Starting phenix.real_space_refine on Fri Jul 3 11:43:32 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8dmb_27533/07_2026/8dmb_27533.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dmb_27533/07_2026/8dmb_27533.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8dmb_27533/07_2026/8dmb_27533.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dmb_27533/07_2026/8dmb_27533.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8dmb_27533/07_2026/8dmb_27533.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dmb_27533/07_2026/8dmb_27533.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8dmb_27533/07_2026/8dmb_27533.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8dmb_27533/07_2026/8dmb_27533.cif" } resolution = 3.1 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= 0.006 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: 7 Type Number sf(0) Gaussians P 274 5.49 5 Mg 2 5.21 5 S 9 5.16 5 C 4303 2.51 5 N 1586 2.21 5 O 2323 1.98 5 H 5728 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 14225 Number of models: 1 Model: "" Number of chains: 5 Chain: "P" Number of atoms: 5376 Number of conformers: 1 Conformer: "" Number of residues, atoms: 328, 5376 Classifications: {'peptide': 328} Link IDs: {'PTRANS': 20, 'TRANS': 307} Chain breaks: 1 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "W" Number of atoms: 7634 Number of conformers: 1 Conformer: "" Number of residues, atoms: 237, 7634 Classifications: {'RNA': 237} Modifications used: {'3*END': 1, 'rna2p_pur': 11, 'rna2p_pyr': 14, 'rna3p_pur': 109, 'rna3p_pyr': 103} Link IDs: {'rna2p': 25, 'rna3p': 211} Chain breaks: 4 Chain: "X" Number of atoms: 893 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 893 Classifications: {'DNA': 28} Link IDs: {'rna3p': 27} Chain: "Y" Number of atoms: 320 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 320 Classifications: {'DNA': 10} Modifications used: {'3*END': 1, '5*END': 1} Link IDs: {'rna3p': 9} Chain: "W" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 2.44, per 1000 atoms: 0.17 Number of scatterers: 14225 At special positions: 0 Unit cell: (108.68, 128.128, 102.96, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 9 16.00 P 274 15.00 Mg 2 11.99 O 2323 8.00 N 1586 7.00 C 4303 6.00 H 5728 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.10 Conformation dependent library (CDL) restraints added in 252.5 milliseconds 648 Ramachandran restraints generated. 324 Oldfield, 0 Emsley, 324 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 604 Finding SS restraints... Secondary structure from input PDB file: 9 helices and 3 sheets defined 34.5% alpha, 21.3% beta 108 base pairs and 159 stacking pairs defined. Time for finding SS restraints: 2.20 Creating SS restraints... Processing helix chain 'P' and resid 22 through 32 Processing helix chain 'P' and resid 92 through 112 Processing helix chain 'P' and resid 130 through 151 removed outlier: 4.105A pdb=" N ILE P 150 " --> pdb=" O GLU P 146 " (cutoff:3.500A) Processing helix chain 'P' and resid 164 through 168 Processing helix chain 'P' and resid 171 through 179 removed outlier: 4.974A pdb=" N VAL P 177 " --> pdb=" O TYR P 173 " (cutoff:3.500A) Processing helix chain 'P' and resid 180 through 192 removed outlier: 3.668A pdb=" N LYS P 190 " --> pdb=" O ARG P 186 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N LEU P 191 " --> pdb=" O GLU P 187 " (cutoff:3.500A) Processing helix chain 'P' and resid 198 through 210 Processing helix chain 'P' and resid 226 through 239 Processing helix chain 'P' and resid 267 through 271 removed outlier: 3.581A pdb=" N VAL P 271 " --> pdb=" O LYS P 268 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'P' and resid 10 through 11 removed outlier: 7.201A pdb=" N VAL P 11 " --> pdb=" O MET P 49 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'P' and resid 193 through 197 removed outlier: 3.640A pdb=" N LEU P 155 " --> pdb=" O VAL P 60 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N GLU P 159 " --> pdb=" O VAL P 64 " (cutoff:3.500A) removed outlier: 5.980A pdb=" N SER P 77 " --> pdb=" O VAL P 81 " (cutoff:3.500A) removed outlier: 5.026A pdb=" N VAL P 81 " --> pdb=" O SER P 77 " (cutoff:3.500A) removed outlier: 8.956A pdb=" N PHE P 249 " --> pdb=" O GLU P 82 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N ARG P 84 " --> pdb=" O PHE P 249 " (cutoff:3.500A) removed outlier: 8.231A pdb=" N TRP P 251 " --> pdb=" O ARG P 84 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N MET P 86 " --> pdb=" O TRP P 251 " (cutoff:3.500A) removed outlier: 8.073A pdb=" N ARG P 253 " --> pdb=" O MET P 86 " (cutoff:3.500A) removed outlier: 7.547A pdb=" N PHE P 88 " --> pdb=" O ARG P 253 " (cutoff:3.500A) removed outlier: 4.666A pdb=" N PHE P 248 " --> pdb=" O VAL P 346 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ARG P 252 " --> pdb=" O SER P 342 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'P' and resid 323 through 327 removed outlier: 6.074A pdb=" N GLY P 315 " --> pdb=" O CYS P 304 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N GLU P 291 " --> pdb=" O LEU P 334 " (cutoff:3.500A) removed outlier: 5.287A pdb=" N LEU P 334 " --> pdb=" O GLU P 291 " (cutoff:3.500A) removed outlier: 7.346A pdb=" N GLU P 293 " --> pdb=" O VAL P 332 " (cutoff:3.500A) removed outlier: 5.931A pdb=" N VAL P 332 " --> pdb=" O GLU P 293 " (cutoff:3.500A) 116 hydrogen bonds defined for protein. 330 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 285 hydrogen bonds 526 hydrogen bond angles 0 basepair planarities 108 basepair parallelities 159 stacking parallelities Total time for adding SS restraints: 2.63 Time building geometry restraints manager: 1.54 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.82 - 1.02: 5725 1.02 - 1.22: 5 1.22 - 1.41: 3882 1.41 - 1.61: 5326 1.61 - 1.81: 29 Bond restraints: 14967 Sorted by residual: bond pdb=" C1' DT Y 2 " pdb=" N1 DT Y 2 " ideal model delta sigma weight residual 1.468 1.552 -0.084 1.40e-02 5.10e+03 3.62e+01 bond pdb=" C3' DT Y 2 " pdb=" C2' DT Y 2 " ideal model delta sigma weight residual 1.516 1.560 -0.044 8.00e-03 1.56e+04 3.06e+01 bond pdb=" C1' DT Y 10 " pdb=" N1 DT Y 10 " ideal model delta sigma weight residual 1.468 1.545 -0.077 1.40e-02 5.10e+03 3.05e+01 bond pdb=" C3' DT Y 2 " pdb=" O3' DT Y 2 " ideal model delta sigma weight residual 1.435 1.498 -0.063 1.30e-02 5.92e+03 2.31e+01 bond pdb=" C1' DT X 3 " pdb=" N1 DT X 3 " ideal model delta sigma weight residual 1.468 1.534 -0.066 1.40e-02 5.10e+03 2.24e+01 ... (remaining 14962 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.02: 25348 2.02 - 4.04: 1402 4.04 - 6.05: 115 6.05 - 8.07: 6 8.07 - 10.09: 1 Bond angle restraints: 26872 Sorted by residual: angle pdb=" O4' DA X 28 " pdb=" C4' DA X 28 " pdb=" C3' DA X 28 " ideal model delta sigma weight residual 106.00 101.74 4.26 6.00e-01 2.78e+00 5.05e+01 angle pdb=" O4' DT X 3 " pdb=" C1' DT X 3 " pdb=" N1 DT X 3 " ideal model delta sigma weight residual 108.00 112.84 -4.84 7.00e-01 2.04e+00 4.79e+01 angle pdb=" O4' DG X 14 " pdb=" C1' DG X 14 " pdb=" N9 DG X 14 " ideal model delta sigma weight residual 108.00 112.20 -4.20 7.00e-01 2.04e+00 3.61e+01 angle pdb=" O5' DG Y 3 " pdb=" C5' DG Y 3 " pdb=" C4' DG Y 3 " ideal model delta sigma weight residual 109.40 113.79 -4.39 8.00e-01 1.56e+00 3.00e+01 angle pdb=" O4' DC X 19 " pdb=" C4' DC X 19 " pdb=" C3' DC X 19 " ideal model delta sigma weight residual 106.00 102.74 3.26 6.00e-01 2.78e+00 2.95e+01 ... (remaining 26867 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.61: 5858 35.61 - 71.23: 353 71.23 - 106.84: 66 106.84 - 142.46: 1 142.46 - 178.07: 2 Dihedral angle restraints: 6280 sinusoidal: 5177 harmonic: 1103 Sorted by residual: dihedral pdb=" O4' U W 255 " pdb=" C1' U W 255 " pdb=" N1 U W 255 " pdb=" C2 U W 255 " ideal model delta sinusoidal sigma weight residual 232.00 53.93 178.07 1 1.70e+01 3.46e-03 6.64e+01 dihedral pdb=" O4' C W 146 " pdb=" C1' C W 146 " pdb=" N1 C W 146 " pdb=" C2 C W 146 " ideal model delta sinusoidal sigma weight residual -128.00 44.32 -172.32 1 1.70e+01 3.46e-03 6.61e+01 dihedral pdb=" O4' C W 147 " pdb=" C1' C W 147 " pdb=" N1 C W 147 " pdb=" C2 C W 147 " ideal model delta sinusoidal sigma weight residual -160.00 -86.23 -73.77 1 1.50e+01 4.44e-03 3.07e+01 ... (remaining 6277 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 1298 0.052 - 0.104: 305 0.104 - 0.157: 91 0.157 - 0.209: 21 0.209 - 0.261: 7 Chirality restraints: 1722 Sorted by residual: chirality pdb=" C1' A W 11 " pdb=" O4' A W 11 " pdb=" C2' A W 11 " pdb=" N9 A W 11 " both_signs ideal model delta sigma weight residual False 2.46 2.20 0.26 2.00e-01 2.50e+01 1.70e+00 chirality pdb=" C1' A W 251 " pdb=" O4' A W 251 " pdb=" C2' A W 251 " pdb=" N9 A W 251 " both_signs ideal model delta sigma weight residual False 2.46 2.20 0.25 2.00e-01 2.50e+01 1.60e+00 chirality pdb=" C1' A W 189 " pdb=" O4' A W 189 " pdb=" C2' A W 189 " pdb=" N9 A W 189 " both_signs ideal model delta sigma weight residual False 2.46 2.21 0.25 2.00e-01 2.50e+01 1.54e+00 ... (remaining 1719 not shown) Planarity restraints: 1284 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG P 108 " 0.369 9.50e-02 1.11e+02 1.25e-01 2.38e+01 pdb=" NE ARG P 108 " 0.001 2.00e-02 2.50e+03 pdb=" CZ ARG P 108 " -0.007 2.00e-02 2.50e+03 pdb=" NH1 ARG P 108 " -0.036 2.00e-02 2.50e+03 pdb=" NH2 ARG P 108 " -0.028 2.00e-02 2.50e+03 pdb="HH11 ARG P 108 " -0.000 2.00e-02 2.50e+03 pdb="HH12 ARG P 108 " 0.024 2.00e-02 2.50e+03 pdb="HH21 ARG P 108 " 0.001 2.00e-02 2.50e+03 pdb="HH22 ARG P 108 " 0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG P 253 " 0.295 9.50e-02 1.11e+02 1.00e-01 1.75e+01 pdb=" NE ARG P 253 " 0.004 2.00e-02 2.50e+03 pdb=" CZ ARG P 253 " -0.004 2.00e-02 2.50e+03 pdb=" NH1 ARG P 253 " -0.036 2.00e-02 2.50e+03 pdb=" NH2 ARG P 253 " -0.024 2.00e-02 2.50e+03 pdb="HH11 ARG P 253 " -0.001 2.00e-02 2.50e+03 pdb="HH12 ARG P 253 " 0.025 2.00e-02 2.50e+03 pdb="HH21 ARG P 253 " -0.001 2.00e-02 2.50e+03 pdb="HH22 ARG P 253 " 0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN P 170 " 0.025 2.00e-02 2.50e+03 3.26e-02 1.59e+01 pdb=" CG ASN P 170 " -0.020 2.00e-02 2.50e+03 pdb=" OD1 ASN P 170 " -0.001 2.00e-02 2.50e+03 pdb=" ND2 ASN P 170 " -0.054 2.00e-02 2.50e+03 pdb="HD21 ASN P 170 " 0.000 2.00e-02 2.50e+03 pdb="HD22 ASN P 170 " 0.049 2.00e-02 2.50e+03 ... (remaining 1281 not shown) Histogram of nonbonded interaction distances: 1.68 - 2.26: 1437 2.26 - 2.85: 24223 2.85 - 3.43: 33487 3.43 - 4.02: 52883 4.02 - 4.60: 74867 Nonbonded interactions: 186897 Sorted by model distance: nonbonded pdb="HO2' A W 152 " pdb=" OP2 U W 154 " model vdw 1.677 2.450 nonbonded pdb="HO2' G W 72 " pdb=" O2 C W 98 " model vdw 1.688 2.450 nonbonded pdb=" HZ1 LYS P 142 " pdb=" OP1 G W 250 " model vdw 1.717 2.450 nonbonded pdb=" O ARG P 108 " pdb=" HG1 THR P 112 " model vdw 1.718 2.450 nonbonded pdb=" OD1 ASP P 91 " pdb=" HZ1 LYS P 136 " model vdw 1.728 2.450 ... (remaining 186892 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 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: 0.380 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.060 Extract box with map and model: 0.280 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 14.730 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 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 : 0.005 0.084 9239 Z= 0.386 Angle : 0.929 10.089 13808 Z= 0.611 Chirality : 0.054 0.261 1722 Planarity : 0.014 0.143 751 Dihedral : 16.044 178.072 4307 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 0.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 0.74 % Allowed : 3.70 % Favored : 95.56 % 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 are not related in a simple way. whole: 0.39 (0.46), residues: 324 helix: 0.05 (0.48), residues: 95 sheet: 0.92 (0.62), residues: 76 loop : 0.21 (0.51), residues: 153 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.003 ARG P 263 TYR 0.018 0.004 TYR P 127 PHE 0.010 0.002 PHE P 135 TRP 0.011 0.003 TRP P 251 HIS 0.003 0.002 HIS P 78 Details of bonding type rmsd/Z covalent geometry : bond 0.00548 / 0.39 ( 9239) covalent geometry : angle 0.92864 / 0.61 (13808) hydrogen bonds : bond 0.10658 / 7.28 ( 401) hydrogen bonds : angle 4.91605 / 3.76 ( 856) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 648 Ramachandran restraints generated. 324 Oldfield, 0 Emsley, 324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 648 Ramachandran restraints generated. 324 Oldfield, 0 Emsley, 324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 40 time to evaluate : 0.235 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 41 average time/residue: 0.4064 time to fit residues: 19.4471 Evaluate side-chains 30 residues out of total 272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 29 time to evaluate : 0.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 226 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 54 optimal weight: 9.9990 chunk 24 optimal weight: 0.8980 chunk 48 optimal weight: 9.9990 chunk 56 optimal weight: 6.9990 chunk 26 optimal weight: 4.9990 chunk 2 optimal weight: 4.9990 chunk 16 optimal weight: 10.0000 chunk 32 optimal weight: 7.9990 chunk 31 optimal weight: 2.9990 chunk 25 optimal weight: 0.9990 chunk 50 optimal weight: 9.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... P 226 HIS P 264 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.146180 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.114266 restraints weight = 28171.387| |-----------------------------------------------------------------------------| r_work (start): 0.3365 rms_B_bonded: 1.35 r_work: 0.3075 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3075 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8258 moved from start: 0.1300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 9239 Z= 0.216 Angle : 0.710 7.363 13808 Z= 0.394 Chirality : 0.043 0.246 1722 Planarity : 0.007 0.048 751 Dihedral : 15.672 178.376 3645 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 1.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.93 % Favored : 99.07 % Rotamer: Outliers : 1.11 % Allowed : 5.93 % Favored : 92.96 % 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 are not related in a simple way. whole: 0.52 (0.47), residues: 324 helix: 1.05 (0.51), residues: 98 sheet: 0.04 (0.56), residues: 84 loop : 0.22 (0.54), residues: 142 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG P 253 TYR 0.015 0.002 TYR P 70 PHE 0.010 0.001 PHE P 135 TRP 0.009 0.002 TRP P 343 HIS 0.004 0.001 HIS P 165 Details of bonding type rmsd/Z covalent geometry : bond 0.00420 / 0.22 ( 9239) covalent geometry : angle 0.70985 / 0.39 (13808) hydrogen bonds : bond 0.05837 / 3.92 ( 401) hydrogen bonds : angle 3.84479 / 2.86 ( 856) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 648 Ramachandran restraints generated. 324 Oldfield, 0 Emsley, 324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 648 Ramachandran restraints generated. 324 Oldfield, 0 Emsley, 324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 31 residues out of total 272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 28 time to evaluate : 0.146 Fit side-chains REVERT: P 24 ARG cc_start: 0.8306 (tmt90) cc_final: 0.8021 (tmt90) outliers start: 3 outliers final: 1 residues processed: 30 average time/residue: 0.3651 time to fit residues: 13.0277 Evaluate side-chains 26 residues out of total 272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 25 time to evaluate : 0.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 71 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 25 optimal weight: 4.9990 chunk 12 optimal weight: 3.9990 chunk 6 optimal weight: 6.9990 chunk 56 optimal weight: 10.0000 chunk 53 optimal weight: 10.0000 chunk 20 optimal weight: 10.0000 chunk 0 optimal weight: 5.9990 chunk 31 optimal weight: 0.9980 chunk 45 optimal weight: 5.9990 chunk 24 optimal weight: 1.9990 chunk 26 optimal weight: 0.8980 overall best weight: 2.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.146166 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.114108 restraints weight = 28097.158| |-----------------------------------------------------------------------------| r_work (start): 0.3370 rms_B_bonded: 1.29 r_work: 0.3086 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3086 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8255 moved from start: 0.1660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9239 Z= 0.183 Angle : 0.620 6.084 13808 Z= 0.352 Chirality : 0.039 0.216 1722 Planarity : 0.006 0.049 751 Dihedral : 15.638 178.432 3643 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 1.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 0.37 % Allowed : 7.78 % Favored : 91.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.66 (0.46), residues: 324 helix: 1.58 (0.51), residues: 98 sheet: -0.09 (0.51), residues: 96 loop : 0.14 (0.56), residues: 130 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG P 253 TYR 0.011 0.002 TYR P 70 PHE 0.010 0.001 PHE P 135 TRP 0.008 0.001 TRP P 343 HIS 0.004 0.001 HIS P 165 Details of bonding type rmsd/Z covalent geometry : bond 0.00343 / 0.18 ( 9239) covalent geometry : angle 0.61961 / 0.35 (13808) hydrogen bonds : bond 0.05496 / 3.76 ( 401) hydrogen bonds : angle 3.43362 / 2.53 ( 856) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 648 Ramachandran restraints generated. 324 Oldfield, 0 Emsley, 324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 648 Ramachandran restraints generated. 324 Oldfield, 0 Emsley, 324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 27 residues out of total 272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 26 time to evaluate : 0.166 Fit side-chains REVERT: P 24 ARG cc_start: 0.8238 (tmt90) cc_final: 0.7976 (tmt90) outliers start: 1 outliers final: 1 residues processed: 26 average time/residue: 0.3226 time to fit residues: 10.0698 Evaluate side-chains 27 residues out of total 272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 26 time to evaluate : 0.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 71 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 56 optimal weight: 10.0000 chunk 38 optimal weight: 20.0000 chunk 49 optimal weight: 10.0000 chunk 31 optimal weight: 3.9990 chunk 42 optimal weight: 10.0000 chunk 19 optimal weight: 5.9990 chunk 46 optimal weight: 7.9990 chunk 32 optimal weight: 10.0000 chunk 6 optimal weight: 6.9990 chunk 11 optimal weight: 0.9990 chunk 47 optimal weight: 7.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.142170 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.108808 restraints weight = 27980.867| |-----------------------------------------------------------------------------| r_work (start): 0.3289 rms_B_bonded: 1.42 r_work: 0.3014 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3014 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8321 moved from start: 0.2199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 9239 Z= 0.309 Angle : 0.732 6.790 13808 Z= 0.400 Chirality : 0.044 0.293 1722 Planarity : 0.008 0.053 751 Dihedral : 15.900 179.904 3643 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 2.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 0.74 % Allowed : 8.89 % Favored : 90.37 % 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 are not related in a simple way. whole: -0.04 (0.45), residues: 324 helix: 1.18 (0.50), residues: 98 sheet: -0.50 (0.50), residues: 101 loop : -0.43 (0.53), residues: 125 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG P 79 TYR 0.012 0.003 TYR P 46 PHE 0.017 0.002 PHE P 135 TRP 0.011 0.003 TRP P 289 HIS 0.008 0.002 HIS P 165 Details of bonding type rmsd/Z covalent geometry : bond 0.00623 / 0.31 ( 9239) covalent geometry : angle 0.73170 / 0.40 (13808) hydrogen bonds : bond 0.06457 / 4.29 ( 401) hydrogen bonds : angle 3.53140 / 2.59 ( 856) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 648 Ramachandran restraints generated. 324 Oldfield, 0 Emsley, 324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 648 Ramachandran restraints generated. 324 Oldfield, 0 Emsley, 324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 25 residues out of total 272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 23 time to evaluate : 0.168 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 24 average time/residue: 0.3553 time to fit residues: 10.1603 Evaluate side-chains 23 residues out of total 272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 22 time to evaluate : 0.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 71 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 43 optimal weight: 6.9990 chunk 24 optimal weight: 3.9990 chunk 56 optimal weight: 10.0000 chunk 42 optimal weight: 8.9990 chunk 47 optimal weight: 7.9990 chunk 41 optimal weight: 8.9990 chunk 48 optimal weight: 6.9990 chunk 30 optimal weight: 4.9990 chunk 14 optimal weight: 0.9990 chunk 10 optimal weight: 2.9990 chunk 36 optimal weight: 10.0000 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.143586 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.110234 restraints weight = 27923.767| |-----------------------------------------------------------------------------| r_work (start): 0.3319 rms_B_bonded: 1.32 r_work: 0.3048 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3048 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8304 moved from start: 0.2310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 9239 Z= 0.238 Angle : 0.635 6.167 13808 Z= 0.356 Chirality : 0.040 0.230 1722 Planarity : 0.007 0.054 751 Dihedral : 15.868 179.738 3643 Min Nonbonded Distance : 1.883 Molprobity Statistics. All-atom Clashscore : 2.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 0.74 % Allowed : 10.00 % Favored : 89.26 % 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 are not related in a simple way. whole: 0.12 (0.46), residues: 324 helix: 1.30 (0.50), residues: 98 sheet: -0.42 (0.52), residues: 96 loop : -0.32 (0.54), residues: 130 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG P 323 TYR 0.011 0.002 TYR P 46 PHE 0.013 0.001 PHE P 135 TRP 0.009 0.002 TRP P 343 HIS 0.005 0.002 HIS P 242 Details of bonding type rmsd/Z covalent geometry : bond 0.00470 / 0.24 ( 9239) covalent geometry : angle 0.63493 / 0.36 (13808) hydrogen bonds : bond 0.05672 / 3.79 ( 401) hydrogen bonds : angle 3.31092 / 2.42 ( 856) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 648 Ramachandran restraints generated. 324 Oldfield, 0 Emsley, 324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 648 Ramachandran restraints generated. 324 Oldfield, 0 Emsley, 324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 25 residues out of total 272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 23 time to evaluate : 0.234 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 24 average time/residue: 0.3765 time to fit residues: 10.8343 Evaluate side-chains 24 residues out of total 272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 22 time to evaluate : 0.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 71 ASP Chi-restraints excluded: chain P residue 320 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 12 optimal weight: 4.9990 chunk 16 optimal weight: 10.0000 chunk 49 optimal weight: 10.0000 chunk 42 optimal weight: 9.9990 chunk 40 optimal weight: 8.9990 chunk 32 optimal weight: 8.9990 chunk 10 optimal weight: 2.9990 chunk 30 optimal weight: 0.3980 chunk 21 optimal weight: 5.9990 chunk 39 optimal weight: 6.9990 chunk 7 optimal weight: 3.9990 overall best weight: 3.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.143651 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.111845 restraints weight = 27803.449| |-----------------------------------------------------------------------------| r_work (start): 0.3339 rms_B_bonded: 1.27 r_work: 0.3051 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3051 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 moved from start: 0.2490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 9239 Z= 0.234 Angle : 0.625 5.854 13808 Z= 0.349 Chirality : 0.039 0.213 1722 Planarity : 0.007 0.053 751 Dihedral : 15.872 179.625 3643 Min Nonbonded Distance : 1.777 Molprobity Statistics. All-atom Clashscore : 2.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 1.48 % Allowed : 9.63 % Favored : 88.89 % 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 are not related in a simple way. whole: 0.08 (0.46), residues: 324 helix: 1.32 (0.50), residues: 98 sheet: -0.45 (0.51), residues: 100 loop : -0.37 (0.55), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG P 79 TYR 0.011 0.002 TYR P 46 PHE 0.013 0.001 PHE P 135 TRP 0.010 0.002 TRP P 343 HIS 0.005 0.002 HIS P 165 Details of bonding type rmsd/Z covalent geometry : bond 0.00463 / 0.23 ( 9239) covalent geometry : angle 0.62522 / 0.35 (13808) hydrogen bonds : bond 0.05516 / 3.68 ( 401) hydrogen bonds : angle 3.23692 / 2.36 ( 856) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 648 Ramachandran restraints generated. 324 Oldfield, 0 Emsley, 324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 648 Ramachandran restraints generated. 324 Oldfield, 0 Emsley, 324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 30 residues out of total 272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 26 time to evaluate : 0.251 Fit side-chains REVERT: P 47 ILE cc_start: 0.8798 (OUTLIER) cc_final: 0.8553 (mt) outliers start: 4 outliers final: 3 residues processed: 29 average time/residue: 0.3546 time to fit residues: 12.2395 Evaluate side-chains 29 residues out of total 272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 25 time to evaluate : 0.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 47 ILE Chi-restraints excluded: chain P residue 71 ASP Chi-restraints excluded: chain P residue 320 ASP Chi-restraints excluded: chain P residue 328 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 13 optimal weight: 3.9990 chunk 5 optimal weight: 0.7980 chunk 36 optimal weight: 10.0000 chunk 22 optimal weight: 0.7980 chunk 37 optimal weight: 9.9990 chunk 21 optimal weight: 0.8980 chunk 41 optimal weight: 10.0000 chunk 0 optimal weight: 5.9990 chunk 9 optimal weight: 3.9990 chunk 11 optimal weight: 0.0980 chunk 2 optimal weight: 2.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.146023 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.113825 restraints weight = 27786.753| |-----------------------------------------------------------------------------| r_work (start): 0.3368 rms_B_bonded: 1.28 r_work: 0.3088 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3088 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 moved from start: 0.2536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 9239 Z= 0.132 Angle : 0.570 5.112 13808 Z= 0.324 Chirality : 0.036 0.169 1722 Planarity : 0.006 0.050 751 Dihedral : 15.790 179.145 3643 Min Nonbonded Distance : 1.859 Molprobity Statistics. All-atom Clashscore : 2.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 0.74 % Allowed : 10.74 % Favored : 88.52 % 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 are not related in a simple way. whole: 0.37 (0.47), residues: 324 helix: 1.60 (0.52), residues: 98 sheet: -0.35 (0.51), residues: 100 loop : -0.17 (0.57), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG P 79 TYR 0.009 0.001 TYR P 46 PHE 0.012 0.001 PHE P 135 TRP 0.007 0.001 TRP P 343 HIS 0.002 0.001 HIS P 165 Details of bonding type rmsd/Z covalent geometry : bond 0.00230 / 0.13 ( 9239) covalent geometry : angle 0.56991 / 0.32 (13808) hydrogen bonds : bond 0.04849 / 3.30 ( 401) hydrogen bonds : angle 3.10118 / 2.26 ( 856) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 648 Ramachandran restraints generated. 324 Oldfield, 0 Emsley, 324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 648 Ramachandran restraints generated. 324 Oldfield, 0 Emsley, 324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 28 residues out of total 272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 26 time to evaluate : 0.263 Fit side-chains revert: symmetry clash outliers start: 2 outliers final: 2 residues processed: 27 average time/residue: 0.4097 time to fit residues: 13.0375 Evaluate side-chains 28 residues out of total 272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 26 time to evaluate : 0.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 71 ASP Chi-restraints excluded: chain P residue 328 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 35 optimal weight: 20.0000 chunk 8 optimal weight: 3.9990 chunk 3 optimal weight: 3.9990 chunk 24 optimal weight: 4.9990 chunk 14 optimal weight: 0.2980 chunk 17 optimal weight: 5.9990 chunk 5 optimal weight: 0.9990 chunk 30 optimal weight: 0.0170 chunk 53 optimal weight: 8.9990 chunk 9 optimal weight: 1.9990 chunk 45 optimal weight: 5.9990 overall best weight: 1.4624 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.146676 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.114951 restraints weight = 27846.422| |-----------------------------------------------------------------------------| r_work (start): 0.3385 rms_B_bonded: 1.25 r_work: 0.3104 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.2628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 9239 Z= 0.129 Angle : 0.548 4.695 13808 Z= 0.313 Chirality : 0.035 0.168 1722 Planarity : 0.005 0.049 751 Dihedral : 15.697 178.101 3643 Min Nonbonded Distance : 1.783 Molprobity Statistics. All-atom Clashscore : 2.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 1.11 % Allowed : 10.00 % Favored : 88.89 % 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 are not related in a simple way. whole: 0.66 (0.47), residues: 324 helix: 1.90 (0.52), residues: 98 sheet: -0.22 (0.51), residues: 98 loop : -0.04 (0.57), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG P 79 TYR 0.009 0.001 TYR P 46 PHE 0.008 0.001 PHE P 135 TRP 0.007 0.001 TRP P 343 HIS 0.002 0.001 HIS P 165 Details of bonding type rmsd/Z covalent geometry : bond 0.00225 / 0.13 ( 9239) covalent geometry : angle 0.54787 / 0.31 (13808) hydrogen bonds : bond 0.04719 / 3.21 ( 401) hydrogen bonds : angle 3.07287 / 2.24 ( 856) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 648 Ramachandran restraints generated. 324 Oldfield, 0 Emsley, 324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 648 Ramachandran restraints generated. 324 Oldfield, 0 Emsley, 324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 30 residues out of total 272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 27 time to evaluate : 0.268 Fit side-chains revert: symmetry clash REVERT: P 47 ILE cc_start: 0.8737 (OUTLIER) cc_final: 0.8487 (mt) outliers start: 3 outliers final: 2 residues processed: 29 average time/residue: 0.4168 time to fit residues: 14.2563 Evaluate side-chains 29 residues out of total 272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 26 time to evaluate : 0.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 47 ILE Chi-restraints excluded: chain P residue 71 ASP Chi-restraints excluded: chain P residue 328 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 16 optimal weight: 10.0000 chunk 28 optimal weight: 0.3980 chunk 6 optimal weight: 6.9990 chunk 56 optimal weight: 9.9990 chunk 41 optimal weight: 9.9990 chunk 19 optimal weight: 4.9990 chunk 5 optimal weight: 0.9980 chunk 13 optimal weight: 3.9990 chunk 4 optimal weight: 0.7980 chunk 33 optimal weight: 5.9990 chunk 48 optimal weight: 8.9990 overall best weight: 2.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.145647 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.113426 restraints weight = 27837.161| |-----------------------------------------------------------------------------| r_work (start): 0.3365 rms_B_bonded: 1.26 r_work: 0.3089 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.2784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9239 Z= 0.157 Angle : 0.549 4.708 13808 Z= 0.312 Chirality : 0.035 0.165 1722 Planarity : 0.005 0.047 751 Dihedral : 15.699 178.877 3643 Min Nonbonded Distance : 1.813 Molprobity Statistics. All-atom Clashscore : 2.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 0.74 % Allowed : 10.37 % Favored : 88.89 % 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 are not related in a simple way. whole: 0.62 (0.47), residues: 324 helix: 1.92 (0.51), residues: 98 sheet: -0.26 (0.50), residues: 98 loop : -0.09 (0.57), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG P 79 TYR 0.009 0.001 TYR P 127 PHE 0.013 0.001 PHE P 135 TRP 0.005 0.001 TRP P 289 HIS 0.002 0.001 HIS P 165 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.16 ( 9239) covalent geometry : angle 0.54887 / 0.31 (13808) hydrogen bonds : bond 0.04872 / 3.29 ( 401) hydrogen bonds : angle 3.05637 / 2.24 ( 856) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 648 Ramachandran restraints generated. 324 Oldfield, 0 Emsley, 324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 648 Ramachandran restraints generated. 324 Oldfield, 0 Emsley, 324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 27 residues out of total 272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 25 time to evaluate : 0.247 Fit side-chains revert: symmetry clash REVERT: P 47 ILE cc_start: 0.8734 (OUTLIER) cc_final: 0.8491 (mt) outliers start: 2 outliers final: 1 residues processed: 26 average time/residue: 0.4365 time to fit residues: 13.2557 Evaluate side-chains 27 residues out of total 272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 25 time to evaluate : 0.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 47 ILE Chi-restraints excluded: chain P residue 71 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 12 optimal weight: 2.9990 chunk 55 optimal weight: 10.0000 chunk 33 optimal weight: 5.9990 chunk 43 optimal weight: 7.9990 chunk 15 optimal weight: 4.9990 chunk 44 optimal weight: 6.9990 chunk 21 optimal weight: 1.9990 chunk 47 optimal weight: 8.9990 chunk 54 optimal weight: 10.0000 chunk 49 optimal weight: 10.0000 chunk 52 optimal weight: 5.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.143148 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.110808 restraints weight = 27725.161| |-----------------------------------------------------------------------------| r_work (start): 0.3324 rms_B_bonded: 1.29 r_work: 0.3049 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3049 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 moved from start: 0.2885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 9239 Z= 0.267 Angle : 0.633 5.756 13808 Z= 0.348 Chirality : 0.039 0.183 1722 Planarity : 0.007 0.063 751 Dihedral : 15.880 179.866 3643 Min Nonbonded Distance : 1.728 Molprobity Statistics. All-atom Clashscore : 2.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 1.11 % Allowed : 10.37 % Favored : 88.52 % 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 are not related in a simple way. whole: 0.23 (0.46), residues: 324 helix: 1.57 (0.50), residues: 98 sheet: -0.41 (0.51), residues: 98 loop : -0.36 (0.55), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG P 79 TYR 0.012 0.002 TYR P 46 PHE 0.015 0.002 PHE P 135 TRP 0.008 0.002 TRP P 289 HIS 0.004 0.002 HIS P 242 Details of bonding type rmsd/Z covalent geometry : bond 0.00534 / 0.27 ( 9239) covalent geometry : angle 0.63287 / 0.35 (13808) hydrogen bonds : bond 0.05731 / 3.80 ( 401) hydrogen bonds : angle 3.14382 / 2.28 ( 856) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 648 Ramachandran restraints generated. 324 Oldfield, 0 Emsley, 324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 648 Ramachandran restraints generated. 324 Oldfield, 0 Emsley, 324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 28 residues out of total 272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 25 time to evaluate : 0.245 Fit side-chains REVERT: P 47 ILE cc_start: 0.8776 (OUTLIER) cc_final: 0.8545 (mt) outliers start: 3 outliers final: 2 residues processed: 27 average time/residue: 0.4256 time to fit residues: 13.5807 Evaluate side-chains 27 residues out of total 272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 24 time to evaluate : 0.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 47 ILE Chi-restraints excluded: chain P residue 71 ASP Chi-restraints excluded: chain P residue 328 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 57 optimal weight: 10.0000 chunk 49 optimal weight: 10.0000 chunk 5 optimal weight: 0.9990 chunk 11 optimal weight: 0.3980 chunk 24 optimal weight: 2.9990 chunk 31 optimal weight: 0.1980 chunk 25 optimal weight: 0.9980 chunk 28 optimal weight: 2.9990 chunk 46 optimal weight: 7.9990 chunk 16 optimal weight: 5.9990 chunk 56 optimal weight: 10.0000 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.146351 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.114566 restraints weight = 27834.488| |-----------------------------------------------------------------------------| r_work (start): 0.3381 rms_B_bonded: 1.22 r_work: 0.3107 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3107 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 moved from start: 0.2937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 9239 Z= 0.124 Angle : 0.531 4.297 13808 Z= 0.303 Chirality : 0.034 0.167 1722 Planarity : 0.006 0.072 751 Dihedral : 15.737 179.121 3643 Min Nonbonded Distance : 1.865 Molprobity Statistics. All-atom Clashscore : 2.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 0.74 % Allowed : 10.37 % Favored : 88.89 % 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 are not related in a simple way. whole: 0.57 (0.47), residues: 324 helix: 1.86 (0.51), residues: 98 sheet: -0.22 (0.51), residues: 98 loop : -0.17 (0.57), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG P 79 TYR 0.007 0.001 TYR P 46 PHE 0.007 0.001 PHE P 135 TRP 0.009 0.001 TRP P 343 HIS 0.002 0.001 HIS P 165 Details of bonding type rmsd/Z covalent geometry : bond 0.00219 / 0.12 ( 9239) covalent geometry : angle 0.53058 / 0.30 (13808) hydrogen bonds : bond 0.04677 / 3.20 ( 401) hydrogen bonds : angle 3.02439 / 2.20 ( 856) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3124.48 seconds wall clock time: 53 minutes 46.11 seconds (3226.11 seconds total)