Starting phenix.real_space_refine on Wed Jul 1 22:26:03 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9iub_60896/07_2026/9iub_60896.cif Found real_map, /net/cci-nas-00/data/ceres_data/9iub_60896/07_2026/9iub_60896.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.08 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9iub_60896/07_2026/9iub_60896.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9iub_60896/07_2026/9iub_60896.map" model { file = "/net/cci-nas-00/data/ceres_data/9iub_60896/07_2026/9iub_60896.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9iub_60896/07_2026/9iub_60896.cif" } resolution = 3.08 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= 0.046 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: 6 Type Number sf(0) Gaussians Zn 1 6.06 5 P 44 5.49 5 S 10 5.16 5 C 1968 2.51 5 N 622 2.21 5 O 701 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 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: 3346 Number of models: 1 Model: "" Number of chains: 4 Chain: "G2" Number of atoms: 447 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 447 Classifications: {'DNA': 22} Link IDs: {'rna3p': 21} Chain: "H2" Number of atoms: 455 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 455 Classifications: {'DNA': 22} Link IDs: {'rna3p': 21} Chain: "D" Number of atoms: 2443 Number of conformers: 1 Conformer: "" Number of residues, atoms: 304, 2443 Classifications: {'peptide': 304} Link IDs: {'PTRANS': 19, 'TRANS': 284} Chain breaks: 5 Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2320 SG CYS D 304 42.983 25.595 37.022 1.00166.48 S ATOM 2338 SG CYS D 307 43.487 28.501 34.758 1.00166.00 S ATOM 2489 SG CYS D 326 40.592 28.401 36.037 1.00159.94 S ATOM 2561 SG CYS D 335 41.262 25.414 33.741 1.00167.81 S Time building chain proxies: 1.04, per 1000 atoms: 0.31 Number of scatterers: 3346 At special positions: 0 Unit cell: (79.9564, 83.4839, 81.1323, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 1 29.99 S 10 16.00 P 44 15.00 O 701 8.00 N 622 7.00 C 1968 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.33 Conformation dependent library (CDL) restraints added in 93.9 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D1000 " pdb="ZN ZN D1000 " - pdb=" SG CYS D 335 " pdb="ZN ZN D1000 " - pdb=" SG CYS D 304 " pdb="ZN ZN D1000 " - pdb=" SG CYS D 326 " pdb="ZN ZN D1000 " - pdb=" SG CYS D 307 " Number of angles added : 6 584 Ramachandran restraints generated. 292 Oldfield, 0 Emsley, 292 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 560 Finding SS restraints... Secondary structure from input PDB file: 12 helices and 6 sheets defined 40.8% alpha, 14.8% beta 22 base pairs and 35 stacking pairs defined. Time for finding SS restraints: 0.59 Creating SS restraints... Processing helix chain 'D' and resid 58 through 66 removed outlier: 3.658A pdb=" N TRP D 64 " --> pdb=" O ASN D 60 " (cutoff:3.500A) Processing helix chain 'D' and resid 177 through 193 Processing helix chain 'D' and resid 197 through 208 Processing helix chain 'D' and resid 212 through 221 Processing helix chain 'D' and resid 231 through 240 Processing helix chain 'D' and resid 241 through 245 Processing helix chain 'D' and resid 271 through 283 Processing helix chain 'D' and resid 328 through 331 Processing helix chain 'D' and resid 342 through 358 Processing helix chain 'D' and resid 439 through 446 Processing helix chain 'D' and resid 447 through 458 Processing helix chain 'D' and resid 478 through 484 Processing sheet with id=AA1, first strand: chain 'D' and resid 7 through 9 removed outlier: 6.509A pdb=" N ILE D 7 " --> pdb=" O ASP D 43 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'D' and resid 163 through 164 Processing sheet with id=AA3, first strand: chain 'D' and resid 253 through 255 removed outlier: 5.551A pdb=" N ALA D 248 " --> pdb=" O VAL D 255 " (cutoff:3.500A) removed outlier: 5.737A pdb=" N LEU D 263 " --> pdb=" O ALA D 248 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 302 through 304 Processing sheet with id=AA5, first strand: chain 'D' and resid 311 through 314 Processing sheet with id=AA6, first strand: chain 'D' and resid 361 through 368 removed outlier: 7.053A pdb=" N ARG D 362 " --> pdb=" O THR D 435 " (cutoff:3.500A) 104 hydrogen bonds defined for protein. 282 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 58 hydrogen bonds 116 hydrogen bond angles 0 basepair planarities 22 basepair parallelities 35 stacking parallelities Total time for adding SS restraints: 0.59 Time building geometry restraints manager: 0.43 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: 750 1.34 - 1.46: 1133 1.46 - 1.57: 1526 1.57 - 1.69: 86 1.69 - 1.81: 15 Bond restraints: 3510 Sorted by residual: bond pdb=" N1 DCG2 28 " pdb=" C6 DCG2 28 " ideal model delta sigma weight residual 1.367 1.344 0.023 6.00e-03 2.78e+04 1.43e+01 bond pdb=" N1 DCG2 31 " pdb=" C6 DCG2 31 " ideal model delta sigma weight residual 1.367 1.346 0.021 6.00e-03 2.78e+04 1.17e+01 bond pdb=" N1 DCG2 27 " pdb=" C6 DCG2 27 " ideal model delta sigma weight residual 1.367 1.350 0.017 6.00e-03 2.78e+04 7.64e+00 bond pdb=" CA SER D 157 " pdb=" CB SER D 157 " ideal model delta sigma weight residual 1.530 1.485 0.046 1.69e-02 3.50e+03 7.31e+00 bond pdb=" CA PRO D 159 " pdb=" CB PRO D 159 " ideal model delta sigma weight residual 1.539 1.517 0.023 9.30e-03 1.16e+04 5.97e+00 ... (remaining 3505 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.11: 4611 3.11 - 6.22: 284 6.22 - 9.33: 37 9.33 - 12.44: 2 12.44 - 15.56: 1 Bond angle restraints: 4935 Sorted by residual: angle pdb=" N ARG D 323 " pdb=" CA ARG D 323 " pdb=" CB ARG D 323 " ideal model delta sigma weight residual 111.53 95.97 15.56 1.86e+00 2.89e-01 6.99e+01 angle pdb=" CA HIS D 199 " pdb=" CB HIS D 199 " pdb=" CG HIS D 199 " ideal model delta sigma weight residual 113.80 122.05 -8.25 1.00e+00 1.00e+00 6.81e+01 angle pdb=" O5' DTG2 30 " pdb=" C5' DTG2 30 " pdb=" C4' DTG2 30 " ideal model delta sigma weight residual 109.40 115.97 -6.57 8.00e-01 1.56e+00 6.75e+01 angle pdb=" O3' DCG2 34 " pdb=" P DAG2 35 " pdb=" O5' DAG2 35 " ideal model delta sigma weight residual 104.00 93.25 10.75 1.50e+00 4.44e-01 5.13e+01 angle pdb=" O4' DCH2 18 " pdb=" C1' DCH2 18 " pdb=" C2' DCH2 18 " ideal model delta sigma weight residual 105.90 100.78 5.12 8.00e-01 1.56e+00 4.10e+01 ... (remaining 4930 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.85: 1541 17.85 - 35.70: 227 35.70 - 53.54: 154 53.54 - 71.39: 36 71.39 - 89.24: 6 Dihedral angle restraints: 1964 sinusoidal: 1098 harmonic: 866 Sorted by residual: dihedral pdb=" CA LEU D 282 " pdb=" C LEU D 282 " pdb=" N VAL D 283 " pdb=" CA VAL D 283 " ideal model delta harmonic sigma weight residual -180.00 -146.75 -33.25 0 5.00e+00 4.00e-02 4.42e+01 dihedral pdb=" N ARG D 323 " pdb=" C ARG D 323 " pdb=" CA ARG D 323 " pdb=" CB ARG D 323 " ideal model delta harmonic sigma weight residual 122.80 108.64 14.16 0 2.50e+00 1.60e-01 3.21e+01 dihedral pdb=" CD ARG D 58 " pdb=" NE ARG D 58 " pdb=" CZ ARG D 58 " pdb=" NH1 ARG D 58 " ideal model delta sinusoidal sigma weight residual 0.00 36.44 -36.44 1 1.00e+01 1.00e-02 1.88e+01 ... (remaining 1961 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.130: 472 0.130 - 0.260: 52 0.260 - 0.390: 5 0.390 - 0.520: 1 0.520 - 0.649: 1 Chirality restraints: 531 Sorted by residual: chirality pdb=" P DCH2 1 " pdb=" OP1 DCH2 1 " pdb=" OP2 DCH2 1 " pdb=" O5' DCH2 1 " both_signs ideal model delta sigma weight residual True 2.34 -2.98 -0.65 2.00e-01 2.50e+01 1.05e+01 chirality pdb=" P DCG2 31 " pdb=" OP1 DCG2 31 " pdb=" OP2 DCG2 31 " pdb=" O5' DCG2 31 " both_signs ideal model delta sigma weight residual True 2.34 -2.81 -0.47 2.00e-01 2.50e+01 5.62e+00 chirality pdb=" P DCG2 25 " pdb=" OP1 DCG2 25 " pdb=" OP2 DCG2 25 " pdb=" O5' DCG2 25 " both_signs ideal model delta sigma weight residual True 2.34 2.68 -0.35 2.00e-01 2.50e+01 3.03e+00 ... (remaining 528 not shown) Planarity restraints: 485 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG D 58 " 0.545 9.50e-02 1.11e+02 2.45e-01 4.11e+01 pdb=" NE ARG D 58 " -0.045 2.00e-02 2.50e+03 pdb=" CZ ARG D 58 " 0.030 2.00e-02 2.50e+03 pdb=" NH1 ARG D 58 " -0.016 2.00e-02 2.50e+03 pdb=" NH2 ARG D 58 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DGG2 29 " 0.062 2.00e-02 2.50e+03 2.62e-02 2.06e+01 pdb=" N9 DGG2 29 " -0.052 2.00e-02 2.50e+03 pdb=" C8 DGG2 29 " -0.006 2.00e-02 2.50e+03 pdb=" N7 DGG2 29 " -0.014 2.00e-02 2.50e+03 pdb=" C5 DGG2 29 " 0.011 2.00e-02 2.50e+03 pdb=" C6 DGG2 29 " 0.020 2.00e-02 2.50e+03 pdb=" O6 DGG2 29 " 0.015 2.00e-02 2.50e+03 pdb=" N1 DGG2 29 " 0.005 2.00e-02 2.50e+03 pdb=" C2 DGG2 29 " -0.021 2.00e-02 2.50e+03 pdb=" N2 DGG2 29 " 0.003 2.00e-02 2.50e+03 pdb=" N3 DGG2 29 " -0.008 2.00e-02 2.50e+03 pdb=" C4 DGG2 29 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DGH2 16 " -0.058 2.00e-02 2.50e+03 2.43e-02 1.77e+01 pdb=" N9 DGH2 16 " 0.042 2.00e-02 2.50e+03 pdb=" C8 DGH2 16 " -0.001 2.00e-02 2.50e+03 pdb=" N7 DGH2 16 " 0.006 2.00e-02 2.50e+03 pdb=" C5 DGH2 16 " 0.015 2.00e-02 2.50e+03 pdb=" C6 DGH2 16 " -0.010 2.00e-02 2.50e+03 pdb=" O6 DGH2 16 " -0.013 2.00e-02 2.50e+03 pdb=" N1 DGH2 16 " -0.024 2.00e-02 2.50e+03 pdb=" C2 DGH2 16 " -0.001 2.00e-02 2.50e+03 pdb=" N2 DGH2 16 " 0.006 2.00e-02 2.50e+03 pdb=" N3 DGH2 16 " 0.024 2.00e-02 2.50e+03 pdb=" C4 DGH2 16 " 0.014 2.00e-02 2.50e+03 ... (remaining 482 not shown) Histogram of nonbonded interaction distances: 1.61 - 2.27: 2 2.27 - 2.93: 1211 2.93 - 3.59: 5006 3.59 - 4.24: 8562 4.24 - 4.90: 13047 Nonbonded interactions: 27828 Sorted by model distance: nonbonded pdb=" P DCG2 25 " pdb=" OG SER D 10 " model vdw 1.614 3.400 nonbonded pdb=" N LEU D 363 " pdb=" OH TYR D 482 " model vdw 2.117 3.120 nonbonded pdb=" OP2 DAG2 35 " pdb=" OH TYR D 312 " model vdw 2.336 3.040 nonbonded pdb=" OD2 ASP D 204 " pdb=" NH1 ARG D 208 " model vdw 2.392 3.120 nonbonded pdb=" O5' DCG2 31 " pdb=" O4' DCG2 31 " model vdw 2.404 2.432 ... (remaining 27823 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: 1.390 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.070 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 6.480 Find NCS groups from input model: 0.010 Set up NCS constraints: 0.000 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 8.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5186 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 : 0.009 0.082 3514 Z= 0.630 Angle : 1.673 21.849 4941 Z= 1.103 Chirality : 0.089 0.649 531 Planarity : 0.021 0.245 485 Dihedral : 22.239 89.237 1404 Min Nonbonded Distance : 1.614 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 4.33 % Allowed : 5.91 % Favored : 89.76 % Cbeta Deviations : 0.71 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.36 % 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: 0.16 (0.47), residues: 292 helix: 0.13 (0.45), residues: 113 sheet: 0.08 (0.77), residues: 44 loop : 0.30 (0.55), residues: 135 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.037 0.004 ARG D 58 TYR 0.019 0.005 TYR D 188 PHE 0.022 0.005 PHE D 439 TRP 0.031 0.004 TRP D 432 HIS 0.025 0.006 HIS D 199 Details of bonding type rmsd/Z covalent geometry : bond 0.00921 / 0.63 ( 3510) covalent geometry : angle 1.63391 / 1.10 ( 4935) hydrogen bonds : bond 0.16093 / 16.69 ( 162) hydrogen bonds : angle 6.21066 / 8.00 ( 398) metal coordination : bond 0.05617 / 3.15 ( 4) metal coordination : angle 10.38354 / 23.35 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 584 Ramachandran restraints generated. 292 Oldfield, 0 Emsley, 292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 584 Ramachandran restraints generated. 292 Oldfield, 0 Emsley, 292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 67 time to evaluate : 0.120 Fit side-chains revert: symmetry clash REVERT: D 40 VAL cc_start: 0.6795 (t) cc_final: 0.6530 (t) REVERT: D 163 TYR cc_start: 0.6263 (m-80) cc_final: 0.5955 (m-80) REVERT: D 254 THR cc_start: 0.7859 (OUTLIER) cc_final: 0.7447 (m) REVERT: D 287 ARG cc_start: 0.4443 (OUTLIER) cc_final: 0.4195 (ppt170) REVERT: D 313 LYS cc_start: 0.6835 (ttpp) cc_final: 0.6505 (tttt) REVERT: D 361 GLU cc_start: 0.6434 (OUTLIER) cc_final: 0.5655 (pm20) REVERT: D 444 ARG cc_start: 0.6828 (mtt90) cc_final: 0.6551 (mtt90) REVERT: D 472 ARG cc_start: 0.7067 (mtm180) cc_final: 0.6810 (ptm160) REVERT: D 473 THR cc_start: 0.5764 (m) cc_final: 0.5135 (p) outliers start: 11 outliers final: 3 residues processed: 74 average time/residue: 0.0824 time to fit residues: 7.1218 Evaluate side-chains 49 residues out of total 254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 43 time to evaluate : 0.100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 10 SER Chi-restraints excluded: chain D residue 254 THR Chi-restraints excluded: chain D residue 287 ARG Chi-restraints excluded: chain D residue 361 GLU Chi-restraints excluded: chain D residue 463 THR Chi-restraints excluded: chain D residue 466 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 34 random chunks: chunk 24 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 2 optimal weight: 10.0000 chunk 16 optimal weight: 0.5980 chunk 32 optimal weight: 1.9990 chunk 31 optimal weight: 0.9990 chunk 25 optimal weight: 0.9980 chunk 19 optimal weight: 0.9980 chunk 30 optimal weight: 5.9990 chunk 22 optimal weight: 0.8980 chunk 13 optimal weight: 0.8980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 189 HIS D 194 ASN D 452 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.177069 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.144636 restraints weight = 3252.586| |-----------------------------------------------------------------------------| r_work (start): 0.3641 rms_B_bonded: 1.37 r_work: 0.3286 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3286 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8308 moved from start: 0.1963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 3514 Z= 0.206 Angle : 0.737 9.844 4941 Z= 0.409 Chirality : 0.050 0.203 531 Planarity : 0.007 0.078 485 Dihedral : 25.835 88.526 816 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 6.30 % Allowed : 8.66 % Favored : 85.04 % 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: 0.74 (0.49), residues: 292 helix: 0.83 (0.47), residues: 119 sheet: -0.52 (0.78), residues: 42 loop : 0.77 (0.57), residues: 131 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 58 TYR 0.013 0.002 TYR D 482 PHE 0.015 0.002 PHE D 464 TRP 0.010 0.002 TRP D 161 HIS 0.008 0.002 HIS D 199 Details of bonding type rmsd/Z covalent geometry : bond 0.00431 / 0.21 ( 3510) covalent geometry : angle 0.71179 / 0.41 ( 4935) hydrogen bonds : bond 0.05317 / 5.27 ( 162) hydrogen bonds : angle 4.45076 / 5.89 ( 398) metal coordination : bond 0.01409 / 1.26 ( 4) metal coordination : angle 5.57734 / 11.25 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 584 Ramachandran restraints generated. 292 Oldfield, 0 Emsley, 292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 584 Ramachandran restraints generated. 292 Oldfield, 0 Emsley, 292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 42 time to evaluate : 0.105 Fit side-chains revert: symmetry clash REVERT: D 163 TYR cc_start: 0.8497 (m-80) cc_final: 0.7993 (m-80) REVERT: D 265 ARG cc_start: 0.8039 (ttp-170) cc_final: 0.7646 (ttp-170) REVERT: D 282 LEU cc_start: 0.8056 (OUTLIER) cc_final: 0.7829 (mt) REVERT: D 361 GLU cc_start: 0.7467 (OUTLIER) cc_final: 0.6558 (pm20) REVERT: D 473 THR cc_start: 0.8152 (m) cc_final: 0.7753 (p) REVERT: D 480 GLN cc_start: 0.7341 (mt0) cc_final: 0.7089 (mp10) outliers start: 16 outliers final: 8 residues processed: 55 average time/residue: 0.0937 time to fit residues: 6.0460 Evaluate side-chains 50 residues out of total 254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 40 time to evaluate : 0.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 10 SER Chi-restraints excluded: chain D residue 282 LEU Chi-restraints excluded: chain D residue 287 ARG Chi-restraints excluded: chain D residue 328 SER Chi-restraints excluded: chain D residue 351 GLU Chi-restraints excluded: chain D residue 354 LEU Chi-restraints excluded: chain D residue 361 GLU Chi-restraints excluded: chain D residue 441 ASP Chi-restraints excluded: chain D residue 453 THR Chi-restraints excluded: chain D residue 463 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 34 random chunks: chunk 24 optimal weight: 10.0000 chunk 3 optimal weight: 4.9990 chunk 7 optimal weight: 0.7980 chunk 21 optimal weight: 0.5980 chunk 10 optimal weight: 0.9990 chunk 17 optimal weight: 5.9990 chunk 28 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 26 optimal weight: 0.7980 chunk 30 optimal weight: 3.9990 chunk 23 optimal weight: 0.7980 overall best weight: 0.7982 ------------------------------------------------------------------------------- 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 = 0.3951 r_free = 0.3951 target = 0.177146 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.134396 restraints weight = 3264.108| |-----------------------------------------------------------------------------| r_work (start): 0.3496 rms_B_bonded: 1.24 r_work: 0.3302 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3167 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8363 moved from start: 0.2579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.022 3514 Z= 0.175 Angle : 0.626 6.833 4941 Z= 0.353 Chirality : 0.043 0.170 531 Planarity : 0.006 0.062 485 Dihedral : 26.719 88.144 814 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 3.94 % Allowed : 11.02 % Favored : 85.04 % 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: 0.68 (0.51), residues: 292 helix: 0.93 (0.49), residues: 119 sheet: -1.57 (0.72), residues: 44 loop : 1.03 (0.59), residues: 129 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 11 TYR 0.019 0.003 TYR D 482 PHE 0.015 0.002 PHE D 464 TRP 0.009 0.001 TRP D 230 HIS 0.006 0.001 HIS D 199 Details of bonding type rmsd/Z covalent geometry : bond 0.00351 / 0.17 ( 3510) covalent geometry : angle 0.61961 / 0.35 ( 4935) hydrogen bonds : bond 0.05044 / 5.29 ( 162) hydrogen bonds : angle 4.27346 / 5.77 ( 398) metal coordination : bond 0.00830 / 0.58 ( 4) metal coordination : angle 2.68371 / 5.50 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 584 Ramachandran restraints generated. 292 Oldfield, 0 Emsley, 292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 584 Ramachandran restraints generated. 292 Oldfield, 0 Emsley, 292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 41 time to evaluate : 0.063 Fit side-chains REVERT: D 163 TYR cc_start: 0.8580 (m-80) cc_final: 0.7743 (m-80) REVERT: D 229 GLU cc_start: 0.8656 (pt0) cc_final: 0.8452 (pt0) REVERT: D 287 ARG cc_start: 0.6994 (OUTLIER) cc_final: 0.4588 (ptm160) REVERT: D 473 THR cc_start: 0.8197 (m) cc_final: 0.7747 (p) REVERT: D 480 GLN cc_start: 0.7595 (mt0) cc_final: 0.7293 (mp10) outliers start: 10 outliers final: 5 residues processed: 48 average time/residue: 0.0812 time to fit residues: 4.5628 Evaluate side-chains 41 residues out of total 254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 35 time to evaluate : 0.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 287 ARG Chi-restraints excluded: chain D residue 301 VAL Chi-restraints excluded: chain D residue 328 SER Chi-restraints excluded: chain D residue 351 GLU Chi-restraints excluded: chain D residue 453 THR Chi-restraints excluded: chain D residue 463 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 34 random chunks: chunk 5 optimal weight: 2.9990 chunk 14 optimal weight: 1.9990 chunk 25 optimal weight: 0.0970 chunk 27 optimal weight: 2.9990 chunk 1 optimal weight: 5.9990 chunk 9 optimal weight: 0.8980 chunk 18 optimal weight: 0.8980 chunk 19 optimal weight: 0.5980 chunk 2 optimal weight: 10.0000 chunk 13 optimal weight: 0.7980 chunk 31 optimal weight: 0.7980 overall best weight: 0.6378 ------------------------------------------------------------------------------- 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 = 0.3955 r_free = 0.3955 target = 0.176982 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.135555 restraints weight = 3242.356| |-----------------------------------------------------------------------------| r_work (start): 0.3496 rms_B_bonded: 1.22 r_work: 0.3330 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3192 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.3192 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8332 moved from start: 0.2834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3514 Z= 0.156 Angle : 0.592 6.606 4941 Z= 0.337 Chirality : 0.041 0.155 531 Planarity : 0.005 0.052 485 Dihedral : 26.559 86.656 810 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 3.94 % Allowed : 11.81 % Favored : 84.25 % 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: 0.59 (0.51), residues: 292 helix: 0.95 (0.49), residues: 120 sheet: -1.76 (0.70), residues: 44 loop : 0.93 (0.59), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 472 TYR 0.014 0.002 TYR D 482 PHE 0.013 0.001 PHE D 464 TRP 0.008 0.001 TRP D 230 HIS 0.005 0.001 HIS D 199 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.16 ( 3510) covalent geometry : angle 0.58491 / 0.34 ( 4935) hydrogen bonds : bond 0.04245 / 4.37 ( 162) hydrogen bonds : angle 4.16968 / 5.68 ( 398) metal coordination : bond 0.00602 / 0.44 ( 4) metal coordination : angle 2.62064 / 5.36 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 584 Ramachandran restraints generated. 292 Oldfield, 0 Emsley, 292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 584 Ramachandran restraints generated. 292 Oldfield, 0 Emsley, 292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 37 time to evaluate : 0.101 Fit side-chains REVERT: D 163 TYR cc_start: 0.8556 (m-80) cc_final: 0.7779 (m-80) REVERT: D 287 ARG cc_start: 0.7007 (OUTLIER) cc_final: 0.4744 (ptm160) REVERT: D 480 GLN cc_start: 0.7558 (mt0) cc_final: 0.7281 (mp10) outliers start: 10 outliers final: 8 residues processed: 45 average time/residue: 0.0834 time to fit residues: 4.4295 Evaluate side-chains 41 residues out of total 254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 32 time to evaluate : 0.103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 10 SER Chi-restraints excluded: chain D residue 64 TRP Chi-restraints excluded: chain D residue 187 VAL Chi-restraints excluded: chain D residue 287 ARG Chi-restraints excluded: chain D residue 294 THR Chi-restraints excluded: chain D residue 328 SER Chi-restraints excluded: chain D residue 351 GLU Chi-restraints excluded: chain D residue 453 THR Chi-restraints excluded: chain D residue 463 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 34 random chunks: chunk 15 optimal weight: 0.9990 chunk 0 optimal weight: 4.9990 chunk 27 optimal weight: 2.9990 chunk 21 optimal weight: 0.7980 chunk 25 optimal weight: 0.9980 chunk 24 optimal weight: 5.9990 chunk 29 optimal weight: 0.9990 chunk 7 optimal weight: 0.8980 chunk 33 optimal weight: 0.8980 chunk 28 optimal weight: 3.9990 chunk 16 optimal weight: 0.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 446 GLN D 480 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.174804 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.132596 restraints weight = 3216.423| |-----------------------------------------------------------------------------| r_work (start): 0.3458 rms_B_bonded: 1.24 r_work: 0.3305 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3172 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.3172 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8338 moved from start: 0.3086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 3514 Z= 0.185 Angle : 0.616 6.656 4941 Z= 0.345 Chirality : 0.043 0.171 531 Planarity : 0.005 0.037 485 Dihedral : 26.625 87.061 810 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 5.12 % Allowed : 12.20 % Favored : 82.68 % 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: 0.44 (0.51), residues: 292 helix: 0.91 (0.49), residues: 119 sheet: -2.03 (0.68), residues: 44 loop : 0.83 (0.59), residues: 129 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 8 TYR 0.019 0.002 TYR D 482 PHE 0.015 0.002 PHE D 464 TRP 0.008 0.001 TRP D 230 HIS 0.005 0.001 HIS D 199 Details of bonding type rmsd/Z covalent geometry : bond 0.00384 / 0.18 ( 3510) covalent geometry : angle 0.60894 / 0.34 ( 4935) hydrogen bonds : bond 0.04643 / 4.93 ( 162) hydrogen bonds : angle 4.13401 / 5.65 ( 398) metal coordination : bond 0.00970 / 0.68 ( 4) metal coordination : angle 2.81948 / 5.75 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 584 Ramachandran restraints generated. 292 Oldfield, 0 Emsley, 292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 584 Ramachandran restraints generated. 292 Oldfield, 0 Emsley, 292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 34 time to evaluate : 0.102 Fit side-chains REVERT: D 43 ASP cc_start: 0.7516 (m-30) cc_final: 0.7280 (m-30) REVERT: D 163 TYR cc_start: 0.8588 (m-80) cc_final: 0.7700 (m-80) REVERT: D 287 ARG cc_start: 0.7098 (OUTLIER) cc_final: 0.5128 (ptm160) REVERT: D 313 LYS cc_start: 0.8651 (ttpp) cc_final: 0.8428 (tttt) REVERT: D 480 GLN cc_start: 0.7606 (mt0) cc_final: 0.7282 (mp10) REVERT: D 481 GLU cc_start: 0.7369 (tt0) cc_final: 0.7139 (tt0) outliers start: 13 outliers final: 9 residues processed: 44 average time/residue: 0.0886 time to fit residues: 4.6170 Evaluate side-chains 42 residues out of total 254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 32 time to evaluate : 0.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 10 SER Chi-restraints excluded: chain D residue 64 TRP Chi-restraints excluded: chain D residue 187 VAL Chi-restraints excluded: chain D residue 287 ARG Chi-restraints excluded: chain D residue 294 THR Chi-restraints excluded: chain D residue 301 VAL Chi-restraints excluded: chain D residue 328 SER Chi-restraints excluded: chain D residue 351 GLU Chi-restraints excluded: chain D residue 453 THR Chi-restraints excluded: chain D residue 473 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 34 random chunks: chunk 26 optimal weight: 0.9980 chunk 6 optimal weight: 2.9990 chunk 12 optimal weight: 0.4980 chunk 8 optimal weight: 0.7980 chunk 30 optimal weight: 0.9990 chunk 28 optimal weight: 2.9990 chunk 19 optimal weight: 1.9990 chunk 22 optimal weight: 0.7980 chunk 11 optimal weight: 0.7980 chunk 2 optimal weight: 10.0000 chunk 14 optimal weight: 2.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 = 0.3931 r_free = 0.3931 target = 0.175324 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.145041 restraints weight = 3200.513| |-----------------------------------------------------------------------------| r_work (start): 0.3609 rms_B_bonded: 1.06 r_work: 0.3325 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3194 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.3194 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 moved from start: 0.3280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 3514 Z= 0.162 Angle : 0.571 6.062 4941 Z= 0.326 Chirality : 0.041 0.155 531 Planarity : 0.005 0.033 485 Dihedral : 26.630 87.084 809 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.03 % Favored : 98.97 % Rotamer: Outliers : 4.72 % Allowed : 14.17 % Favored : 81.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.40 (0.51), residues: 292 helix: 1.02 (0.49), residues: 118 sheet: -2.16 (0.68), residues: 44 loop : 0.70 (0.59), residues: 130 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 265 TYR 0.017 0.002 TYR D 482 PHE 0.013 0.001 PHE D 464 TRP 0.008 0.001 TRP D 230 HIS 0.006 0.001 HIS D 199 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.16 ( 3510) covalent geometry : angle 0.56421 / 0.33 ( 4935) hydrogen bonds : bond 0.04143 / 4.33 ( 162) hydrogen bonds : angle 3.99287 / 5.48 ( 398) metal coordination : bond 0.00713 / 0.50 ( 4) metal coordination : angle 2.57847 / 5.03 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 584 Ramachandran restraints generated. 292 Oldfield, 0 Emsley, 292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 584 Ramachandran restraints generated. 292 Oldfield, 0 Emsley, 292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 34 time to evaluate : 0.104 Fit side-chains REVERT: D 163 TYR cc_start: 0.8571 (m-80) cc_final: 0.7706 (m-80) REVERT: D 287 ARG cc_start: 0.7132 (OUTLIER) cc_final: 0.5501 (ptm160) REVERT: D 313 LYS cc_start: 0.8644 (ttpp) cc_final: 0.8430 (tttt) REVERT: D 480 GLN cc_start: 0.7645 (mt0) cc_final: 0.7292 (mp10) REVERT: D 481 GLU cc_start: 0.7528 (tt0) cc_final: 0.7266 (tt0) outliers start: 12 outliers final: 10 residues processed: 44 average time/residue: 0.0873 time to fit residues: 4.5750 Evaluate side-chains 42 residues out of total 254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 31 time to evaluate : 0.103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 10 SER Chi-restraints excluded: chain D residue 64 TRP Chi-restraints excluded: chain D residue 187 VAL Chi-restraints excluded: chain D residue 287 ARG Chi-restraints excluded: chain D residue 294 THR Chi-restraints excluded: chain D residue 301 VAL Chi-restraints excluded: chain D residue 328 SER Chi-restraints excluded: chain D residue 351 GLU Chi-restraints excluded: chain D residue 453 THR Chi-restraints excluded: chain D residue 463 THR Chi-restraints excluded: chain D residue 479 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 34 random chunks: chunk 29 optimal weight: 3.9990 chunk 15 optimal weight: 0.6980 chunk 20 optimal weight: 2.9990 chunk 26 optimal weight: 0.8980 chunk 3 optimal weight: 5.9990 chunk 0 optimal weight: 3.9990 chunk 14 optimal weight: 0.8980 chunk 30 optimal weight: 0.0470 chunk 21 optimal weight: 0.5980 chunk 16 optimal weight: 0.9980 chunk 19 optimal weight: 0.9980 overall best weight: 0.6278 ------------------------------------------------------------------------------- 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 = 0.3916 r_free = 0.3916 target = 0.174271 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.144520 restraints weight = 3316.967| |-----------------------------------------------------------------------------| r_work (start): 0.3605 rms_B_bonded: 1.10 r_work: 0.3334 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3204 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.3204 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8358 moved from start: 0.3437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.018 3514 Z= 0.146 Angle : 0.554 6.167 4941 Z= 0.317 Chirality : 0.040 0.146 531 Planarity : 0.005 0.033 485 Dihedral : 26.536 85.444 809 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 4.72 % Allowed : 14.57 % Favored : 80.71 % 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 (0.52), residues: 292 helix: 1.21 (0.50), residues: 118 sheet: -2.11 (0.70), residues: 44 loop : 0.75 (0.60), residues: 130 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 461 TYR 0.017 0.002 TYR D 482 PHE 0.012 0.001 PHE D 464 TRP 0.007 0.001 TRP D 230 HIS 0.005 0.001 HIS D 199 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.15 ( 3510) covalent geometry : angle 0.54740 / 0.32 ( 4935) hydrogen bonds : bond 0.04051 / 4.27 ( 162) hydrogen bonds : angle 3.90004 / 5.34 ( 398) metal coordination : bond 0.00669 / 0.48 ( 4) metal coordination : angle 2.51498 / 4.90 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 584 Ramachandran restraints generated. 292 Oldfield, 0 Emsley, 292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 584 Ramachandran restraints generated. 292 Oldfield, 0 Emsley, 292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 33 time to evaluate : 0.065 Fit side-chains REVERT: D 163 TYR cc_start: 0.8549 (m-80) cc_final: 0.7681 (m-80) REVERT: D 287 ARG cc_start: 0.6946 (OUTLIER) cc_final: 0.5353 (ptm160) REVERT: D 480 GLN cc_start: 0.7661 (mt0) cc_final: 0.7402 (mp10) REVERT: D 481 GLU cc_start: 0.7568 (tt0) cc_final: 0.7305 (tt0) outliers start: 12 outliers final: 10 residues processed: 42 average time/residue: 0.0770 time to fit residues: 3.8279 Evaluate side-chains 42 residues out of total 254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 31 time to evaluate : 0.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 9 LEU Chi-restraints excluded: chain D residue 10 SER Chi-restraints excluded: chain D residue 64 TRP Chi-restraints excluded: chain D residue 187 VAL Chi-restraints excluded: chain D residue 287 ARG Chi-restraints excluded: chain D residue 301 VAL Chi-restraints excluded: chain D residue 328 SER Chi-restraints excluded: chain D residue 351 GLU Chi-restraints excluded: chain D residue 453 THR Chi-restraints excluded: chain D residue 473 THR Chi-restraints excluded: chain D residue 479 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 34 random chunks: chunk 7 optimal weight: 0.9980 chunk 5 optimal weight: 0.0980 chunk 26 optimal weight: 0.5980 chunk 23 optimal weight: 0.5980 chunk 6 optimal weight: 0.0770 chunk 22 optimal weight: 0.6980 chunk 30 optimal weight: 0.9980 chunk 24 optimal weight: 0.9980 chunk 13 optimal weight: 0.5980 chunk 33 optimal weight: 0.5980 chunk 2 optimal weight: 9.9990 overall best weight: 0.3938 ------------------------------------------------------------------------------- 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 = 0.3957 r_free = 0.3957 target = 0.178094 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.145741 restraints weight = 3273.377| |-----------------------------------------------------------------------------| r_work (start): 0.3630 rms_B_bonded: 1.14 r_work: 0.3354 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3227 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3227 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8335 moved from start: 0.3544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 3514 Z= 0.125 Angle : 0.536 6.880 4941 Z= 0.308 Chirality : 0.038 0.130 531 Planarity : 0.004 0.032 485 Dihedral : 26.467 84.826 809 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 2.76 % Allowed : 17.32 % Favored : 79.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.60 (0.52), residues: 292 helix: 1.27 (0.49), residues: 119 sheet: -2.17 (0.67), residues: 44 loop : 0.77 (0.60), residues: 129 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 362 TYR 0.015 0.002 TYR D 482 PHE 0.010 0.001 PHE D 464 TRP 0.008 0.001 TRP D 345 HIS 0.004 0.001 HIS D 199 Details of bonding type rmsd/Z covalent geometry : bond 0.00226 / 0.13 ( 3510) covalent geometry : angle 0.53063 / 0.31 ( 4935) hydrogen bonds : bond 0.03662 / 3.75 ( 162) hydrogen bonds : angle 3.81007 / 5.23 ( 398) metal coordination : bond 0.00468 / 0.33 ( 4) metal coordination : angle 2.21447 / 4.22 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 584 Ramachandran restraints generated. 292 Oldfield, 0 Emsley, 292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 584 Ramachandran restraints generated. 292 Oldfield, 0 Emsley, 292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 31 time to evaluate : 0.108 Fit side-chains REVERT: D 163 TYR cc_start: 0.8552 (m-80) cc_final: 0.7716 (m-80) REVERT: D 287 ARG cc_start: 0.6925 (OUTLIER) cc_final: 0.5521 (ptm160) REVERT: D 480 GLN cc_start: 0.7674 (mt0) cc_final: 0.7426 (mp10) REVERT: D 481 GLU cc_start: 0.7591 (tt0) cc_final: 0.7309 (tt0) outliers start: 7 outliers final: 5 residues processed: 36 average time/residue: 0.0899 time to fit residues: 3.8782 Evaluate side-chains 36 residues out of total 254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 30 time to evaluate : 0.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 10 SER Chi-restraints excluded: chain D residue 64 TRP Chi-restraints excluded: chain D residue 287 ARG Chi-restraints excluded: chain D residue 294 THR Chi-restraints excluded: chain D residue 301 VAL Chi-restraints excluded: chain D residue 351 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 34 random chunks: chunk 23 optimal weight: 0.7980 chunk 10 optimal weight: 0.5980 chunk 9 optimal weight: 0.7980 chunk 24 optimal weight: 1.9990 chunk 14 optimal weight: 0.8980 chunk 3 optimal weight: 4.9990 chunk 11 optimal weight: 0.9990 chunk 17 optimal weight: 0.0980 chunk 27 optimal weight: 4.9990 chunk 2 optimal weight: 9.9990 chunk 21 optimal weight: 0.6980 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 = 0.3922 r_free = 0.3922 target = 0.174663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.141077 restraints weight = 3268.433| |-----------------------------------------------------------------------------| r_work (start): 0.3574 rms_B_bonded: 1.23 r_work: 0.3320 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3179 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.3179 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8337 moved from start: 0.3595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 3514 Z= 0.141 Angle : 0.548 6.079 4941 Z= 0.313 Chirality : 0.039 0.137 531 Planarity : 0.004 0.032 485 Dihedral : 26.488 85.187 809 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 2.76 % Allowed : 16.93 % Favored : 80.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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 (0.52), residues: 292 helix: 1.28 (0.49), residues: 119 sheet: -2.14 (0.67), residues: 44 loop : 0.78 (0.61), residues: 129 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 444 TYR 0.015 0.002 TYR D 482 PHE 0.012 0.001 PHE D 464 TRP 0.006 0.001 TRP D 230 HIS 0.005 0.001 HIS D 199 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.14 ( 3510) covalent geometry : angle 0.54246 / 0.31 ( 4935) hydrogen bonds : bond 0.03916 / 4.14 ( 162) hydrogen bonds : angle 3.83712 / 5.24 ( 398) metal coordination : bond 0.00644 / 0.46 ( 4) metal coordination : angle 2.35235 / 4.56 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 584 Ramachandran restraints generated. 292 Oldfield, 0 Emsley, 292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 584 Ramachandran restraints generated. 292 Oldfield, 0 Emsley, 292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 29 time to evaluate : 0.101 Fit side-chains REVERT: D 163 TYR cc_start: 0.8566 (m-80) cc_final: 0.7719 (m-80) REVERT: D 287 ARG cc_start: 0.6846 (OUTLIER) cc_final: 0.5408 (ptm160) REVERT: D 480 GLN cc_start: 0.7685 (mt0) cc_final: 0.7419 (mp10) outliers start: 7 outliers final: 5 residues processed: 34 average time/residue: 0.0985 time to fit residues: 3.9525 Evaluate side-chains 35 residues out of total 254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 29 time to evaluate : 0.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 10 SER Chi-restraints excluded: chain D residue 64 TRP Chi-restraints excluded: chain D residue 287 ARG Chi-restraints excluded: chain D residue 294 THR Chi-restraints excluded: chain D residue 301 VAL Chi-restraints excluded: chain D residue 351 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 34 random chunks: chunk 13 optimal weight: 0.5980 chunk 14 optimal weight: 0.5980 chunk 28 optimal weight: 0.7980 chunk 29 optimal weight: 0.7980 chunk 27 optimal weight: 0.7980 chunk 10 optimal weight: 0.6980 chunk 18 optimal weight: 3.9990 chunk 21 optimal weight: 0.9980 chunk 32 optimal weight: 0.9990 chunk 30 optimal weight: 0.9990 chunk 7 optimal weight: 0.0870 overall best weight: 0.5558 ------------------------------------------------------------------------------- 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 = 0.3951 r_free = 0.3951 target = 0.177420 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.145474 restraints weight = 3187.812| |-----------------------------------------------------------------------------| r_work (start): 0.3604 rms_B_bonded: 1.10 r_work: 0.3340 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3205 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.3205 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8350 moved from start: 0.3659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.017 3514 Z= 0.135 Angle : 0.538 5.827 4941 Z= 0.308 Chirality : 0.038 0.123 531 Planarity : 0.004 0.032 485 Dihedral : 26.486 85.293 809 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 2.76 % Allowed : 16.93 % Favored : 80.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.75 (0.52), residues: 292 helix: 1.38 (0.50), residues: 118 sheet: -2.11 (0.67), residues: 44 loop : 0.87 (0.61), residues: 130 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 444 TYR 0.015 0.002 TYR D 482 PHE 0.011 0.001 PHE D 464 TRP 0.007 0.001 TRP D 345 HIS 0.004 0.001 HIS D 199 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.14 ( 3510) covalent geometry : angle 0.53252 / 0.31 ( 4935) hydrogen bonds : bond 0.03743 / 3.90 ( 162) hydrogen bonds : angle 3.80554 / 5.20 ( 398) metal coordination : bond 0.00570 / 0.41 ( 4) metal coordination : angle 2.29529 / 4.44 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 584 Ramachandran restraints generated. 292 Oldfield, 0 Emsley, 292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 584 Ramachandran restraints generated. 292 Oldfield, 0 Emsley, 292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 29 time to evaluate : 0.102 Fit side-chains REVERT: D 163 TYR cc_start: 0.8558 (m-80) cc_final: 0.7612 (m-80) REVERT: D 287 ARG cc_start: 0.6875 (OUTLIER) cc_final: 0.5500 (ptm160) REVERT: D 480 GLN cc_start: 0.7722 (mt0) cc_final: 0.7500 (mp10) outliers start: 7 outliers final: 6 residues processed: 35 average time/residue: 0.1006 time to fit residues: 4.1317 Evaluate side-chains 36 residues out of total 254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 29 time to evaluate : 0.103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 10 SER Chi-restraints excluded: chain D residue 64 TRP Chi-restraints excluded: chain D residue 287 ARG Chi-restraints excluded: chain D residue 294 THR Chi-restraints excluded: chain D residue 301 VAL Chi-restraints excluded: chain D residue 351 GLU Chi-restraints excluded: chain D residue 463 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 34 random chunks: chunk 30 optimal weight: 0.0050 chunk 7 optimal weight: 0.9980 chunk 25 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 33 optimal weight: 0.7980 chunk 6 optimal weight: 0.8980 chunk 12 optimal weight: 0.6980 chunk 17 optimal weight: 5.9990 chunk 16 optimal weight: 0.7980 chunk 9 optimal weight: 0.7980 chunk 15 optimal weight: 0.5980 overall best weight: 0.5794 ------------------------------------------------------------------------------- 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 = 0.3947 r_free = 0.3947 target = 0.177004 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.146142 restraints weight = 3289.312| |-----------------------------------------------------------------------------| r_work (start): 0.3616 rms_B_bonded: 1.07 r_work: 0.3335 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3206 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.3206 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8358 moved from start: 0.3721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.018 3514 Z= 0.138 Angle : 0.542 6.036 4941 Z= 0.309 Chirality : 0.039 0.125 531 Planarity : 0.004 0.032 485 Dihedral : 26.484 85.029 809 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 2.76 % Allowed : 16.93 % Favored : 80.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.77 (0.52), residues: 292 helix: 1.41 (0.50), residues: 118 sheet: -2.13 (0.67), residues: 44 loop : 0.88 (0.61), residues: 130 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 444 TYR 0.014 0.001 TYR D 482 PHE 0.012 0.001 PHE D 464 TRP 0.006 0.001 TRP D 230 HIS 0.005 0.001 HIS D 199 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.14 ( 3510) covalent geometry : angle 0.53546 / 0.31 ( 4935) hydrogen bonds : bond 0.03817 / 4.01 ( 162) hydrogen bonds : angle 3.82743 / 5.21 ( 398) metal coordination : bond 0.00611 / 0.45 ( 4) metal coordination : angle 2.38971 / 4.76 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1136.46 seconds wall clock time: 20 minutes 3.05 seconds (1203.05 seconds total)