Starting phenix.real_space_refine on Mon Feb 10 20:26:28 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7vv0_32133/02_2025/7vv0_32133.cif Found real_map, /net/cci-nas-00/data/ceres_data/7vv0_32133/02_2025/7vv0_32133.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/7vv0_32133/02_2025/7vv0_32133.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7vv0_32133/02_2025/7vv0_32133.map" model { file = "/net/cci-nas-00/data/ceres_data/7vv0_32133/02_2025/7vv0_32133.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7vv0_32133/02_2025/7vv0_32133.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= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 18 5.16 5 C 1477 2.51 5 N 340 2.21 5 O 340 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 2175 Number of models: 1 Model: "" Number of chains: 3 Chain: "L" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 54 Classifications: {'peptide': 5} Link IDs: {'TRANS': 4} Chain: "R" Number of atoms: 2093 Number of conformers: 1 Conformer: "" Number of residues, atoms: 263, 2093 Classifications: {'peptide': 263} Link IDs: {'PTRANS': 8, 'TRANS': 254} Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'CLR': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.04, per 1000 atoms: 0.94 Number of scatterers: 2175 At special positions: 0 Unit cell: (65.4594, 72.0882, 61.3164, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 18 16.00 O 340 8.00 N 340 7.00 C 1477 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS R 26 " - pdb=" SG CYS R 258 " distance=2.03 Simple disulfide: pdb=" SG CYS R 168 " - pdb=" SG CYS R 180 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.54 Conformation dependent library (CDL) restraints added in 252.5 milliseconds 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 502 Finding SS restraints... Secondary structure from input PDB file: 11 helices and 0 sheets defined 82.8% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.20 Creating SS restraints... Processing helix chain 'R' and resid 30 through 58 removed outlier: 3.523A pdb=" N VAL R 34 " --> pdb=" O THR R 30 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LEU R 42 " --> pdb=" O LEU R 38 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ARG R 58 " --> pdb=" O LEU R 54 " (cutoff:3.500A) Processing helix chain 'R' and resid 62 through 94 Processing helix chain 'R' and resid 103 through 133 removed outlier: 3.950A pdb=" N THR R 107 " --> pdb=" O SER R 103 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N LEU R 120 " --> pdb=" O GLY R 116 " (cutoff:3.500A) Processing helix chain 'R' and resid 133 through 140 Processing helix chain 'R' and resid 145 through 166 removed outlier: 4.357A pdb=" N LEU R 163 " --> pdb=" O LEU R 159 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N GLU R 164 " --> pdb=" O LEU R 160 " (cutoff:3.500A) Processing helix chain 'R' and resid 176 through 213 removed outlier: 3.992A pdb=" N THR R 182 " --> pdb=" O GLY R 178 " (cutoff:3.500A) Processing helix chain 'R' and resid 217 through 235 Processing helix chain 'R' and resid 236 through 245 removed outlier: 4.390A pdb=" N GLY R 240 " --> pdb=" O GLY R 236 " (cutoff:3.500A) Processing helix chain 'R' and resid 245 through 250 Processing helix chain 'R' and resid 256 through 274 Proline residue: R 262 - end of helix Processing helix chain 'R' and resid 274 through 280 166 hydrogen bonds defined for protein. 498 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: 0.58 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: 1.16 - 1.29: 299 1.29 - 1.42: 660 1.42 - 1.55: 1251 1.55 - 1.68: 9 1.68 - 1.81: 22 Bond restraints: 2241 Sorted by residual: bond pdb=" C LEU R 237 " pdb=" N PRO R 238 " ideal model delta sigma weight residual 1.335 1.426 -0.090 1.36e-02 5.41e+03 4.39e+01 bond pdb=" C LEU R 38 " pdb=" O LEU R 38 " ideal model delta sigma weight residual 1.236 1.157 0.080 1.32e-02 5.74e+03 3.64e+01 bond pdb=" C17 CLR R 401 " pdb=" C20 CLR R 401 " ideal model delta sigma weight residual 1.535 1.619 -0.084 2.00e-02 2.50e+03 1.78e+01 bond pdb=" N TRP R 179 " pdb=" CA TRP R 179 " ideal model delta sigma weight residual 1.458 1.406 0.052 1.30e-02 5.92e+03 1.62e+01 bond pdb=" C TRP R 179 " pdb=" O TRP R 179 " ideal model delta sigma weight residual 1.233 1.174 0.059 1.53e-02 4.27e+03 1.48e+01 ... (remaining 2236 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.03: 2910 3.03 - 6.06: 115 6.06 - 9.09: 15 9.09 - 12.11: 12 12.11 - 15.14: 2 Bond angle restraints: 3054 Sorted by residual: angle pdb=" N ARG R 286 " pdb=" CA ARG R 286 " pdb=" C ARG R 286 " ideal model delta sigma weight residual 111.28 123.19 -11.91 1.09e+00 8.42e-01 1.19e+02 angle pdb=" N SER R 284 " pdb=" CA SER R 284 " pdb=" C SER R 284 " ideal model delta sigma weight residual 112.30 122.92 -10.62 1.36e+00 5.41e-01 6.10e+01 angle pdb=" N TRP R 179 " pdb=" CA TRP R 179 " pdb=" C TRP R 179 " ideal model delta sigma weight residual 113.55 104.34 9.21 1.26e+00 6.30e-01 5.34e+01 angle pdb=" N LYS L 11 " pdb=" CA LYS L 11 " pdb=" C LYS L 11 " ideal model delta sigma weight residual 107.93 119.23 -11.30 1.65e+00 3.67e-01 4.69e+01 angle pdb=" C PHE R 285 " pdb=" N ARG R 286 " pdb=" CA ARG R 286 " ideal model delta sigma weight residual 120.28 127.44 -7.16 1.34e+00 5.57e-01 2.85e+01 ... (remaining 3049 not shown) Histogram of dihedral angle deviations from ideal: 0.01 - 11.66: 1071 11.66 - 23.31: 162 23.31 - 34.96: 59 34.96 - 46.61: 20 46.61 - 58.26: 9 Dihedral angle restraints: 1321 sinusoidal: 547 harmonic: 774 Sorted by residual: dihedral pdb=" CB CYS R 26 " pdb=" SG CYS R 26 " pdb=" SG CYS R 258 " pdb=" CB CYS R 258 " ideal model delta sinusoidal sigma weight residual 93.00 151.26 -58.26 1 1.00e+01 1.00e-02 4.55e+01 dihedral pdb=" CA GLU R 164 " pdb=" C GLU R 164 " pdb=" N GLY R 165 " pdb=" CA GLY R 165 " ideal model delta harmonic sigma weight residual -180.00 -158.60 -21.40 0 5.00e+00 4.00e-02 1.83e+01 dihedral pdb=" C ILE R 32 " pdb=" N ILE R 32 " pdb=" CA ILE R 32 " pdb=" CB ILE R 32 " ideal model delta harmonic sigma weight residual -122.00 -132.39 10.39 0 2.50e+00 1.60e-01 1.73e+01 ... (remaining 1318 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.151: 342 0.151 - 0.303: 14 0.303 - 0.454: 3 0.454 - 0.605: 1 0.605 - 0.757: 1 Chirality restraints: 361 Sorted by residual: chirality pdb=" CB ILE R 32 " pdb=" CA ILE R 32 " pdb=" CG1 ILE R 32 " pdb=" CG2 ILE R 32 " both_signs ideal model delta sigma weight residual False 2.64 1.89 0.76 2.00e-01 2.50e+01 1.43e+01 chirality pdb=" CA SER R 284 " pdb=" N SER R 284 " pdb=" C SER R 284 " pdb=" CB SER R 284 " both_signs ideal model delta sigma weight residual False 2.51 1.95 0.56 2.00e-01 2.50e+01 7.78e+00 chirality pdb=" CA ARG R 286 " pdb=" N ARG R 286 " pdb=" C ARG R 286 " pdb=" CB ARG R 286 " both_signs ideal model delta sigma weight residual False 2.51 2.08 0.43 2.00e-01 2.50e+01 4.66e+00 ... (remaining 358 not shown) Planarity restraints: 354 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE R 37 " -0.020 2.00e-02 2.50e+03 3.99e-02 1.59e+01 pdb=" C ILE R 37 " 0.069 2.00e-02 2.50e+03 pdb=" O ILE R 37 " -0.025 2.00e-02 2.50e+03 pdb=" N LEU R 38 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL R 149 " 0.019 2.00e-02 2.50e+03 3.81e-02 1.45e+01 pdb=" C VAL R 149 " -0.066 2.00e-02 2.50e+03 pdb=" O VAL R 149 " 0.025 2.00e-02 2.50e+03 pdb=" N CYS R 150 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL R 151 " -0.018 2.00e-02 2.50e+03 3.66e-02 1.34e+01 pdb=" C VAL R 151 " 0.063 2.00e-02 2.50e+03 pdb=" O VAL R 151 " -0.024 2.00e-02 2.50e+03 pdb=" N LEU R 152 " -0.021 2.00e-02 2.50e+03 ... (remaining 351 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.59: 17 2.59 - 3.16: 1669 3.16 - 3.74: 3446 3.74 - 4.32: 4483 4.32 - 4.90: 7429 Nonbonded interactions: 17044 Sorted by model distance: nonbonded pdb=" CD1 LEU R 38 " pdb=" CD1 ILE R 83 " model vdw 2.007 3.880 nonbonded pdb=" O LYS L 12 " pdb=" CE1 PHE R 257 " model vdw 2.215 3.340 nonbonded pdb=" CZ2 TRP L 13 " pdb=" CH2 TRP R 243 " model vdw 2.304 3.640 nonbonded pdb=" NH1 ARG L 10 " pdb=" OD2 ASP R 184 " model vdw 2.311 3.120 nonbonded pdb=" O SER R 284 " pdb=" OG SER R 284 " model vdw 2.317 3.040 ... (remaining 17039 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== 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: 0.360 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: 0.090 Check model and map are aligned: 0.010 Set scattering table: 0.030 Process input model: 10.470 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: 13.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7720 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 : 0.010 0.090 2241 Z= 0.654 Angle : 1.491 15.143 3054 Z= 0.808 Chirality : 0.091 0.757 361 Planarity : 0.012 0.083 354 Dihedral : 14.054 56.619 813 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 11.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 2.93 % Allowed : 1.67 % Favored : 95.40 % Cbeta Deviations : 0.40 % 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: -3.44 (0.39), residues: 264 helix: -2.01 (0.28), residues: 205 sheet: None (None), residues: 0 loop : -2.48 (0.60), residues: 59 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP R 243 HIS 0.004 0.001 HIS R 261 PHE 0.028 0.003 PHE R 244 TYR 0.012 0.003 TYR R 279 ARG 0.027 0.002 ARG R 140 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 31 residues out of total 239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 24 time to evaluate : 0.204 Fit side-chains outliers start: 7 outliers final: 6 residues processed: 30 average time/residue: 0.2502 time to fit residues: 8.4081 Evaluate side-chains 26 residues out of total 239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 20 time to evaluate : 0.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 12 LYS Chi-restraints excluded: chain R residue 179 TRP Chi-restraints excluded: chain R residue 242 GLN Chi-restraints excluded: chain R residue 282 VAL Chi-restraints excluded: chain R residue 285 PHE Chi-restraints excluded: chain R residue 287 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 22 optimal weight: 0.9980 chunk 20 optimal weight: 0.6980 chunk 11 optimal weight: 1.9990 chunk 6 optimal weight: 0.6980 chunk 13 optimal weight: 0.7980 chunk 10 optimal weight: 0.9980 chunk 21 optimal weight: 0.9980 chunk 8 optimal weight: 6.9990 chunk 12 optimal weight: 0.6980 chunk 15 optimal weight: 0.9990 chunk 24 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 275 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 = 0.3974 r_free = 0.3974 target = 0.166837 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.139771 restraints weight = 2316.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.143380 restraints weight = 1415.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.145764 restraints weight = 1059.253| |-----------------------------------------------------------------------------| r_work (final): 0.3745 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7739 moved from start: 0.1739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 2241 Z= 0.229 Angle : 0.683 7.351 3054 Z= 0.338 Chirality : 0.046 0.345 361 Planarity : 0.006 0.051 354 Dihedral : 9.559 59.722 366 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 2.93 % Allowed : 8.79 % Favored : 88.28 % 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: -0.17 (0.49), residues: 264 helix: 0.45 (0.35), residues: 210 sheet: None (None), residues: 0 loop : -2.09 (0.73), residues: 54 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP R 133 HIS 0.001 0.001 HIS R 261 PHE 0.012 0.001 PHE R 244 TYR 0.004 0.001 TYR R 222 ARG 0.004 0.001 ARG R 140 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 29 time to evaluate : 0.215 Fit side-chains REVERT: R 45 LEU cc_start: 0.8589 (mm) cc_final: 0.8376 (mm) REVERT: R 287 LYS cc_start: 0.6831 (OUTLIER) cc_final: 0.6498 (tmtt) outliers start: 7 outliers final: 4 residues processed: 34 average time/residue: 0.1903 time to fit residues: 7.4199 Evaluate side-chains 29 residues out of total 239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 24 time to evaluate : 0.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 99 ILE Chi-restraints excluded: chain R residue 129 LEU Chi-restraints excluded: chain R residue 179 TRP Chi-restraints excluded: chain R residue 196 MET Chi-restraints excluded: chain R residue 287 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 26 optimal weight: 0.5980 chunk 4 optimal weight: 0.0370 chunk 10 optimal weight: 0.5980 chunk 7 optimal weight: 4.9990 chunk 23 optimal weight: 2.9990 chunk 13 optimal weight: 0.5980 chunk 24 optimal weight: 0.0040 chunk 19 optimal weight: 0.6980 chunk 16 optimal weight: 0.7980 chunk 11 optimal weight: 0.6980 chunk 15 optimal weight: 0.9980 overall best weight: 0.3670 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 261 HIS ** R 275 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 = 0.4039 r_free = 0.4039 target = 0.176947 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.149641 restraints weight = 2251.290| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.153767 restraints weight = 1280.998| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.156611 restraints weight = 920.061| |-----------------------------------------------------------------------------| r_work (final): 0.3805 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7639 moved from start: 0.2296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 2241 Z= 0.157 Angle : 0.571 5.940 3054 Z= 0.279 Chirality : 0.042 0.314 361 Planarity : 0.005 0.041 354 Dihedral : 7.931 57.722 356 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 3.35 % Allowed : 10.46 % Favored : 86.19 % 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: 1.37 (0.53), residues: 264 helix: 1.58 (0.37), residues: 210 sheet: None (None), residues: 0 loop : -1.77 (0.74), residues: 54 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP R 133 HIS 0.001 0.000 HIS R 259 PHE 0.010 0.001 PHE R 244 TYR 0.005 0.001 TYR R 113 ARG 0.005 0.000 ARG R 140 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 29 residues out of total 239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 21 time to evaluate : 0.231 Fit side-chains REVERT: R 45 LEU cc_start: 0.8440 (mm) cc_final: 0.8208 (mm) REVERT: R 60 ARG cc_start: 0.7488 (ttm110) cc_final: 0.7278 (ttm-80) REVERT: R 287 LYS cc_start: 0.6813 (OUTLIER) cc_final: 0.6441 (tmtt) outliers start: 8 outliers final: 4 residues processed: 26 average time/residue: 0.2161 time to fit residues: 6.5239 Evaluate side-chains 23 residues out of total 239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 18 time to evaluate : 0.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 99 ILE Chi-restraints excluded: chain R residue 119 MET Chi-restraints excluded: chain R residue 179 TRP Chi-restraints excluded: chain R residue 196 MET Chi-restraints excluded: chain R residue 287 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 25 optimal weight: 3.9990 chunk 26 optimal weight: 0.0030 chunk 24 optimal weight: 0.9990 chunk 23 optimal weight: 0.0970 chunk 16 optimal weight: 0.9990 chunk 22 optimal weight: 0.5980 chunk 5 optimal weight: 0.9980 chunk 12 optimal weight: 0.5980 chunk 0 optimal weight: 6.9990 chunk 9 optimal weight: 0.8980 chunk 11 optimal weight: 0.0670 overall best weight: 0.2726 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 261 HIS ** R 275 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 = 0.3955 r_free = 0.3955 target = 0.168339 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.140054 restraints weight = 2300.213| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.144234 restraints weight = 1316.181| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.146640 restraints weight = 943.809| |-----------------------------------------------------------------------------| r_work (final): 0.3692 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7592 moved from start: 0.2646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 2241 Z= 0.135 Angle : 0.518 5.472 3054 Z= 0.253 Chirality : 0.038 0.274 361 Planarity : 0.004 0.038 354 Dihedral : 7.254 57.269 356 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 5.02 % Allowed : 10.88 % Favored : 84.10 % 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: 2.16 (0.53), residues: 264 helix: 2.15 (0.37), residues: 209 sheet: None (None), residues: 0 loop : -1.47 (0.76), residues: 55 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.000 TRP R 133 HIS 0.000 0.000 HIS R 261 PHE 0.009 0.001 PHE R 81 TYR 0.008 0.001 TYR R 279 ARG 0.006 0.000 ARG R 140 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 32 residues out of total 239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 20 time to evaluate : 0.216 Fit side-chains REVERT: R 285 PHE cc_start: 0.6281 (OUTLIER) cc_final: 0.6029 (m-80) REVERT: R 287 LYS cc_start: 0.6585 (OUTLIER) cc_final: 0.6260 (tmtt) outliers start: 12 outliers final: 7 residues processed: 25 average time/residue: 0.2048 time to fit residues: 5.9881 Evaluate side-chains 28 residues out of total 239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 19 time to evaluate : 0.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 86 CYS Chi-restraints excluded: chain R residue 99 ILE Chi-restraints excluded: chain R residue 129 LEU Chi-restraints excluded: chain R residue 179 TRP Chi-restraints excluded: chain R residue 196 MET Chi-restraints excluded: chain R residue 226 LEU Chi-restraints excluded: chain R residue 273 SER Chi-restraints excluded: chain R residue 285 PHE Chi-restraints excluded: chain R residue 287 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 8 optimal weight: 5.9990 chunk 3 optimal weight: 0.6980 chunk 9 optimal weight: 1.9990 chunk 7 optimal weight: 0.6980 chunk 26 optimal weight: 0.9990 chunk 23 optimal weight: 0.8980 chunk 15 optimal weight: 3.9990 chunk 22 optimal weight: 0.8980 chunk 13 optimal weight: 0.9990 chunk 25 optimal weight: 0.9990 chunk 6 optimal weight: 0.5980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 275 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 = 0.3979 r_free = 0.3979 target = 0.166933 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.140428 restraints weight = 2234.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.143854 restraints weight = 1361.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.145838 restraints weight = 1010.316| |-----------------------------------------------------------------------------| r_work (final): 0.3758 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7734 moved from start: 0.2602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 2241 Z= 0.199 Angle : 0.584 6.360 3054 Z= 0.280 Chirality : 0.042 0.291 361 Planarity : 0.004 0.036 354 Dihedral : 7.280 56.058 356 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 4.60 % Allowed : 14.64 % Favored : 80.75 % 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 (0.53), residues: 264 helix: 2.10 (0.37), residues: 210 sheet: None (None), residues: 0 loop : -1.41 (0.77), residues: 54 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP R 190 HIS 0.001 0.000 HIS R 259 PHE 0.009 0.001 PHE R 244 TYR 0.006 0.001 TYR R 279 ARG 0.006 0.000 ARG R 140 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 22 time to evaluate : 0.223 Fit side-chains REVERT: R 45 LEU cc_start: 0.8413 (OUTLIER) cc_final: 0.8103 (mm) REVERT: R 285 PHE cc_start: 0.6761 (OUTLIER) cc_final: 0.6422 (m-80) REVERT: R 287 LYS cc_start: 0.6597 (OUTLIER) cc_final: 0.6320 (tmtt) outliers start: 11 outliers final: 7 residues processed: 28 average time/residue: 0.1906 time to fit residues: 6.2312 Evaluate side-chains 32 residues out of total 239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 22 time to evaluate : 0.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 45 LEU Chi-restraints excluded: chain R residue 99 ILE Chi-restraints excluded: chain R residue 119 MET Chi-restraints excluded: chain R residue 129 LEU Chi-restraints excluded: chain R residue 179 TRP Chi-restraints excluded: chain R residue 196 MET Chi-restraints excluded: chain R residue 226 LEU Chi-restraints excluded: chain R residue 273 SER Chi-restraints excluded: chain R residue 285 PHE Chi-restraints excluded: chain R residue 287 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 3 optimal weight: 2.9990 chunk 23 optimal weight: 0.8980 chunk 18 optimal weight: 0.9980 chunk 19 optimal weight: 0.6980 chunk 7 optimal weight: 1.9990 chunk 11 optimal weight: 0.7980 chunk 13 optimal weight: 0.8980 chunk 0 optimal weight: 7.9990 chunk 4 optimal weight: 0.4980 chunk 1 optimal weight: 0.3980 chunk 6 optimal weight: 0.5980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 261 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 275 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 = 0.4002 r_free = 0.4002 target = 0.169220 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.141931 restraints weight = 2251.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.145749 restraints weight = 1339.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.148094 restraints weight = 986.672| |-----------------------------------------------------------------------------| r_work (final): 0.3774 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7700 moved from start: 0.2756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 2241 Z= 0.170 Angle : 0.561 6.428 3054 Z= 0.271 Chirality : 0.040 0.270 361 Planarity : 0.004 0.036 354 Dihedral : 7.314 59.264 356 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 5.44 % Allowed : 14.64 % Favored : 79.92 % 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 (0.53), residues: 264 helix: 2.26 (0.37), residues: 210 sheet: None (None), residues: 0 loop : -1.30 (0.79), residues: 54 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP R 243 HIS 0.001 0.000 HIS R 259 PHE 0.007 0.001 PHE R 244 TYR 0.005 0.001 TYR R 279 ARG 0.005 0.000 ARG R 140 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 21 time to evaluate : 0.229 Fit side-chains REVERT: R 45 LEU cc_start: 0.8380 (OUTLIER) cc_final: 0.8160 (mt) REVERT: R 285 PHE cc_start: 0.6583 (OUTLIER) cc_final: 0.6278 (m-80) outliers start: 13 outliers final: 8 residues processed: 27 average time/residue: 0.2289 time to fit residues: 7.0829 Evaluate side-chains 30 residues out of total 239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 20 time to evaluate : 0.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 45 LEU Chi-restraints excluded: chain R residue 86 CYS Chi-restraints excluded: chain R residue 99 ILE Chi-restraints excluded: chain R residue 119 MET Chi-restraints excluded: chain R residue 129 LEU Chi-restraints excluded: chain R residue 179 TRP Chi-restraints excluded: chain R residue 196 MET Chi-restraints excluded: chain R residue 226 LEU Chi-restraints excluded: chain R residue 273 SER Chi-restraints excluded: chain R residue 285 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 10 optimal weight: 0.8980 chunk 6 optimal weight: 0.6980 chunk 13 optimal weight: 0.9990 chunk 1 optimal weight: 0.9980 chunk 9 optimal weight: 0.7980 chunk 11 optimal weight: 0.8980 chunk 4 optimal weight: 0.7980 chunk 2 optimal weight: 0.5980 chunk 18 optimal weight: 0.9980 chunk 8 optimal weight: 3.9990 chunk 7 optimal weight: 0.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 261 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 275 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 = 0.3843 r_free = 0.3843 target = 0.157567 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.130660 restraints weight = 2335.135| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.134107 restraints weight = 1385.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.136122 restraints weight = 1016.431| |-----------------------------------------------------------------------------| r_work (final): 0.3617 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7711 moved from start: 0.2870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 2241 Z= 0.199 Angle : 0.589 6.751 3054 Z= 0.282 Chirality : 0.042 0.277 361 Planarity : 0.004 0.035 354 Dihedral : 7.085 58.734 352 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 4.60 % Allowed : 15.06 % Favored : 80.33 % 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: 2.34 (0.53), residues: 264 helix: 2.22 (0.37), residues: 210 sheet: None (None), residues: 0 loop : -1.20 (0.80), residues: 54 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP R 243 HIS 0.001 0.000 HIS R 259 PHE 0.009 0.001 PHE R 183 TYR 0.005 0.001 TYR R 279 ARG 0.005 0.000 ARG R 140 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 28 residues out of total 239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 17 time to evaluate : 0.219 Fit side-chains REVERT: R 285 PHE cc_start: 0.6582 (OUTLIER) cc_final: 0.6285 (m-80) outliers start: 11 outliers final: 8 residues processed: 23 average time/residue: 0.1833 time to fit residues: 4.9994 Evaluate side-chains 28 residues out of total 239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 19 time to evaluate : 0.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 86 CYS Chi-restraints excluded: chain R residue 99 ILE Chi-restraints excluded: chain R residue 119 MET Chi-restraints excluded: chain R residue 129 LEU Chi-restraints excluded: chain R residue 179 TRP Chi-restraints excluded: chain R residue 196 MET Chi-restraints excluded: chain R residue 226 LEU Chi-restraints excluded: chain R residue 273 SER Chi-restraints excluded: chain R residue 285 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 21 optimal weight: 0.0000 chunk 0 optimal weight: 8.9990 chunk 26 optimal weight: 0.7980 chunk 23 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 6 optimal weight: 0.5980 chunk 25 optimal weight: 50.0000 chunk 3 optimal weight: 0.8980 chunk 9 optimal weight: 0.7980 chunk 7 optimal weight: 0.5980 overall best weight: 0.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 261 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 275 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 = 0.3843 r_free = 0.3843 target = 0.157994 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.131742 restraints weight = 2338.162| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.134949 restraints weight = 1431.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.137066 restraints weight = 1068.752| |-----------------------------------------------------------------------------| r_work (final): 0.3629 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7674 moved from start: 0.2994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 2241 Z= 0.166 Angle : 0.535 5.794 3054 Z= 0.262 Chirality : 0.039 0.251 361 Planarity : 0.004 0.035 354 Dihedral : 6.952 58.046 352 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 4.18 % Allowed : 16.32 % Favored : 79.50 % 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: 2.55 (0.54), residues: 264 helix: 2.37 (0.37), residues: 210 sheet: None (None), residues: 0 loop : -1.14 (0.81), residues: 54 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP R 243 HIS 0.001 0.000 HIS R 259 PHE 0.008 0.001 PHE R 81 TYR 0.006 0.001 TYR R 113 ARG 0.006 0.000 ARG R 140 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 30 residues out of total 239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 20 time to evaluate : 0.233 Fit side-chains REVERT: R 285 PHE cc_start: 0.6468 (OUTLIER) cc_final: 0.6200 (m-80) outliers start: 10 outliers final: 8 residues processed: 24 average time/residue: 0.2298 time to fit residues: 6.3206 Evaluate side-chains 28 residues out of total 239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 19 time to evaluate : 0.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 86 CYS Chi-restraints excluded: chain R residue 99 ILE Chi-restraints excluded: chain R residue 119 MET Chi-restraints excluded: chain R residue 129 LEU Chi-restraints excluded: chain R residue 179 TRP Chi-restraints excluded: chain R residue 196 MET Chi-restraints excluded: chain R residue 226 LEU Chi-restraints excluded: chain R residue 273 SER Chi-restraints excluded: chain R residue 285 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 0 optimal weight: 6.9990 chunk 19 optimal weight: 0.7980 chunk 6 optimal weight: 0.8980 chunk 3 optimal weight: 0.0980 chunk 4 optimal weight: 0.8980 chunk 2 optimal weight: 1.9990 chunk 12 optimal weight: 0.0770 chunk 7 optimal weight: 2.9990 chunk 8 optimal weight: 0.9990 chunk 16 optimal weight: 0.6980 chunk 15 optimal weight: 0.9990 overall best weight: 0.5138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 261 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 275 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 = 0.3871 r_free = 0.3871 target = 0.160383 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.134643 restraints weight = 2293.277| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.137773 restraints weight = 1408.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.139624 restraints weight = 1056.420| |-----------------------------------------------------------------------------| r_work (final): 0.3647 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7677 moved from start: 0.3061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 2241 Z= 0.158 Angle : 0.528 5.816 3054 Z= 0.259 Chirality : 0.039 0.242 361 Planarity : 0.005 0.046 354 Dihedral : 6.900 57.010 352 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 3.77 % Allowed : 17.99 % Favored : 78.24 % 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: 2.53 (0.54), residues: 264 helix: 2.34 (0.37), residues: 210 sheet: None (None), residues: 0 loop : -1.10 (0.81), residues: 54 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP R 243 HIS 0.001 0.000 HIS R 259 PHE 0.008 0.001 PHE R 244 TYR 0.005 0.001 TYR R 113 ARG 0.006 0.000 ARG R 140 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 28 residues out of total 239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 19 time to evaluate : 0.225 Fit side-chains REVERT: R 285 PHE cc_start: 0.6449 (OUTLIER) cc_final: 0.6131 (m-80) outliers start: 9 outliers final: 8 residues processed: 23 average time/residue: 0.1921 time to fit residues: 5.2178 Evaluate side-chains 28 residues out of total 239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 19 time to evaluate : 0.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 86 CYS Chi-restraints excluded: chain R residue 99 ILE Chi-restraints excluded: chain R residue 119 MET Chi-restraints excluded: chain R residue 129 LEU Chi-restraints excluded: chain R residue 179 TRP Chi-restraints excluded: chain R residue 196 MET Chi-restraints excluded: chain R residue 226 LEU Chi-restraints excluded: chain R residue 273 SER Chi-restraints excluded: chain R residue 285 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 4 optimal weight: 1.9990 chunk 25 optimal weight: 0.2980 chunk 1 optimal weight: 0.0870 chunk 3 optimal weight: 1.9990 chunk 20 optimal weight: 0.5980 chunk 5 optimal weight: 0.6980 chunk 24 optimal weight: 0.9980 chunk 8 optimal weight: 7.9990 chunk 21 optimal weight: 0.9980 chunk 13 optimal weight: 1.9990 chunk 7 optimal weight: 0.8980 overall best weight: 0.5158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 261 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 275 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 = 0.3866 r_free = 0.3866 target = 0.159812 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.134307 restraints weight = 2253.697| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.137223 restraints weight = 1412.069| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.138603 restraints weight = 1061.672| |-----------------------------------------------------------------------------| r_work (final): 0.3661 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7690 moved from start: 0.3174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 2241 Z= 0.158 Angle : 0.517 5.668 3054 Z= 0.256 Chirality : 0.038 0.212 361 Planarity : 0.005 0.042 354 Dihedral : 6.757 52.669 352 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 4.18 % Allowed : 17.99 % Favored : 77.82 % 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: 2.56 (0.54), residues: 264 helix: 2.33 (0.37), residues: 211 sheet: None (None), residues: 0 loop : -0.97 (0.85), residues: 53 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP R 243 HIS 0.001 0.000 HIS R 259 PHE 0.008 0.001 PHE R 81 TYR 0.005 0.001 TYR R 113 ARG 0.007 0.000 ARG R 140 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 30 residues out of total 239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 20 time to evaluate : 0.242 Fit side-chains REVERT: R 285 PHE cc_start: 0.6536 (OUTLIER) cc_final: 0.6222 (m-80) outliers start: 10 outliers final: 8 residues processed: 24 average time/residue: 0.1791 time to fit residues: 5.1748 Evaluate side-chains 29 residues out of total 239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 20 time to evaluate : 0.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 86 CYS Chi-restraints excluded: chain R residue 99 ILE Chi-restraints excluded: chain R residue 119 MET Chi-restraints excluded: chain R residue 129 LEU Chi-restraints excluded: chain R residue 179 TRP Chi-restraints excluded: chain R residue 196 MET Chi-restraints excluded: chain R residue 226 LEU Chi-restraints excluded: chain R residue 273 SER Chi-restraints excluded: chain R residue 285 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 6 optimal weight: 0.9980 chunk 7 optimal weight: 1.9990 chunk 8 optimal weight: 0.9990 chunk 17 optimal weight: 1.9990 chunk 24 optimal weight: 0.5980 chunk 10 optimal weight: 0.9990 chunk 16 optimal weight: 1.9990 chunk 11 optimal weight: 0.4980 chunk 1 optimal weight: 0.0970 chunk 2 optimal weight: 0.8980 chunk 26 optimal weight: 0.0020 overall best weight: 0.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 261 HIS ** R 275 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 = 0.3920 r_free = 0.3920 target = 0.165015 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.138825 restraints weight = 2285.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.142288 restraints weight = 1347.217| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.144605 restraints weight = 979.144| |-----------------------------------------------------------------------------| r_work (final): 0.3689 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7651 moved from start: 0.3258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 2241 Z= 0.143 Angle : 0.507 5.681 3054 Z= 0.251 Chirality : 0.037 0.193 361 Planarity : 0.004 0.036 354 Dihedral : 6.725 51.239 352 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 3.77 % Allowed : 18.41 % Favored : 77.82 % 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: 2.67 (0.54), residues: 264 helix: 2.40 (0.37), residues: 211 sheet: None (None), residues: 0 loop : -0.93 (0.84), residues: 53 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP R 243 HIS 0.000 0.000 HIS R 259 PHE 0.008 0.001 PHE R 81 TYR 0.006 0.001 TYR R 113 ARG 0.007 0.000 ARG R 140 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1202.39 seconds wall clock time: 22 minutes 6.06 seconds (1326.06 seconds total)