 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.133627 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.122520 restraints weight = 2119.734| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.124548 restraints weight = 1298.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.126157 restraints weight = 907.554| |-----------------------------------------------------------------------------| r_work (final): 0.3466 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7388 moved from start: 0.3806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.150 1435 Z= 0.209 Angle : 0.619 4.017 1964 Z= 0.309 Chirality : 0.042 0.139 219 Planarity : 0.005 0.036 249 Dihedral : 12.945 55.085 247 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 10.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 6.15 % Allowed : 13.85 % Favored : 80.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.07 (0.65), residues: 169 helix: 2.29 (0.49), residues: 107 sheet: None (None), residues: 0 loop : -0.25 (0.83), residues: 62 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.012 0.002 PHE Q 171 TYR 0.012 0.002 TYR Q 133 ARG 0.002 0.001 ARG Q 155 Details of bonding type rmsd hydrogen bonds : bond 0.04279 ( 88) hydrogen bonds : angle 3.57966 ( 261) covalent geometry : bond 0.00484 ( 1433) covalent geometry : angle 0.61914 ( 1964) Misc. bond : bond 0.10739 ( 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 26 residues out of total 130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 18 time to evaluate : 0.135 Fit side-chains REVERT: Q 61 LYS cc_start: 0.6845 (mmtt) cc_final: 0.6565 (tmtt) REVERT: Q 173 GLU cc_start: 0.7043 (OUTLIER) cc_final: 0.6221 (mt-10) REVERT: Q 175 LEU cc_start: 0.7197 (OUTLIER) cc_final: 0.6960 (pp) outliers start: 8 outliers final: 4 residues processed: 25 average time/residue: 0.0873 time to fit residues: 2.6851 Evaluate side-chains 23 residues out of total 130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 17 time to evaluate : 0.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 62 THR Chi-restraints excluded: chain Q residue 171 PHE Chi-restraints excluded: chain Q residue 173 GLU Chi-restraints excluded: chain Q residue 175 LEU Chi-restraints excluded: chain Q residue 183 LEU Chi-restraints excluded: chain Q residue 192 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 17 random chunks: chunk 9 optimal weight: 0.7980 chunk 15 optimal weight: 0.6980 chunk 14 optimal weight: 0.0870 chunk 4 optimal weight: 0.3980 chunk 12 optimal weight: 0.5980 chunk 13 optimal weight: 0.3980 chunk 1 optimal weight: 0.0470 chunk 3 optimal weight: 0.4980 chunk 2 optimal weight: 0.9980 chunk 11 optimal weight: 0.5980 chunk 16 optimal weight: 0.6980 overall best weight: 0.2856 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Q 88 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.137103 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.126122 restraints weight = 2090.052| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.128255 restraints weight = 1274.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.129798 restraints weight = 878.756| |-----------------------------------------------------------------------------| r_work (final): 0.3499 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7338 moved from start: 0.3924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.158 1435 Z= 0.148 Angle : 0.536 3.763 1964 Z= 0.274 Chirality : 0.038 0.126 219 Planarity : 0.004 0.038 249 Dihedral : 12.940 56.019 247 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 7.69 % Allowed : 11.54 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.24 (0.65), residues: 169 helix: 2.47 (0.49), residues: 107 sheet: None (None), residues: 0 loop : -0.28 (0.81), residues: 62 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.011 0.002 PHE Q 171 TYR 0.009 0.001 TYR Q 133 ARG 0.001 0.000 ARG Q 155 Details of bonding type rmsd hydrogen bonds : bond 0.03790 ( 88) hydrogen bonds : angle 3.47930 ( 261) covalent geometry : bond 0.00324 ( 1433) covalent geometry : angle 0.53565 ( 1964) Misc. bond : bond 0.11177 ( 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 26 residues out of total 130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 16 time to evaluate : 0.149 Fit side-chains REVERT: Q 61 LYS cc_start: 0.6838 (mmtt) cc_final: 0.6570 (tmtt) REVERT: Q 173 GLU cc_start: 0.6978 (OUTLIER) cc_final: 0.6136 (mt-10) REVERT: Q 175 LEU cc_start: 0.7163 (OUTLIER) cc_final: 0.6959 (pp) outliers start: 10 outliers final: 5 residues processed: 26 average time/residue: 0.0874 time to fit residues: 2.8059 Evaluate side-chains 22 residues out of total 130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 15 time to evaluate : 0.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 91 SER Chi-restraints excluded: chain Q residue 171 PHE Chi-restraints excluded: chain Q residue 173 GLU Chi-restraints excluded: chain Q residue 175 LEU 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 17 random chunks: chunk 12 optimal weight: 0.9980 chunk 13 optimal weight: 0.5980 chunk 0 optimal weight: 0.9990 chunk 5 optimal weight: 0.9990 chunk 3 optimal weight: 0.5980 chunk 9 optimal weight: 0.8980 chunk 2 optimal weight: 0.9980 chunk 15 optimal weight: 0.5980 chunk 7 optimal weight: 0.1980 chunk 6 optimal weight: 0.9980 chunk 11 optimal weight: 0.8980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Q 88 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.131722 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.121631 restraints weight = 2112.323| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.123425 restraints weight = 1363.895| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.124745 restraints weight = 982.278| |-----------------------------------------------------------------------------| r_work (final): 0.3455 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7411 moved from start: 0.4006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.088 1435 Z= 0.235 Angle : 0.646 4.069 1964 Z= 0.323 Chirality : 0.043 0.146 219 Planarity : 0.005 0.035 249 Dihedral : 13.071 58.111 247 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 6.92 % Allowed : 12.31 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.94 (0.65), residues: 169 helix: 2.24 (0.49), residues: 107 sheet: None (None), residues: 0 loop : -0.41 (0.79), residues: 62 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.012 0.002 PHE Q 171 TYR 0.015 0.002 TYR Q 133 ARG 0.003 0.001 ARG Q 155 Details of bonding type rmsd hydrogen bonds : bond 0.04375 ( 88) hydrogen bonds : angle 3.60900 ( 261) covalent geometry : bond 0.00554 ( 1433) covalent geometry : angle 0.64557 ( 1964) Misc. bond : bond 0.06428 ( 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 25 residues out of total 130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 16 time to evaluate : 0.157 Fit side-chains REVERT: Q 173 GLU cc_start: 0.7134 (OUTLIER) cc_final: 0.6304 (mt-10) REVERT: Q 175 LEU cc_start: 0.7292 (OUTLIER) cc_final: 0.7058 (pp) outliers start: 9 outliers final: 5 residues processed: 25 average time/residue: 0.0891 time to fit residues: 2.7587 Evaluate side-chains 23 residues out of total 130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 16 time to evaluate : 0.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 91 SER Chi-restraints excluded: chain Q residue 171 PHE Chi-restraints excluded: chain Q residue 173 GLU Chi-restraints excluded: chain Q residue 175 LEU 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: 0.1980 chunk 4 optimal weight: 0.6980 chunk 11 optimal weight: 0.9980 chunk 12 optimal weight: 0.9980 chunk 3 optimal weight: 0.5980 chunk 16 optimal weight: 0.9990 chunk 2 optimal weight: 0.5980 chunk 0 optimal weight: 0.1980 chunk 14 optimal weight: 0.5980 chunk 9 optimal weight: 0.6980 chunk 1 optimal weight: 0.0670 overall best weight: 0.3318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Q 88 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.138210 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.127455 restraints weight = 2110.080| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.129520 restraints weight = 1281.434| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.131135 restraints weight = 888.786| |-----------------------------------------------------------------------------| r_work (final): 0.3540 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7353 moved from start: 0.4198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.130 1435 Z= 0.165 Angle : 0.577 4.085 1964 Z= 0.293 Chirality : 0.040 0.130 219 Planarity : 0.004 0.038 249 Dihedral : 12.959 56.800 247 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 6.92 % Allowed : 12.31 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.14 (0.65), residues: 169 helix: 2.40 (0.49), residues: 107 sheet: None (None), residues: 0 loop : -0.36 (0.80), residues: 62 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.011 0.002 PHE Q 171 TYR 0.011 0.002 TYR Q 133 ARG 0.002 0.000 ARG Q 155 Details of bonding type rmsd hydrogen bonds : bond 0.03910 ( 88) hydrogen bonds : angle 3.53510 ( 261) covalent geometry : bond 0.00376 ( 1433) covalent geometry : angle 0.57736 ( 1964) Misc. bond : bond 0.09272 ( 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 24 residues out of total 130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 15 time to evaluate : 0.151 Fit side-chains REVERT: Q 173 GLU cc_start: 0.7005 (OUTLIER) cc_final: 0.6187 (mt-10) outliers start: 9 outliers final: 5 residues processed: 24 average time/residue: 0.0893 time to fit residues: 2.6878 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 : 0.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 91 SER Chi-restraints excluded: chain Q residue 171 PHE Chi-restraints excluded: chain Q residue 173 GLU 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: 0.8980 chunk 4 optimal weight: 0.9990 chunk 12 optimal weight: 0.9990 chunk 2 optimal weight: 0.0570 chunk 15 optimal weight: 0.9980 chunk 16 optimal weight: 0.9980 chunk 1 optimal weight: 0.0970 chunk 7 optimal weight: 0.0980 chunk 6 optimal weight: 0.6980 chunk 13 optimal weight: 0.6980 chunk 9 optimal weight: 0.0980 overall best weight: 0.2096 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Q 88 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.143395 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.133208 restraints weight = 2047.924| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.135262 restraints weight = 1241.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.136633 restraints weight = 855.050| |-----------------------------------------------------------------------------| r_work (final): 0.3582 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7319 moved from start: 0.4298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.131 1435 Z= 0.137 Angle : 0.551 3.859 1964 Z= 0.282 Chirality : 0.038 0.120 219 Planarity : 0.004 0.039 249 Dihedral : 12.894 57.615 247 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 9.14 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.28 (0.66), residues: 169 helix: 2.53 (0.50), residues: 107 sheet: None (None), residues: 0 loop : -0.32 (0.80), residues: 62 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.011 0.001 PHE Q 171 TYR 0.010 0.001 TYR Q 133 ARG 0.001 0.000 ARG Q 155 Details of bonding type rmsd hydrogen bonds : bond 0.03693 ( 88) hydrogen bonds : angle 3.48894 ( 261) covalent geometry : bond 0.00305 ( 1433) covalent geometry : angle 0.55070 ( 1964) Misc. bond : bond 0.09298 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1012.09 seconds wall clock time: 18 minutes 26.61 seconds (1106.61 seconds total)