Starting phenix.real_space_refine on Wed Sep 17 03:00:34 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7dwv_30887/09_2025/7dwv_30887.cif Found real_map, /net/cci-nas-00/data/ceres_data/7dwv_30887/09_2025/7dwv_30887.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.07 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7dwv_30887/09_2025/7dwv_30887.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7dwv_30887/09_2025/7dwv_30887.map" model { file = "/net/cci-nas-00/data/ceres_data/7dwv_30887/09_2025/7dwv_30887.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7dwv_30887/09_2025/7dwv_30887.cif" } resolution = 3.07 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 30 5.16 5 C 1278 2.51 5 N 354 2.21 5 O 402 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 2064 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 344 Classifications: {'peptide': 43} Link IDs: {'TRANS': 42} Restraints were copied for chains: B, C, D, E, F Time building chain proxies: 0.57, per 1000 atoms: 0.28 Number of scatterers: 2064 At special positions: 0 Unit cell: (98.358, 84.162, 31.434, 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 30 16.00 O 402 8.00 N 354 7.00 C 1278 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 179 " - pdb=" SG CYS A 214 " distance=2.03 Simple disulfide: pdb=" SG CYS B 179 " - pdb=" SG CYS B 214 " distance=2.02 Simple disulfide: pdb=" SG CYS C 179 " - pdb=" SG CYS C 214 " distance=2.02 Simple disulfide: pdb=" SG CYS D 179 " - pdb=" SG CYS D 214 " distance=2.02 Simple disulfide: pdb=" SG CYS E 179 " - pdb=" SG CYS E 214 " distance=2.02 Simple disulfide: pdb=" SG CYS F 179 " - pdb=" SG CYS F 214 " 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: 0.16 Conformation dependent library (CDL) restraints added in 84.4 milliseconds Enol-peptide restraints added in 1.2 microseconds 492 Ramachandran restraints generated. 246 Oldfield, 0 Emsley, 246 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 504 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 2 sheets defined 0.0% alpha, 4.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.06 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 180 through 182 Processing sheet with id=AA2, first strand: chain 'D' and resid 180 through 182 8 hydrogen bonds defined for protein. 24 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: 0.26 Time building geometry restraints manager: 0.23 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 672 1.34 - 1.45: 200 1.45 - 1.57: 1162 1.57 - 1.69: 0 1.69 - 1.80: 48 Bond restraints: 2082 Sorted by residual: bond pdb=" CB THR A 193 " pdb=" CG2 THR A 193 " ideal model delta sigma weight residual 1.521 1.466 0.055 3.30e-02 9.18e+02 2.74e+00 bond pdb=" CB THR D 193 " pdb=" CG2 THR D 193 " ideal model delta sigma weight residual 1.521 1.467 0.054 3.30e-02 9.18e+02 2.72e+00 bond pdb=" CB THR C 193 " pdb=" CG2 THR C 193 " ideal model delta sigma weight residual 1.521 1.467 0.054 3.30e-02 9.18e+02 2.70e+00 bond pdb=" CB THR F 193 " pdb=" CG2 THR F 193 " ideal model delta sigma weight residual 1.521 1.467 0.054 3.30e-02 9.18e+02 2.67e+00 bond pdb=" CB THR E 193 " pdb=" CG2 THR E 193 " ideal model delta sigma weight residual 1.521 1.467 0.054 3.30e-02 9.18e+02 2.67e+00 ... (remaining 2077 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.86: 2269 0.86 - 1.72: 410 1.72 - 2.58: 93 2.58 - 3.45: 12 3.45 - 4.31: 18 Bond angle restraints: 2802 Sorted by residual: angle pdb=" N ASN C 181 " pdb=" CA ASN C 181 " pdb=" C ASN C 181 " ideal model delta sigma weight residual 107.93 112.24 -4.31 1.65e+00 3.67e-01 6.82e+00 angle pdb=" N ASN D 181 " pdb=" CA ASN D 181 " pdb=" C ASN D 181 " ideal model delta sigma weight residual 107.93 112.21 -4.28 1.65e+00 3.67e-01 6.74e+00 angle pdb=" N ASN F 181 " pdb=" CA ASN F 181 " pdb=" C ASN F 181 " ideal model delta sigma weight residual 107.93 112.20 -4.27 1.65e+00 3.67e-01 6.71e+00 angle pdb=" N ASN A 181 " pdb=" CA ASN A 181 " pdb=" C ASN A 181 " ideal model delta sigma weight residual 107.93 112.20 -4.27 1.65e+00 3.67e-01 6.70e+00 angle pdb=" N ASN B 181 " pdb=" CA ASN B 181 " pdb=" C ASN B 181 " ideal model delta sigma weight residual 107.93 112.20 -4.27 1.65e+00 3.67e-01 6.69e+00 ... (remaining 2797 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.64: 984 11.64 - 23.29: 210 23.29 - 34.93: 90 34.93 - 46.57: 6 46.57 - 58.21: 6 Dihedral angle restraints: 1296 sinusoidal: 540 harmonic: 756 Sorted by residual: dihedral pdb=" CA MET C 206 " pdb=" C MET C 206 " pdb=" N GLU C 207 " pdb=" CA GLU C 207 " ideal model delta harmonic sigma weight residual -180.00 -165.64 -14.36 0 5.00e+00 4.00e-02 8.25e+00 dihedral pdb=" CA MET E 206 " pdb=" C MET E 206 " pdb=" N GLU E 207 " pdb=" CA GLU E 207 " ideal model delta harmonic sigma weight residual -180.00 -165.65 -14.35 0 5.00e+00 4.00e-02 8.24e+00 dihedral pdb=" CA MET A 206 " pdb=" C MET A 206 " pdb=" N GLU A 207 " pdb=" CA GLU A 207 " ideal model delta harmonic sigma weight residual -180.00 -165.65 -14.35 0 5.00e+00 4.00e-02 8.24e+00 ... (remaining 1293 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 115 0.030 - 0.060: 127 0.060 - 0.091: 62 0.091 - 0.121: 32 0.121 - 0.151: 24 Chirality restraints: 360 Sorted by residual: chirality pdb=" CB THR C 183 " pdb=" CA THR C 183 " pdb=" OG1 THR C 183 " pdb=" CG2 THR C 183 " both_signs ideal model delta sigma weight residual False 2.55 2.40 0.15 2.00e-01 2.50e+01 5.69e-01 chirality pdb=" CB THR A 183 " pdb=" CA THR A 183 " pdb=" OG1 THR A 183 " pdb=" CG2 THR A 183 " both_signs ideal model delta sigma weight residual False 2.55 2.40 0.15 2.00e-01 2.50e+01 5.57e-01 chirality pdb=" CB THR D 183 " pdb=" CA THR D 183 " pdb=" OG1 THR D 183 " pdb=" CG2 THR D 183 " both_signs ideal model delta sigma weight residual False 2.55 2.40 0.15 2.00e-01 2.50e+01 5.47e-01 ... (remaining 357 not shown) Planarity restraints: 342 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB HIS C 187 " -0.009 2.00e-02 2.50e+03 9.09e-03 1.24e+00 pdb=" CG HIS C 187 " 0.019 2.00e-02 2.50e+03 pdb=" ND1 HIS C 187 " -0.003 2.00e-02 2.50e+03 pdb=" CD2 HIS C 187 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 HIS C 187 " -0.001 2.00e-02 2.50e+03 pdb=" NE2 HIS C 187 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS E 187 " -0.010 2.00e-02 2.50e+03 9.07e-03 1.23e+00 pdb=" CG HIS E 187 " 0.019 2.00e-02 2.50e+03 pdb=" ND1 HIS E 187 " -0.002 2.00e-02 2.50e+03 pdb=" CD2 HIS E 187 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 HIS E 187 " -0.001 2.00e-02 2.50e+03 pdb=" NE2 HIS E 187 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS B 187 " -0.009 2.00e-02 2.50e+03 8.96e-03 1.20e+00 pdb=" CG HIS B 187 " 0.019 2.00e-02 2.50e+03 pdb=" ND1 HIS B 187 " -0.003 2.00e-02 2.50e+03 pdb=" CD2 HIS B 187 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 HIS B 187 " -0.001 2.00e-02 2.50e+03 pdb=" NE2 HIS B 187 " -0.004 2.00e-02 2.50e+03 ... (remaining 339 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 485 2.79 - 3.31: 2050 3.31 - 3.84: 3171 3.84 - 4.37: 3321 4.37 - 4.90: 7268 Nonbonded interactions: 16295 Sorted by model distance: nonbonded pdb=" OD1 ASN B 197 " pdb=" OG1 THR B 199 " model vdw 2.258 3.040 nonbonded pdb=" OD1 ASN A 197 " pdb=" OG1 THR A 199 " model vdw 2.258 3.040 nonbonded pdb=" OD1 ASN C 197 " pdb=" OG1 THR C 199 " model vdw 2.258 3.040 nonbonded pdb=" OD1 ASN F 197 " pdb=" OG1 THR F 199 " model vdw 2.258 3.040 nonbonded pdb=" OD1 ASN E 197 " pdb=" OG1 THR E 199 " model vdw 2.258 3.040 ... (remaining 16290 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.350 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: 0.040 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 4.210 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:1.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.170 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7220 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 : 0.007 0.055 2088 Z= 0.286 Angle : 0.798 4.308 2814 Z= 0.475 Chirality : 0.062 0.151 360 Planarity : 0.003 0.009 342 Dihedral : 14.691 58.214 774 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 16.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 26.83 % Favored : 73.17 % Rotamer: Outliers : 0.00 % Allowed : 28.57 % Favored : 71.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -7.45 (0.29), residues: 246 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -5.67 (0.22), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG E 208 PHE 0.007 0.002 PHE D 175 HIS 0.009 0.003 HIS D 187 Details of bonding type rmsd covalent geometry : bond 0.00672 ( 2082) covalent geometry : angle 0.79902 ( 2802) SS BOND : bond 0.00659 ( 6) SS BOND : angle 0.65468 ( 12) hydrogen bonds : bond 0.41923 ( 8) hydrogen bonds : angle 13.54441 ( 24) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 492 Ramachandran restraints generated. 246 Oldfield, 0 Emsley, 246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 492 Ramachandran restraints generated. 246 Oldfield, 0 Emsley, 246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 65 time to evaluate : 0.130 Fit side-chains REVERT: A 194 LYS cc_start: 0.8742 (mmmt) cc_final: 0.8526 (tppp) REVERT: D 212 GLN cc_start: 0.8385 (mt0) cc_final: 0.8012 (mt0) REVERT: E 217 GLN cc_start: 0.7454 (mt0) cc_final: 0.7237 (mt0) outliers start: 0 outliers final: 0 residues processed: 65 average time/residue: 0.0599 time to fit residues: 4.6450 Evaluate side-chains 63 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 63 time to evaluate : 0.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 12 optimal weight: 3.9990 chunk 13 optimal weight: 3.9990 chunk 1 optimal weight: 4.9990 chunk 8 optimal weight: 5.9990 chunk 16 optimal weight: 3.9990 chunk 15 optimal weight: 0.4980 chunk 9 optimal weight: 2.9990 chunk 11 optimal weight: 3.9990 chunk 18 optimal weight: 0.9980 chunk 6 optimal weight: 0.7980 chunk 4 optimal weight: 2.9990 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 217 GLN F 177 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4358 r_free = 0.4358 target = 0.131105 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4241 r_free = 0.4241 target = 0.122629 restraints weight = 3495.253| |-----------------------------------------------------------------------------| r_work (start): 0.4251 rms_B_bonded: 2.48 r_work: 0.4160 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.4047 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.4047 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7463 moved from start: 0.1600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 2088 Z= 0.241 Angle : 0.760 5.562 2814 Z= 0.438 Chirality : 0.059 0.146 360 Planarity : 0.003 0.011 342 Dihedral : 6.525 15.188 258 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 12.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 29.27 % Favored : 70.73 % Rotamer: Outliers : 15.48 % Allowed : 20.63 % Favored : 63.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -7.13 (0.31), residues: 246 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -5.43 (0.23), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 208 PHE 0.011 0.002 PHE F 175 HIS 0.011 0.004 HIS B 187 Details of bonding type rmsd covalent geometry : bond 0.00547 ( 2082) covalent geometry : angle 0.76087 ( 2802) SS BOND : bond 0.00679 ( 6) SS BOND : angle 0.54571 ( 12) hydrogen bonds : bond 0.07805 ( 8) hydrogen bonds : angle 9.12327 ( 24) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 492 Ramachandran restraints generated. 246 Oldfield, 0 Emsley, 246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 492 Ramachandran restraints generated. 246 Oldfield, 0 Emsley, 246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 62 time to evaluate : 0.087 Fit side-chains REVERT: A 194 LYS cc_start: 0.8763 (mmmt) cc_final: 0.8538 (tppp) REVERT: E 181 ASN cc_start: 0.7680 (OUTLIER) cc_final: 0.7468 (p0) REVERT: F 177 HIS cc_start: 0.7062 (m-70) cc_final: 0.6797 (m170) outliers start: 39 outliers final: 34 residues processed: 93 average time/residue: 0.0440 time to fit residues: 5.0062 Evaluate side-chains 95 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 60 time to evaluate : 0.087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 176 VAL Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 191 THR Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 181 ASN Chi-restraints excluded: chain B residue 183 THR Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 191 THR Chi-restraints excluded: chain C residue 176 VAL Chi-restraints excluded: chain C residue 181 ASN Chi-restraints excluded: chain C residue 183 THR Chi-restraints excluded: chain C residue 189 VAL Chi-restraints excluded: chain C residue 191 THR Chi-restraints excluded: chain C residue 193 THR Chi-restraints excluded: chain C residue 209 VAL Chi-restraints excluded: chain D residue 176 VAL Chi-restraints excluded: chain D residue 183 THR Chi-restraints excluded: chain D residue 189 VAL Chi-restraints excluded: chain D residue 191 THR Chi-restraints excluded: chain D residue 193 THR Chi-restraints excluded: chain D residue 209 VAL Chi-restraints excluded: chain E residue 176 VAL Chi-restraints excluded: chain E residue 181 ASN Chi-restraints excluded: chain E residue 183 THR Chi-restraints excluded: chain E residue 189 VAL Chi-restraints excluded: chain E residue 191 THR Chi-restraints excluded: chain F residue 176 VAL Chi-restraints excluded: chain F residue 181 ASN Chi-restraints excluded: chain F residue 183 THR Chi-restraints excluded: chain F residue 189 VAL Chi-restraints excluded: chain F residue 191 THR Chi-restraints excluded: chain F residue 192 THR Chi-restraints excluded: chain F residue 193 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 20 optimal weight: 6.9990 chunk 22 optimal weight: 3.9990 chunk 6 optimal weight: 4.9990 chunk 19 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 3 optimal weight: 0.0970 chunk 8 optimal weight: 2.9990 chunk 23 optimal weight: 0.4980 chunk 5 optimal weight: 2.9990 chunk 12 optimal weight: 0.5980 chunk 2 optimal weight: 0.6980 overall best weight: 0.9780 ------------------------------------------------------------------------------- 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 = 0.4396 r_free = 0.4396 target = 0.133660 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.4276 r_free = 0.4276 target = 0.124392 restraints weight = 3911.577| |-----------------------------------------------------------------------------| r_work (start): 0.4317 rms_B_bonded: 3.04 r_work: 0.4218 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.4218 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7091 moved from start: 0.1980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 2088 Z= 0.155 Angle : 0.645 4.445 2814 Z= 0.371 Chirality : 0.053 0.141 360 Planarity : 0.003 0.012 342 Dihedral : 5.553 12.003 258 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 12.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 25.20 % Favored : 74.80 % Rotamer: Outliers : 13.89 % Allowed : 28.17 % Favored : 57.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -6.84 (0.33), residues: 246 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -5.21 (0.25), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG C 208 PHE 0.006 0.001 PHE D 175 HIS 0.008 0.003 HIS B 187 Details of bonding type rmsd covalent geometry : bond 0.00345 ( 2082) covalent geometry : angle 0.64584 ( 2802) SS BOND : bond 0.00270 ( 6) SS BOND : angle 0.47957 ( 12) hydrogen bonds : bond 0.06242 ( 8) hydrogen bonds : angle 8.04256 ( 24) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 492 Ramachandran restraints generated. 246 Oldfield, 0 Emsley, 246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 492 Ramachandran restraints generated. 246 Oldfield, 0 Emsley, 246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 65 time to evaluate : 0.095 Fit side-chains REVERT: A 194 LYS cc_start: 0.8562 (mmmt) cc_final: 0.8254 (tppp) REVERT: D 212 GLN cc_start: 0.8534 (mt0) cc_final: 0.8134 (mt0) REVERT: F 177 HIS cc_start: 0.6656 (m-70) cc_final: 0.6318 (m170) outliers start: 35 outliers final: 22 residues processed: 93 average time/residue: 0.0454 time to fit residues: 5.1560 Evaluate side-chains 85 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 63 time to evaluate : 0.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 183 THR Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain C residue 176 VAL Chi-restraints excluded: chain C residue 183 THR Chi-restraints excluded: chain C residue 189 VAL Chi-restraints excluded: chain C residue 190 THR Chi-restraints excluded: chain D residue 176 VAL Chi-restraints excluded: chain D residue 183 THR Chi-restraints excluded: chain D residue 190 THR Chi-restraints excluded: chain E residue 176 VAL Chi-restraints excluded: chain E residue 183 THR Chi-restraints excluded: chain E residue 189 VAL Chi-restraints excluded: chain E residue 193 THR Chi-restraints excluded: chain E residue 209 VAL Chi-restraints excluded: chain F residue 183 THR Chi-restraints excluded: chain F residue 189 VAL Chi-restraints excluded: chain F residue 192 THR Chi-restraints excluded: chain F residue 206 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 3 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 23 optimal weight: 0.5980 chunk 9 optimal weight: 3.9990 chunk 12 optimal weight: 3.9990 chunk 1 optimal weight: 1.9990 chunk 18 optimal weight: 4.9990 chunk 8 optimal weight: 2.9990 chunk 10 optimal weight: 0.5980 chunk 14 optimal weight: 0.7980 chunk 2 optimal weight: 0.8980 overall best weight: 0.9782 ------------------------------------------------------------------------------- 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 = 0.4411 r_free = 0.4411 target = 0.135951 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.4306 r_free = 0.4306 target = 0.127025 restraints weight = 3438.341| |-----------------------------------------------------------------------------| r_work (start): 0.4294 rms_B_bonded: 2.55 r_work: 0.4193 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.4086 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.4086 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7362 moved from start: 0.2299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 2088 Z= 0.154 Angle : 0.680 4.193 2814 Z= 0.389 Chirality : 0.053 0.140 360 Planarity : 0.003 0.013 342 Dihedral : 5.628 12.941 258 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 15.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 23.98 % Favored : 76.02 % Rotamer: Outliers : 18.65 % Allowed : 24.21 % Favored : 57.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -6.68 (0.34), residues: 246 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -5.09 (0.26), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG B 208 PHE 0.008 0.001 PHE B 175 HIS 0.007 0.002 HIS B 187 Details of bonding type rmsd covalent geometry : bond 0.00341 ( 2082) covalent geometry : angle 0.68049 ( 2802) SS BOND : bond 0.00292 ( 6) SS BOND : angle 0.44994 ( 12) hydrogen bonds : bond 0.05615 ( 8) hydrogen bonds : angle 7.86751 ( 24) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 492 Ramachandran restraints generated. 246 Oldfield, 0 Emsley, 246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 492 Ramachandran restraints generated. 246 Oldfield, 0 Emsley, 246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 62 time to evaluate : 0.103 Fit side-chains revert: symmetry clash REVERT: A 194 LYS cc_start: 0.8799 (mmmt) cc_final: 0.8506 (tppp) REVERT: F 190 THR cc_start: 0.8098 (OUTLIER) cc_final: 0.7894 (m) outliers start: 47 outliers final: 42 residues processed: 102 average time/residue: 0.0429 time to fit residues: 5.4043 Evaluate side-chains 105 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 62 time to evaluate : 0.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 176 VAL Chi-restraints excluded: chain A residue 181 ASN Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 191 THR Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 181 ASN Chi-restraints excluded: chain B residue 183 THR Chi-restraints excluded: chain B residue 190 THR Chi-restraints excluded: chain B residue 191 THR Chi-restraints excluded: chain B residue 193 THR Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain C residue 176 VAL Chi-restraints excluded: chain C residue 183 THR Chi-restraints excluded: chain C residue 189 VAL Chi-restraints excluded: chain C residue 191 THR Chi-restraints excluded: chain C residue 193 THR Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain D residue 176 VAL Chi-restraints excluded: chain D residue 183 THR Chi-restraints excluded: chain D residue 191 THR Chi-restraints excluded: chain D residue 209 VAL Chi-restraints excluded: chain E residue 176 VAL Chi-restraints excluded: chain E residue 181 ASN Chi-restraints excluded: chain E residue 183 THR Chi-restraints excluded: chain E residue 189 VAL Chi-restraints excluded: chain E residue 190 THR Chi-restraints excluded: chain E residue 191 THR Chi-restraints excluded: chain E residue 193 THR Chi-restraints excluded: chain E residue 209 VAL Chi-restraints excluded: chain F residue 176 VAL Chi-restraints excluded: chain F residue 183 THR Chi-restraints excluded: chain F residue 189 VAL Chi-restraints excluded: chain F residue 190 THR Chi-restraints excluded: chain F residue 191 THR Chi-restraints excluded: chain F residue 192 THR Chi-restraints excluded: chain F residue 193 THR Chi-restraints excluded: chain F residue 203 VAL Chi-restraints excluded: chain F residue 206 MET Chi-restraints excluded: chain F residue 209 VAL Chi-restraints excluded: chain F residue 213 MET Chi-restraints excluded: chain F residue 214 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 15 optimal weight: 0.0970 chunk 8 optimal weight: 5.9990 chunk 6 optimal weight: 4.9990 chunk 14 optimal weight: 3.9990 chunk 21 optimal weight: 0.0970 chunk 5 optimal weight: 0.9990 chunk 19 optimal weight: 1.9990 chunk 18 optimal weight: 0.8980 chunk 12 optimal weight: 2.9990 chunk 11 optimal weight: 2.9990 chunk 13 optimal weight: 4.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 177 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4440 r_free = 0.4440 target = 0.137943 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4334 r_free = 0.4334 target = 0.128832 restraints weight = 3482.563| |-----------------------------------------------------------------------------| r_work (start): 0.4326 rms_B_bonded: 2.69 r_work: 0.4219 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work (final): 0.4219 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7275 moved from start: 0.2501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 2088 Z= 0.137 Angle : 0.655 4.442 2814 Z= 0.373 Chirality : 0.052 0.138 360 Planarity : 0.003 0.014 342 Dihedral : 5.284 13.316 258 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 14.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 21.54 % Favored : 78.46 % Rotamer: Outliers : 19.05 % Allowed : 24.21 % Favored : 56.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -6.49 (0.36), residues: 246 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.94 (0.27), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 208 PHE 0.008 0.001 PHE B 175 HIS 0.006 0.002 HIS B 187 Details of bonding type rmsd covalent geometry : bond 0.00296 ( 2082) covalent geometry : angle 0.65399 ( 2802) SS BOND : bond 0.00333 ( 6) SS BOND : angle 0.87783 ( 12) hydrogen bonds : bond 0.05422 ( 8) hydrogen bonds : angle 7.64222 ( 24) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 492 Ramachandran restraints generated. 246 Oldfield, 0 Emsley, 246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 492 Ramachandran restraints generated. 246 Oldfield, 0 Emsley, 246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 61 time to evaluate : 0.085 Fit side-chains revert: symmetry clash REVERT: A 194 LYS cc_start: 0.8755 (mmmt) cc_final: 0.8468 (tppp) REVERT: B 214 CYS cc_start: 0.7379 (OUTLIER) cc_final: 0.7136 (m) REVERT: F 177 HIS cc_start: 0.6847 (m-70) cc_final: 0.6502 (m170) outliers start: 48 outliers final: 46 residues processed: 103 average time/residue: 0.0408 time to fit residues: 5.1739 Evaluate side-chains 107 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 60 time to evaluate : 0.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 176 VAL Chi-restraints excluded: chain A residue 181 ASN Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 191 THR Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 181 ASN Chi-restraints excluded: chain B residue 183 THR Chi-restraints excluded: chain B residue 184 ILE Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 190 THR Chi-restraints excluded: chain B residue 191 THR Chi-restraints excluded: chain B residue 206 MET Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain B residue 214 CYS Chi-restraints excluded: chain C residue 176 VAL Chi-restraints excluded: chain C residue 181 ASN Chi-restraints excluded: chain C residue 183 THR Chi-restraints excluded: chain C residue 189 VAL Chi-restraints excluded: chain C residue 190 THR Chi-restraints excluded: chain C residue 191 THR Chi-restraints excluded: chain C residue 193 THR Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain C residue 209 VAL Chi-restraints excluded: chain D residue 176 VAL Chi-restraints excluded: chain D residue 183 THR Chi-restraints excluded: chain D residue 190 THR Chi-restraints excluded: chain D residue 191 THR Chi-restraints excluded: chain D residue 209 VAL Chi-restraints excluded: chain E residue 176 VAL Chi-restraints excluded: chain E residue 183 THR Chi-restraints excluded: chain E residue 189 VAL Chi-restraints excluded: chain E residue 190 THR Chi-restraints excluded: chain E residue 191 THR Chi-restraints excluded: chain E residue 193 THR Chi-restraints excluded: chain E residue 209 VAL Chi-restraints excluded: chain F residue 176 VAL Chi-restraints excluded: chain F residue 183 THR Chi-restraints excluded: chain F residue 189 VAL Chi-restraints excluded: chain F residue 191 THR Chi-restraints excluded: chain F residue 192 THR Chi-restraints excluded: chain F residue 203 VAL Chi-restraints excluded: chain F residue 206 MET Chi-restraints excluded: chain F residue 209 VAL Chi-restraints excluded: chain F residue 213 MET Chi-restraints excluded: chain F residue 214 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 4 optimal weight: 4.9990 chunk 9 optimal weight: 2.9990 chunk 17 optimal weight: 3.9990 chunk 7 optimal weight: 2.9990 chunk 20 optimal weight: 4.9990 chunk 16 optimal weight: 3.9990 chunk 10 optimal weight: 0.7980 chunk 21 optimal weight: 0.8980 chunk 13 optimal weight: 4.9990 chunk 18 optimal weight: 2.9990 chunk 2 optimal weight: 2.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 177 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4318 r_free = 0.4318 target = 0.129389 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.4212 r_free = 0.4212 target = 0.120833 restraints weight = 3503.537| |-----------------------------------------------------------------------------| r_work (start): 0.4217 rms_B_bonded: 2.51 r_work: 0.4114 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.4006 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.4006 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7508 moved from start: 0.2504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.046 2088 Z= 0.304 Angle : 0.829 5.441 2814 Z= 0.473 Chirality : 0.060 0.145 360 Planarity : 0.004 0.015 342 Dihedral : 6.854 17.477 258 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 15.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 29.67 % Favored : 70.33 % Rotamer: Outliers : 26.98 % Allowed : 16.27 % Favored : 56.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -6.88 (0.33), residues: 246 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -5.24 (0.25), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 208 PHE 0.013 0.003 PHE D 198 HIS 0.012 0.004 HIS E 187 Details of bonding type rmsd covalent geometry : bond 0.00690 ( 2082) covalent geometry : angle 0.82939 ( 2802) SS BOND : bond 0.00956 ( 6) SS BOND : angle 0.71311 ( 12) hydrogen bonds : bond 0.06437 ( 8) hydrogen bonds : angle 8.49455 ( 24) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 492 Ramachandran restraints generated. 246 Oldfield, 0 Emsley, 246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 492 Ramachandran restraints generated. 246 Oldfield, 0 Emsley, 246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 56 time to evaluate : 0.088 Fit side-chains revert: symmetry clash REVERT: A 187 HIS cc_start: 0.8113 (OUTLIER) cc_final: 0.7746 (p-80) REVERT: A 194 LYS cc_start: 0.8910 (mmmt) cc_final: 0.8615 (tppp) REVERT: C 205 MET cc_start: 0.7793 (OUTLIER) cc_final: 0.7571 (ptm) REVERT: F 177 HIS cc_start: 0.7155 (m-70) cc_final: 0.6883 (m-70) outliers start: 68 outliers final: 57 residues processed: 110 average time/residue: 0.0363 time to fit residues: 5.0277 Evaluate side-chains 113 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 54 time to evaluate : 0.086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 176 VAL Chi-restraints excluded: chain A residue 181 ASN Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 187 HIS Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 191 THR Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain A residue 206 MET Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 181 ASN Chi-restraints excluded: chain B residue 183 THR Chi-restraints excluded: chain B residue 184 ILE Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 190 THR Chi-restraints excluded: chain B residue 191 THR Chi-restraints excluded: chain B residue 193 THR Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 206 MET Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain C residue 176 VAL Chi-restraints excluded: chain C residue 181 ASN Chi-restraints excluded: chain C residue 183 THR Chi-restraints excluded: chain C residue 189 VAL Chi-restraints excluded: chain C residue 190 THR Chi-restraints excluded: chain C residue 191 THR Chi-restraints excluded: chain C residue 193 THR Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain C residue 205 MET Chi-restraints excluded: chain C residue 209 VAL Chi-restraints excluded: chain D residue 176 VAL Chi-restraints excluded: chain D residue 183 THR Chi-restraints excluded: chain D residue 190 THR Chi-restraints excluded: chain D residue 191 THR Chi-restraints excluded: chain D residue 193 THR Chi-restraints excluded: chain D residue 209 VAL Chi-restraints excluded: chain E residue 176 VAL Chi-restraints excluded: chain E residue 183 THR Chi-restraints excluded: chain E residue 184 ILE Chi-restraints excluded: chain E residue 187 HIS Chi-restraints excluded: chain E residue 189 VAL Chi-restraints excluded: chain E residue 190 THR Chi-restraints excluded: chain E residue 191 THR Chi-restraints excluded: chain E residue 193 THR Chi-restraints excluded: chain E residue 203 VAL Chi-restraints excluded: chain E residue 209 VAL Chi-restraints excluded: chain F residue 176 VAL Chi-restraints excluded: chain F residue 181 ASN Chi-restraints excluded: chain F residue 183 THR Chi-restraints excluded: chain F residue 184 ILE Chi-restraints excluded: chain F residue 189 VAL Chi-restraints excluded: chain F residue 191 THR Chi-restraints excluded: chain F residue 192 THR Chi-restraints excluded: chain F residue 193 THR Chi-restraints excluded: chain F residue 203 VAL Chi-restraints excluded: chain F residue 206 MET Chi-restraints excluded: chain F residue 209 VAL Chi-restraints excluded: chain F residue 214 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 3 optimal weight: 0.9990 chunk 7 optimal weight: 0.8980 chunk 11 optimal weight: 1.9990 chunk 16 optimal weight: 3.9990 chunk 1 optimal weight: 2.9990 chunk 10 optimal weight: 0.0980 chunk 17 optimal weight: 0.8980 chunk 18 optimal weight: 0.8980 chunk 2 optimal weight: 1.9990 chunk 21 optimal weight: 0.7980 chunk 15 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 177 HIS D 212 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4445 r_free = 0.4445 target = 0.137743 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4336 r_free = 0.4336 target = 0.128454 restraints weight = 3366.401| |-----------------------------------------------------------------------------| r_work (start): 0.4334 rms_B_bonded: 2.76 r_work: 0.4221 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.4221 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7226 moved from start: 0.2666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 2088 Z= 0.132 Angle : 0.688 5.169 2814 Z= 0.387 Chirality : 0.052 0.141 360 Planarity : 0.003 0.015 342 Dihedral : 5.296 13.473 258 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 14.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 21.54 % Favored : 78.46 % Rotamer: Outliers : 19.44 % Allowed : 23.81 % Favored : 56.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -6.53 (0.36), residues: 246 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.97 (0.27), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 208 PHE 0.008 0.001 PHE B 175 HIS 0.005 0.002 HIS E 187 Details of bonding type rmsd covalent geometry : bond 0.00279 ( 2082) covalent geometry : angle 0.68015 ( 2802) SS BOND : bond 0.00385 ( 6) SS BOND : angle 1.76998 ( 12) hydrogen bonds : bond 0.05282 ( 8) hydrogen bonds : angle 7.82544 ( 24) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 492 Ramachandran restraints generated. 246 Oldfield, 0 Emsley, 246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 492 Ramachandran restraints generated. 246 Oldfield, 0 Emsley, 246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 60 time to evaluate : 0.098 Fit side-chains revert: symmetry clash REVERT: A 194 LYS cc_start: 0.8711 (mmmt) cc_final: 0.8421 (tppp) REVERT: F 177 HIS cc_start: 0.6830 (m170) cc_final: 0.6421 (m-70) outliers start: 49 outliers final: 46 residues processed: 102 average time/residue: 0.0398 time to fit residues: 5.0425 Evaluate side-chains 105 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 59 time to evaluate : 0.076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 176 VAL Chi-restraints excluded: chain A residue 181 ASN Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 191 THR Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 181 ASN Chi-restraints excluded: chain B residue 183 THR Chi-restraints excluded: chain B residue 184 ILE Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 190 THR Chi-restraints excluded: chain B residue 191 THR Chi-restraints excluded: chain B residue 206 MET Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain C residue 181 ASN Chi-restraints excluded: chain C residue 183 THR Chi-restraints excluded: chain C residue 189 VAL Chi-restraints excluded: chain C residue 190 THR Chi-restraints excluded: chain C residue 191 THR Chi-restraints excluded: chain C residue 193 THR Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain C residue 209 VAL Chi-restraints excluded: chain D residue 176 VAL Chi-restraints excluded: chain D residue 183 THR Chi-restraints excluded: chain D residue 187 HIS Chi-restraints excluded: chain D residue 190 THR Chi-restraints excluded: chain D residue 191 THR Chi-restraints excluded: chain D residue 193 THR Chi-restraints excluded: chain D residue 209 VAL Chi-restraints excluded: chain E residue 176 VAL Chi-restraints excluded: chain E residue 183 THR Chi-restraints excluded: chain E residue 184 ILE Chi-restraints excluded: chain E residue 189 VAL Chi-restraints excluded: chain E residue 190 THR Chi-restraints excluded: chain E residue 191 THR Chi-restraints excluded: chain E residue 193 THR Chi-restraints excluded: chain E residue 209 VAL Chi-restraints excluded: chain F residue 176 VAL Chi-restraints excluded: chain F residue 181 ASN Chi-restraints excluded: chain F residue 183 THR Chi-restraints excluded: chain F residue 184 ILE Chi-restraints excluded: chain F residue 191 THR Chi-restraints excluded: chain F residue 203 VAL Chi-restraints excluded: chain F residue 209 VAL Chi-restraints excluded: chain F residue 214 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 7 optimal weight: 2.9990 chunk 5 optimal weight: 4.9990 chunk 13 optimal weight: 4.9990 chunk 20 optimal weight: 5.9990 chunk 18 optimal weight: 4.9990 chunk 21 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 3 optimal weight: 0.1980 chunk 15 optimal weight: 0.0770 chunk 19 optimal weight: 0.7980 chunk 2 optimal weight: 0.9980 overall best weight: 0.8140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 177 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4447 r_free = 0.4447 target = 0.138642 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4345 r_free = 0.4345 target = 0.129892 restraints weight = 3341.196| |-----------------------------------------------------------------------------| r_work (start): 0.4317 rms_B_bonded: 2.62 r_work: 0.4211 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work (final): 0.4211 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7293 moved from start: 0.2763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 2088 Z= 0.142 Angle : 0.674 4.968 2814 Z= 0.381 Chirality : 0.052 0.140 360 Planarity : 0.003 0.015 342 Dihedral : 5.238 14.015 258 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 14.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 23.17 % Favored : 76.83 % Rotamer: Outliers : 19.84 % Allowed : 24.60 % Favored : 55.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -6.37 (0.37), residues: 246 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.85 (0.29), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG D 208 PHE 0.008 0.001 PHE B 175 HIS 0.006 0.002 HIS C 187 Details of bonding type rmsd covalent geometry : bond 0.00307 ( 2082) covalent geometry : angle 0.66993 ( 2802) SS BOND : bond 0.00491 ( 6) SS BOND : angle 1.29244 ( 12) hydrogen bonds : bond 0.05246 ( 8) hydrogen bonds : angle 7.70380 ( 24) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 492 Ramachandran restraints generated. 246 Oldfield, 0 Emsley, 246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 492 Ramachandran restraints generated. 246 Oldfield, 0 Emsley, 246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 60 time to evaluate : 0.078 Fit side-chains REVERT: A 194 LYS cc_start: 0.8781 (mmmt) cc_final: 0.8501 (tppp) REVERT: F 177 HIS cc_start: 0.6848 (m170) cc_final: 0.6478 (m-70) outliers start: 50 outliers final: 47 residues processed: 106 average time/residue: 0.0367 time to fit residues: 4.7871 Evaluate side-chains 106 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 59 time to evaluate : 0.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 176 VAL Chi-restraints excluded: chain A residue 181 ASN Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 191 THR Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 183 THR Chi-restraints excluded: chain B residue 184 ILE Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 190 THR Chi-restraints excluded: chain B residue 191 THR Chi-restraints excluded: chain B residue 206 MET Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain C residue 176 VAL Chi-restraints excluded: chain C residue 181 ASN Chi-restraints excluded: chain C residue 183 THR Chi-restraints excluded: chain C residue 189 VAL Chi-restraints excluded: chain C residue 190 THR Chi-restraints excluded: chain C residue 191 THR Chi-restraints excluded: chain C residue 193 THR Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain C residue 209 VAL Chi-restraints excluded: chain D residue 176 VAL Chi-restraints excluded: chain D residue 183 THR Chi-restraints excluded: chain D residue 187 HIS Chi-restraints excluded: chain D residue 190 THR Chi-restraints excluded: chain D residue 191 THR Chi-restraints excluded: chain D residue 209 VAL Chi-restraints excluded: chain E residue 176 VAL Chi-restraints excluded: chain E residue 183 THR Chi-restraints excluded: chain E residue 184 ILE Chi-restraints excluded: chain E residue 187 HIS Chi-restraints excluded: chain E residue 189 VAL Chi-restraints excluded: chain E residue 190 THR Chi-restraints excluded: chain E residue 191 THR Chi-restraints excluded: chain E residue 193 THR Chi-restraints excluded: chain E residue 209 VAL Chi-restraints excluded: chain F residue 176 VAL Chi-restraints excluded: chain F residue 181 ASN Chi-restraints excluded: chain F residue 183 THR Chi-restraints excluded: chain F residue 184 ILE Chi-restraints excluded: chain F residue 189 VAL Chi-restraints excluded: chain F residue 191 THR Chi-restraints excluded: chain F residue 203 VAL Chi-restraints excluded: chain F residue 209 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 20 optimal weight: 0.0980 chunk 7 optimal weight: 1.9990 chunk 12 optimal weight: 4.9990 chunk 9 optimal weight: 0.1980 chunk 13 optimal weight: 4.9990 chunk 11 optimal weight: 1.9990 chunk 19 optimal weight: 0.7980 chunk 10 optimal weight: 0.9980 chunk 1 optimal weight: 0.9980 chunk 14 optimal weight: 0.9990 chunk 5 optimal weight: 0.7980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 177 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4490 r_free = 0.4490 target = 0.140543 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4387 r_free = 0.4387 target = 0.131370 restraints weight = 3394.008| |-----------------------------------------------------------------------------| r_work (start): 0.4362 rms_B_bonded: 2.83 r_work: 0.4251 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.4251 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7212 moved from start: 0.2964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 2088 Z= 0.120 Angle : 0.647 4.998 2814 Z= 0.364 Chirality : 0.050 0.137 360 Planarity : 0.003 0.015 342 Dihedral : 4.814 12.637 258 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 13.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 19.11 % Favored : 80.89 % Rotamer: Outliers : 14.68 % Allowed : 30.16 % Favored : 55.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -6.21 (0.39), residues: 246 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.73 (0.30), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 208 PHE 0.008 0.001 PHE B 175 HIS 0.005 0.001 HIS C 187 Details of bonding type rmsd covalent geometry : bond 0.00250 ( 2082) covalent geometry : angle 0.64428 ( 2802) SS BOND : bond 0.00333 ( 6) SS BOND : angle 1.10548 ( 12) hydrogen bonds : bond 0.04611 ( 8) hydrogen bonds : angle 7.66269 ( 24) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 492 Ramachandran restraints generated. 246 Oldfield, 0 Emsley, 246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 492 Ramachandran restraints generated. 246 Oldfield, 0 Emsley, 246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 61 time to evaluate : 0.057 Fit side-chains REVERT: A 194 LYS cc_start: 0.8691 (mmmt) cc_final: 0.8418 (tppp) REVERT: B 187 HIS cc_start: 0.7594 (OUTLIER) cc_final: 0.6880 (p-80) REVERT: F 177 HIS cc_start: 0.6824 (m170) cc_final: 0.6367 (m170) outliers start: 37 outliers final: 36 residues processed: 95 average time/residue: 0.0351 time to fit residues: 4.1901 Evaluate side-chains 98 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 61 time to evaluate : 0.064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 176 VAL Chi-restraints excluded: chain A residue 181 ASN Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 183 THR Chi-restraints excluded: chain B residue 187 HIS Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 190 THR Chi-restraints excluded: chain B residue 191 THR Chi-restraints excluded: chain B residue 206 MET Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain C residue 183 THR Chi-restraints excluded: chain C residue 190 THR Chi-restraints excluded: chain C residue 191 THR Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain C residue 209 VAL Chi-restraints excluded: chain D residue 176 VAL Chi-restraints excluded: chain D residue 181 ASN Chi-restraints excluded: chain D residue 187 HIS Chi-restraints excluded: chain D residue 190 THR Chi-restraints excluded: chain D residue 209 VAL Chi-restraints excluded: chain E residue 176 VAL Chi-restraints excluded: chain E residue 183 THR Chi-restraints excluded: chain E residue 187 HIS Chi-restraints excluded: chain E residue 189 VAL Chi-restraints excluded: chain E residue 190 THR Chi-restraints excluded: chain E residue 191 THR Chi-restraints excluded: chain E residue 209 VAL Chi-restraints excluded: chain F residue 176 VAL Chi-restraints excluded: chain F residue 181 ASN Chi-restraints excluded: chain F residue 183 THR Chi-restraints excluded: chain F residue 184 ILE Chi-restraints excluded: chain F residue 189 VAL Chi-restraints excluded: chain F residue 191 THR Chi-restraints excluded: chain F residue 203 VAL Chi-restraints excluded: chain F residue 209 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 21 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 17 optimal weight: 0.9990 chunk 14 optimal weight: 0.5980 chunk 16 optimal weight: 0.9980 chunk 11 optimal weight: 1.9990 chunk 5 optimal weight: 5.9990 chunk 7 optimal weight: 0.6980 chunk 18 optimal weight: 0.7980 chunk 13 optimal weight: 3.9990 chunk 12 optimal weight: 0.5980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 177 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4471 r_free = 0.4471 target = 0.140022 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4370 r_free = 0.4370 target = 0.130998 restraints weight = 3485.555| |-----------------------------------------------------------------------------| r_work (start): 0.4335 rms_B_bonded: 2.76 r_work: 0.4229 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.4229 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7244 moved from start: 0.2965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 2088 Z= 0.136 Angle : 0.672 5.222 2814 Z= 0.378 Chirality : 0.051 0.137 360 Planarity : 0.003 0.014 342 Dihedral : 5.003 12.525 258 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 14.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 22.76 % Favored : 77.24 % Rotamer: Outliers : 16.27 % Allowed : 28.17 % Favored : 55.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -6.14 (0.39), residues: 246 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.67 (0.30), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG C 208 PHE 0.009 0.001 PHE B 175 HIS 0.006 0.002 HIS C 187 Details of bonding type rmsd covalent geometry : bond 0.00292 ( 2082) covalent geometry : angle 0.66961 ( 2802) SS BOND : bond 0.00427 ( 6) SS BOND : angle 1.14096 ( 12) hydrogen bonds : bond 0.04837 ( 8) hydrogen bonds : angle 7.67083 ( 24) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 492 Ramachandran restraints generated. 246 Oldfield, 0 Emsley, 246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 492 Ramachandran restraints generated. 246 Oldfield, 0 Emsley, 246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 60 time to evaluate : 0.051 Fit side-chains REVERT: A 194 LYS cc_start: 0.8724 (mmmt) cc_final: 0.8431 (tppp) REVERT: A 213 MET cc_start: 0.6935 (ttt) cc_final: 0.6471 (ttt) REVERT: B 187 HIS cc_start: 0.7644 (OUTLIER) cc_final: 0.6825 (p-80) REVERT: B 213 MET cc_start: 0.7185 (tpp) cc_final: 0.6502 (ttt) REVERT: F 177 HIS cc_start: 0.6855 (m170) cc_final: 0.6419 (m-70) outliers start: 41 outliers final: 40 residues processed: 99 average time/residue: 0.0327 time to fit residues: 4.0439 Evaluate side-chains 101 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 60 time to evaluate : 0.051 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 176 VAL Chi-restraints excluded: chain A residue 181 ASN Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 191 THR Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 183 THR Chi-restraints excluded: chain B residue 187 HIS Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 190 THR Chi-restraints excluded: chain B residue 191 THR Chi-restraints excluded: chain B residue 206 MET Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain C residue 176 VAL Chi-restraints excluded: chain C residue 181 ASN Chi-restraints excluded: chain C residue 183 THR Chi-restraints excluded: chain C residue 190 THR Chi-restraints excluded: chain C residue 191 THR Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain C residue 209 VAL Chi-restraints excluded: chain D residue 176 VAL Chi-restraints excluded: chain D residue 187 HIS Chi-restraints excluded: chain D residue 190 THR Chi-restraints excluded: chain D residue 209 VAL Chi-restraints excluded: chain E residue 176 VAL Chi-restraints excluded: chain E residue 183 THR Chi-restraints excluded: chain E residue 184 ILE Chi-restraints excluded: chain E residue 187 HIS Chi-restraints excluded: chain E residue 189 VAL Chi-restraints excluded: chain E residue 190 THR Chi-restraints excluded: chain E residue 191 THR Chi-restraints excluded: chain E residue 209 VAL Chi-restraints excluded: chain F residue 176 VAL Chi-restraints excluded: chain F residue 181 ASN Chi-restraints excluded: chain F residue 183 THR Chi-restraints excluded: chain F residue 184 ILE Chi-restraints excluded: chain F residue 189 VAL Chi-restraints excluded: chain F residue 191 THR Chi-restraints excluded: chain F residue 203 VAL Chi-restraints excluded: chain F residue 209 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 22 optimal weight: 0.0010 chunk 5 optimal weight: 1.9990 chunk 3 optimal weight: 0.4980 chunk 20 optimal weight: 4.9990 chunk 4 optimal weight: 0.9990 chunk 9 optimal weight: 0.5980 chunk 8 optimal weight: 2.9990 chunk 0 optimal weight: 0.5980 chunk 11 optimal weight: 2.9990 chunk 10 optimal weight: 0.9980 chunk 15 optimal weight: 0.9980 overall best weight: 0.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 177 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4529 r_free = 0.4529 target = 0.143859 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4425 r_free = 0.4425 target = 0.134686 restraints weight = 3471.873| |-----------------------------------------------------------------------------| r_work (start): 0.4393 rms_B_bonded: 2.80 r_work: 0.4290 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.4290 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7185 moved from start: 0.3161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 2088 Z= 0.118 Angle : 0.642 5.173 2814 Z= 0.361 Chirality : 0.050 0.132 360 Planarity : 0.003 0.015 342 Dihedral : 4.598 11.711 258 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 13.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 19.11 % Favored : 80.89 % Rotamer: Outliers : 16.27 % Allowed : 29.37 % Favored : 54.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -6.03 (0.40), residues: 246 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.59 (0.31), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 208 PHE 0.009 0.001 PHE B 175 HIS 0.004 0.001 HIS C 187 Details of bonding type rmsd covalent geometry : bond 0.00245 ( 2082) covalent geometry : angle 0.63872 ( 2802) SS BOND : bond 0.00334 ( 6) SS BOND : angle 1.11813 ( 12) hydrogen bonds : bond 0.04523 ( 8) hydrogen bonds : angle 7.38613 ( 24) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 984.59 seconds wall clock time: 17 minutes 31.34 seconds (1051.34 seconds total)