Starting phenix.real_space_refine on Wed Mar 5 14:17:50 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wnw_37674/03_2025/8wnw_37674.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wnw_37674/03_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_37674/03_2025/8wnw_37674.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wnw_37674/03_2025/8wnw_37674.map" model { file = "/net/cci-nas-00/data/ceres_data/8wnw_37674/03_2025/8wnw_37674.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wnw_37674/03_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-5624/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: 2.50, per 1000 atoms: 1.79 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: 0.56 Conformation dependent library (CDL) restraints added in 165.7 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: 0.12 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: 0.60 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: 2.170 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: 0.070 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 10.690 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 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:2.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.890 ------------------------------------------------------------------------------- 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 : 0.013 0.121 1433 Z= 0.857 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 *********************** 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 : 0.127 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: 0.1742 time to fit residues: 4.6477 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 : 0.131 ------------------------------------------------------------------------------- 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: 0.8980 chunk 9 optimal weight: 0.0980 chunk 15 optimal weight: 0.7980 chunk 10 optimal weight: 0.0970 overall best weight: 0.0974 ------------------------------------------------------------------------------- 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 = 0.3786 r_free = 0.3786 target = 0.153684 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.142864 restraints weight = 1941.350| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.144893 restraints weight = 1177.728| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.146371 restraints weight = 815.984| |-----------------------------------------------------------------------------| r_work (final): 0.3706 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6961 moved from start: 0.1749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 1433 Z= 0.157 Angle : 0.592 4.762 1964 Z= 0.308 Chirality : 0.040 0.190 219 Planarity : 0.005 0.041 249 Dihedral : 12.372 58.230 247 Min Nonbonded Distance : 2.610 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 (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: 2.89 (0.66), residues: 169 helix: 2.91 (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 233 TYR 0.008 0.002 TYR Q 137 ARG 0.001 0.000 ARG Q 155 *********************** 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 : 0.144 Fit side-chains REVERT: Q 59 ASP cc_start: 0.8290 (m-30) cc_final: 0.7816 (m-30) REVERT: Q 60 PRO cc_start: 0.9049 (Cg_exo) cc_final: 0.8841 (Cg_endo) REVERT: Q 61 LYS cc_start: 0.6529 (mmtt) cc_final: 0.6070 (tmtt) outliers start: 3 outliers final: 2 residues processed: 19 average time/residue: 0.1195 time to fit residues: 2.7292 Evaluate side-chains 18 residues out of total 130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 16 time to evaluate : 0.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 62 THR Chi-restraints excluded: chain Q residue 231 ILE 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: 0.9980 chunk 6 optimal weight: 0.8980 chunk 0 optimal weight: 0.9990 chunk 2 optimal weight: 0.5980 chunk 15 optimal weight: 0.5980 chunk 9 optimal weight: 0.6980 chunk 1 optimal weight: 1.9990 chunk 5 optimal weight: 0.7980 chunk 8 optimal weight: 0.3980 chunk 7 optimal weight: 0.0980 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 151 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 = 0.3663 r_free = 0.3663 target = 0.142704 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.131391 restraints weight = 1997.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.133121 restraints weight = 1331.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.134449 restraints weight = 981.931| |-----------------------------------------------------------------------------| r_work (final): 0.3568 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7327 moved from start: 0.2577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.031 1433 Z= 0.306 Angle : 0.677 5.216 1964 Z= 0.333 Chirality : 0.043 0.151 219 Planarity : 0.005 0.037 249 Dihedral : 12.713 57.136 247 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % 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: 2.37 (0.64), residues: 169 helix: 2.51 (0.47), residues: 107 sheet: None (None), residues: 0 loop : -0.10 (0.84), residues: 62 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.014 0.002 PHE Q 171 TYR 0.009 0.002 TYR Q 137 ARG 0.002 0.001 ARG Q 136 *********************** 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 26 residues out of total 130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 23 time to evaluate : 0.141 Fit side-chains REVERT: Q 59 ASP cc_start: 0.8198 (m-30) cc_final: 0.7960 (m-30) REVERT: Q 61 LYS cc_start: 0.6868 (mmtt) cc_final: 0.6535 (tmtt) REVERT: Q 175 LEU cc_start: 0.7331 (OUTLIER) cc_final: 0.6994 (pp) outliers start: 3 outliers final: 2 residues processed: 25 average time/residue: 0.1047 time to fit residues: 3.1555 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 : 0.139 ------------------------------------------------------------------------------- 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: 0.5980 chunk 11 optimal weight: 0.4980 chunk 9 optimal weight: 0.6980 chunk 15 optimal weight: 0.9990 chunk 4 optimal weight: 0.6980 chunk 2 optimal weight: 0.3980 chunk 6 optimal weight: 0.8980 chunk 13 optimal weight: 0.5980 chunk 0 optimal weight: 0.9990 chunk 12 optimal weight: 0.8980 chunk 1 optimal weight: 0.7980 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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 = 0.3615 r_free = 0.3615 target = 0.138736 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.128326 restraints weight = 2009.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.129886 restraints weight = 1390.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.130951 restraints weight = 1044.000| |-----------------------------------------------------------------------------| r_work (final): 0.3553 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7384 moved from start: 0.3158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 1433 Z= 0.331 Angle : 0.674 5.602 1964 Z= 0.335 Chirality : 0.044 0.212 219 Planarity : 0.005 0.038 249 Dihedral : 12.785 56.899 247 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % 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 (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: 2.15 (0.66), residues: 169 helix: 2.25 (0.48), residues: 107 sheet: None (None), residues: 0 loop : -0.02 (0.88), residues: 62 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.012 0.002 PHE Q 171 TYR 0.008 0.002 TYR Q 137 ARG 0.001 0.000 ARG Q 155 *********************** 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 24 residues out of total 130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 19 time to evaluate : 0.148 Fit side-chains REVERT: Q 61 LYS cc_start: 0.6938 (mmtt) cc_final: 0.6645 (tmtt) REVERT: Q 175 LEU cc_start: 0.7197 (OUTLIER) cc_final: 0.6975 (pp) REVERT: Q 231 ILE cc_start: 0.6930 (OUTLIER) cc_final: 0.6238 (tp) outliers start: 5 outliers final: 3 residues processed: 22 average time/residue: 0.0939 time to fit residues: 2.5685 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 : 0.148 ------------------------------------------------------------------------------- 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 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: 0.9980 chunk 14 optimal weight: 0.1980 chunk 16 optimal weight: 0.8980 chunk 2 optimal weight: 0.5980 chunk 8 optimal weight: 0.1980 chunk 13 optimal weight: 0.5980 chunk 9 optimal weight: 0.5980 chunk 11 optimal weight: 0.4980 chunk 6 optimal weight: 0.2980 chunk 12 optimal weight: 0.0970 overall best weight: 0.2178 ------------------------------------------------------------------------------- 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 = 0.3658 r_free = 0.3658 target = 0.142901 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.132236 restraints weight = 1978.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.134019 restraints weight = 1324.170| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.135341 restraints weight = 971.521| |-----------------------------------------------------------------------------| r_work (final): 0.3572 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7307 moved from start: 0.3386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 1433 Z= 0.171 Angle : 0.540 4.703 1964 Z= 0.273 Chirality : 0.038 0.131 219 Planarity : 0.004 0.039 249 Dihedral : 12.721 54.892 247 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 3.85 % Allowed : 13.85 % Favored : 82.31 % 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: 2.54 (0.68), residues: 169 helix: 2.60 (0.49), residues: 107 sheet: None (None), residues: 0 loop : 0.07 (0.90), residues: 62 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.010 0.001 PHE Q 171 TYR 0.018 0.002 TYR Q 133 ARG 0.000 0.000 ARG Q 131 *********************** 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 23 residues out of total 130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 18 time to evaluate : 0.147 Fit side-chains REVERT: Q 61 LYS cc_start: 0.6861 (mmtt) cc_final: 0.6574 (tmtt) REVERT: Q 188 ASP cc_start: 0.6702 (m-30) cc_final: 0.6493 (m-30) outliers start: 5 outliers final: 3 residues processed: 21 average time/residue: 0.1180 time to fit residues: 2.9636 Evaluate side-chains 23 residues out of total 130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 20 time to evaluate : 0.144 ------------------------------------------------------------------------------- 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 197 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 17 random chunks: chunk 2 optimal weight: 0.9980 chunk 4 optimal weight: 0.4980 chunk 15 optimal weight: 0.5980 chunk 12 optimal weight: 0.6980 chunk 14 optimal weight: 0.0970 chunk 11 optimal weight: 0.0050 chunk 5 optimal weight: 0.5980 chunk 16 optimal weight: 0.0970 chunk 3 optimal weight: 0.1980 chunk 13 optimal weight: 0.5980 chunk 10 optimal weight: 0.6980 overall best weight: 0.1790 ------------------------------------------------------------------------------- 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 = 0.3685 r_free = 0.3685 target = 0.145476 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.135123 restraints weight = 1982.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.136858 restraints weight = 1339.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.138108 restraints weight = 991.242| |-----------------------------------------------------------------------------| r_work (final): 0.3608 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7287 moved from start: 0.3650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 1433 Z= 0.160 Angle : 0.511 3.922 1964 Z= 0.261 Chirality : 0.037 0.115 219 Planarity : 0.004 0.039 249 Dihedral : 12.637 54.792 247 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.59 % Favored : 99.41 % Rotamer: Outliers : 3.08 % Allowed : 14.62 % Favored : 82.31 % 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: 2.45 (0.67), residues: 169 helix: 2.60 (0.49), residues: 107 sheet: None (None), residues: 0 loop : -0.13 (0.86), residues: 62 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.010 0.001 PHE Q 171 TYR 0.009 0.001 TYR Q 186 ARG 0.001 0.000 ARG Q 155 *********************** 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 23 residues out of total 130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 19 time to evaluate : 0.148 Fit side-chains REVERT: Q 61 LYS cc_start: 0.6886 (mmtt) cc_final: 0.6560 (tmtt) outliers start: 4 outliers final: 3 residues processed: 21 average time/residue: 0.0895 time to fit residues: 2.3956 Evaluate side-chains 22 residues out of total 130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 19 time to evaluate : 0.149 ------------------------------------------------------------------------------- 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 197 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 17 random chunks: chunk 9 optimal weight: 0.5980 chunk 4 optimal weight: 0.2980 chunk 2 optimal weight: 0.8980 chunk 7 optimal weight: 0.0970 chunk 11 optimal weight: 0.5980 chunk 8 optimal weight: 0.2980 chunk 6 optimal weight: 0.7980 chunk 16 optimal weight: 0.0570 chunk 3 optimal weight: 0.2980 chunk 13 optimal weight: 0.3980 chunk 0 optimal weight: 0.0980 overall best weight: 0.1696 ------------------------------------------------------------------------------- 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 = 0.3696 r_free = 0.3696 target = 0.146489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.136462 restraints weight = 2008.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.138120 restraints weight = 1365.785| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.139321 restraints weight = 1005.459| |-----------------------------------------------------------------------------| r_work (final): 0.3620 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7288 moved from start: 0.3769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 1433 Z= 0.153 Angle : 0.493 3.621 1964 Z= 0.254 Chirality : 0.036 0.114 219 Planarity : 0.004 0.038 249 Dihedral : 12.668 56.420 247 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % 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 (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: 2.49 (0.67), residues: 169 helix: 2.65 (0.49), residues: 108 sheet: None (None), residues: 0 loop : -0.20 (0.86), residues: 61 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.010 0.001 PHE Q 171 TYR 0.010 0.001 TYR Q 133 ARG 0.001 0.000 ARG Q 131 *********************** 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: 5 poor density : 18 time to evaluate : 0.147 Fit side-chains REVERT: Q 61 LYS cc_start: 0.6882 (mmtt) cc_final: 0.6618 (tmtt) REVERT: Q 173 GLU cc_start: 0.6926 (OUTLIER) cc_final: 0.6079 (mt-10) outliers start: 5 outliers final: 3 residues processed: 22 average time/residue: 0.0897 time to fit residues: 2.4639 Evaluate side-chains 22 residues out of total 130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 18 time to evaluate : 0.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 171 PHE Chi-restraints excluded: chain Q residue 173 GLU Chi-restraints excluded: chain Q residue 192 SER 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 9 optimal weight: 0.6980 chunk 15 optimal weight: 0.9980 chunk 14 optimal weight: 0.2980 chunk 4 optimal weight: 0.5980 chunk 12 optimal weight: 0.9990 chunk 13 optimal weight: 0.5980 chunk 1 optimal weight: 0.0980 chunk 3 optimal weight: 0.6980 chunk 2 optimal weight: 0.5980 chunk 11 optimal weight: 0.1980 chunk 16 optimal weight: 0.8980 overall best weight: 0.3580 ------------------------------------------------------------------------------- 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 = 0.3630 r_free = 0.3630 target = 0.140794 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.130552 restraints weight = 2063.582| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.132239 restraints weight = 1403.214| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.133327 restraints weight = 1040.413| |-----------------------------------------------------------------------------| r_work (final): 0.3563 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7373 moved from start: 0.3881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 1433 Z= 0.235 Angle : 0.581 5.181 1964 Z= 0.288 Chirality : 0.040 0.145 219 Planarity : 0.004 0.036 249 Dihedral : 12.708 54.970 247 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 3.08 % Allowed : 16.92 % 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: 2.29 (0.66), residues: 169 helix: 2.52 (0.49), residues: 107 sheet: None (None), residues: 0 loop : -0.30 (0.84), residues: 62 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.011 0.002 PHE Q 171 TYR 0.012 0.002 TYR Q 133 ARG 0.001 0.000 ARG Q 155 *********************** 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 24 residues out of total 130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 20 time to evaluate : 0.140 Fit side-chains REVERT: Q 173 GLU cc_start: 0.6997 (OUTLIER) cc_final: 0.6135 (mt-10) outliers start: 4 outliers final: 3 residues processed: 24 average time/residue: 0.0853 time to fit residues: 2.5433 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 : 0.148 ------------------------------------------------------------------------------- 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 192 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 17 random chunks: chunk 12 optimal weight: 0.5980 chunk 13 optimal weight: 0.2980 chunk 0 optimal weight: 0.8980 chunk 5 optimal weight: 0.0670 chunk 3 optimal weight: 0.2980 chunk 9 optimal weight: 0.5980 chunk 2 optimal weight: 0.8980 chunk 15 optimal weight: 0.5980 chunk 7 optimal weight: 0.4980 chunk 6 optimal weight: 0.5980 chunk 11 optimal weight: 0.0070 overall best weight: 0.2336 ------------------------------------------------------------------------------- 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 = 0.3799 r_free = 0.3799 target = 0.156222 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.149054 restraints weight = 1919.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.150184 restraints weight = 1360.684| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.151057 restraints weight = 1048.360| |-----------------------------------------------------------------------------| r_work (final): 0.3622 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7286 moved from start: 0.4139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 1433 Z= 0.180 Angle : 0.535 4.348 1964 Z= 0.274 Chirality : 0.037 0.133 219 Planarity : 0.004 0.037 249 Dihedral : 12.709 55.121 247 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 2.31 % Allowed : 18.46 % Favored : 79.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.33 (0.66), residues: 169 helix: 2.59 (0.49), residues: 107 sheet: None (None), residues: 0 loop : -0.36 (0.81), residues: 62 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.010 0.001 PHE Q 171 TYR 0.012 0.002 TYR Q 133 ARG 0.001 0.000 ARG Q 155 *********************** 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: 3 poor density : 17 time to evaluate : 0.143 Fit side-chains REVERT: Q 173 GLU cc_start: 0.6968 (OUTLIER) cc_final: 0.6115 (mt-10) outliers start: 3 outliers final: 2 residues processed: 20 average time/residue: 0.0828 time to fit residues: 2.1108 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 : 0.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 171 PHE Chi-restraints excluded: chain Q residue 173 GLU Chi-restraints excluded: chain Q residue 192 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 17 random chunks: chunk 6 optimal weight: 0.8980 chunk 4 optimal weight: 0.5980 chunk 11 optimal weight: 0.9990 chunk 12 optimal weight: 0.9980 chunk 3 optimal weight: 0.7980 chunk 16 optimal weight: 0.0770 chunk 2 optimal weight: 0.7980 chunk 0 optimal weight: 0.3980 chunk 14 optimal weight: 0.1980 chunk 9 optimal weight: 0.2980 chunk 1 optimal weight: 0.6980 overall best weight: 0.3138 ------------------------------------------------------------------------------- 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 = 0.3773 r_free = 0.3773 target = 0.153895 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.146471 restraints weight = 1969.978| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.147557 restraints weight = 1382.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.148570 restraints weight = 1055.323| |-----------------------------------------------------------------------------| r_work (final): 0.3602 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7320 moved from start: 0.4193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 1433 Z= 0.217 Angle : 0.565 4.531 1964 Z= 0.284 Chirality : 0.038 0.133 219 Planarity : 0.004 0.036 249 Dihedral : 12.720 54.941 247 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 3.08 % Allowed : 17.69 % Favored : 79.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.22 (0.66), residues: 169 helix: 2.52 (0.49), residues: 107 sheet: None (None), residues: 0 loop : -0.44 (0.82), residues: 62 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.011 0.001 PHE Q 171 TYR 0.013 0.002 TYR Q 133 ARG 0.001 0.000 ARG Q 155 ********************** 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 21 residues out of total 130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 17 time to evaluate : 0.145 Fit side-chains REVERT: Q 173 GLU cc_start: 0.7015 (OUTLIER) cc_final: 0.6140 (mt-10) outliers start: 4 outliers final: 3 residues processed: 21 average time/residue: 0.0966 time to fit residues: 2.6064 Evaluate side-chains 21 residues out of total 130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 17 time to evaluate : 0.208 ------------------------------------------------------------------------------- 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 192 SER 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 4 optimal weight: 0.1980 chunk 12 optimal weight: 0.9980 chunk 2 optimal weight: 0.0570 chunk 15 optimal weight: 0.9980 chunk 16 optimal weight: 0.0270 chunk 1 optimal weight: 0.3980 chunk 7 optimal weight: 0.0870 chunk 6 optimal weight: 0.8980 chunk 13 optimal weight: 0.5980 chunk 9 optimal weight: 0.3980 overall best weight: 0.1534 ------------------------------------------------------------------------------- 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 = 0.3810 r_free = 0.3810 target = 0.157319 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.150037 restraints weight = 1921.671| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.151234 restraints weight = 1349.793| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.152187 restraints weight = 1017.068| |-----------------------------------------------------------------------------| r_work (final): 0.3719 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7272 moved from start: 0.4267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 1433 Z= 0.151 Angle : 0.507 4.339 1964 Z= 0.262 Chirality : 0.036 0.128 219 Planarity : 0.004 0.038 249 Dihedral : 12.706 55.622 247 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 3.08 % Allowed : 17.69 % Favored : 79.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.38 (0.66), residues: 169 helix: 2.65 (0.49), residues: 107 sheet: None (None), residues: 0 loop : -0.37 (0.83), residues: 62 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.010 0.001 PHE Q 171 TYR 0.009 0.001 TYR Q 186 ARG 0.001 0.000 ARG Q 155 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1025.46 seconds wall clock time: 18 minutes 31.11 seconds (1111.11 seconds total)