Starting phenix.real_space_refine on Tue Aug 4 13:38:21 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9iub_60896/08_2026/9iub_60896.cif Found real_map, /net/cci-nas-00/data/ceres_data/9iub_60896/08_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_60896/08_2026/9iub_60896.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9iub_60896/08_2026/9iub_60896.map" model { file = "/net/cci-nas-00/data/ceres_data/9iub_60896/08_2026/9iub_60896.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9iub_60896/08_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-2.2rc3-6140/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: 0.63, per 1000 atoms: 0.19 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: 0.30 Conformation dependent library (CDL) restraints added in 87.8 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: 0.46 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: 0.56 Time building geometry restraints manager: 0.40 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: 4607 3.11 - 6.22: 288 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=" 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 angle pdb=" CA ASP D 478 " pdb=" CB ASP D 478 " pdb=" CG ASP D 478 " ideal model delta sigma weight residual 112.60 118.59 -5.99 1.00e+00 1.00e+00 3.58e+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: 0.880 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.050 Check model and map are aligned: 0.010 Set scattering table: 0.000 Process input model: 5.280 Find NCS groups from input model: 0.010 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 7.400 ------------------------------------------------------------------------------- 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 : 1.678 21.849 4941 Z= 1.097 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 1.63915 / 1.10 ( 4935) hydrogen bonds : bond 0.16093 / 16.78 ( 162) hydrogen bonds : angle 6.21066 / 8.01 ( 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 : 0.110 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: 0.0972 time to fit residues: 8.3425 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 : 0.062 ------------------------------------------------------------------------------- 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 = 0.3942 r_free = 0.3942 target = 0.176451 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.134132 restraints weight = 3281.239| |-----------------------------------------------------------------------------| r_work (start): 0.3507 rms_B_bonded: 1.22 r_work: 0.3327 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3190 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8335 moved from start: 0.1933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 3514 Z= 0.209 Angle : 0.743 9.715 4941 Z= 0.413 Chirality : 0.050 0.197 531 Planarity : 0.007 0.079 485 Dihedral : 25.735 88.191 816 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 5.91 % Allowed : 9.06 % 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: 0.82 (0.47), residues: 119 sheet: -0.47 (0.78), residues: 42 loop : 0.75 (0.57), residues: 131 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 58 TYR 0.015 0.002 TYR D 482 PHE 0.014 0.002 PHE D 464 TRP 0.010 0.001 TRP D 161 HIS 0.009 0.002 HIS D 199 Details of bonding type rmsd/Z covalent geometry : bond 0.00431 / 0.21 ( 3510) covalent geometry : angle 0.71822 / 0.41 ( 4935) hydrogen bonds : bond 0.05412 / 5.39 ( 162) hydrogen bonds : angle 4.45553 / 5.90 ( 398) metal coordination : bond 0.02232 / 1.43 ( 4) metal coordination : angle 5.51253 / 11.08 ( 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 60 residues out of total 254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 45 time to evaluate : 0.059 Fit side-chains revert: symmetry clash REVERT: D 163 TYR cc_start: 0.8533 (m-80) cc_final: 0.8037 (m-80) REVERT: D 265 ARG cc_start: 0.8114 (ttp-170) cc_final: 0.7681 (ttp-170) REVERT: D 282 LEU cc_start: 0.8057 (OUTLIER) cc_final: 0.7839 (mt) REVERT: D 361 GLU cc_start: 0.7527 (OUTLIER) cc_final: 0.6575 (pm20) REVERT: D 473 THR cc_start: 0.8198 (m) cc_final: 0.7780 (p) REVERT: D 480 GLN cc_start: 0.7451 (mt0) cc_final: 0.7125 (mp10) outliers start: 15 outliers final: 7 residues processed: 57 average time/residue: 0.0581 time to fit residues: 3.8762 Evaluate side-chains 48 residues out of total 254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 39 time to evaluate : 0.058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 8.9990 chunk 3 optimal weight: 4.9990 chunk 7 optimal weight: 0.8980 chunk 21 optimal weight: 0.6980 chunk 10 optimal weight: 0.9980 chunk 17 optimal weight: 5.9990 chunk 28 optimal weight: 3.9990 chunk 19 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 30 optimal weight: 0.8980 chunk 23 optimal weight: 0.9980 overall best weight: 0.8980 ------------------------------------------------------------------------------- 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 = 0.3944 r_free = 0.3944 target = 0.176557 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.133523 restraints weight = 3262.937| |-----------------------------------------------------------------------------| r_work (start): 0.3491 rms_B_bonded: 1.28 r_work: 0.3286 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3157 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3157 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8380 moved from start: 0.2570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 3514 Z= 0.186 Angle : 0.648 6.447 4941 Z= 0.361 Chirality : 0.044 0.167 531 Planarity : 0.006 0.051 485 Dihedral : 26.680 88.749 813 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 4.00 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: 0.63 (0.51), residues: 292 helix: 0.88 (0.49), residues: 119 sheet: -1.55 (0.71), residues: 44 loop : 0.99 (0.59), residues: 129 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 472 TYR 0.020 0.003 TYR D 482 PHE 0.015 0.002 PHE D 464 TRP 0.010 0.001 TRP D 230 HIS 0.006 0.001 HIS D 199 Details of bonding type rmsd/Z covalent geometry : bond 0.00383 / 0.19 ( 3510) covalent geometry : angle 0.63978 / 0.36 ( 4935) hydrogen bonds : bond 0.05046 / 5.27 ( 162) hydrogen bonds : angle 4.29273 / 5.81 ( 398) metal coordination : bond 0.00687 / 0.51 ( 4) metal coordination : angle 2.95206 / 5.93 ( 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 : 0.067 Fit side-chains REVERT: D 163 TYR cc_start: 0.8586 (m-80) cc_final: 0.7725 (m-80) REVERT: D 287 ARG cc_start: 0.7029 (OUTLIER) cc_final: 0.4659 (ptm160) REVERT: D 473 THR cc_start: 0.8234 (m) cc_final: 0.7786 (p) REVERT: D 480 GLN cc_start: 0.7609 (mt0) cc_final: 0.7317 (mp10) outliers start: 10 outliers final: 6 residues processed: 48 average time/residue: 0.0533 time to fit residues: 3.0552 Evaluate side-chains 43 residues out of total 254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 36 time to evaluate : 0.066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 10 SER 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: 0.9990 chunk 14 optimal weight: 1.9990 chunk 25 optimal weight: 2.9990 chunk 27 optimal weight: 3.9990 chunk 1 optimal weight: 6.9990 chunk 9 optimal weight: 0.5980 chunk 18 optimal weight: 0.7980 chunk 19 optimal weight: 0.0980 chunk 2 optimal weight: 9.9990 chunk 13 optimal weight: 0.5980 chunk 31 optimal weight: 0.7980 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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 = 0.3960 r_free = 0.3960 target = 0.177415 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.135832 restraints weight = 3236.272| |-----------------------------------------------------------------------------| r_work (start): 0.3495 rms_B_bonded: 1.22 r_work: 0.3343 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3215 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.3215 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8308 moved from start: 0.2840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3514 Z= 0.150 Angle : 0.593 6.725 4941 Z= 0.336 Chirality : 0.041 0.153 531 Planarity : 0.005 0.037 485 Dihedral : 26.488 86.198 810 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 4.33 % Allowed : 11.42 % 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: 0.94 (0.49), residues: 120 sheet: -1.73 (0.70), residues: 44 loop : 0.93 (0.59), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 58 TYR 0.011 0.002 TYR D 482 PHE 0.012 0.001 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 0.00289 / 0.15 ( 3510) covalent geometry : angle 0.58672 / 0.34 ( 4935) hydrogen bonds : bond 0.04211 / 4.42 ( 162) hydrogen bonds : angle 4.13932 / 5.64 ( 398) metal coordination : bond 0.00451 / 0.33 ( 4) metal coordination : angle 2.51549 / 5.14 ( 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 48 residues out of total 254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 37 time to evaluate : 0.068 Fit side-chains REVERT: D 163 TYR cc_start: 0.8542 (m-80) cc_final: 0.7667 (m-80) REVERT: D 287 ARG cc_start: 0.7053 (OUTLIER) cc_final: 0.4839 (ptm160) REVERT: D 480 GLN cc_start: 0.7506 (mt0) cc_final: 0.7275 (mp10) outliers start: 11 outliers final: 8 residues processed: 45 average time/residue: 0.0726 time to fit residues: 3.8427 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 : 0.060 ------------------------------------------------------------------------------- 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: 1.9990 chunk 21 optimal weight: 0.7980 chunk 25 optimal weight: 0.9980 chunk 24 optimal weight: 1.9990 chunk 29 optimal weight: 0.8980 chunk 7 optimal weight: 0.7980 chunk 33 optimal weight: 2.9990 chunk 28 optimal weight: 0.4980 chunk 16 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 = 0.3938 r_free = 0.3938 target = 0.175327 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.133986 restraints weight = 3238.984| |-----------------------------------------------------------------------------| r_work (start): 0.3456 rms_B_bonded: 1.22 r_work: 0.3305 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3170 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.3170 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 moved from start: 0.3063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3514 Z= 0.171 Angle : 0.604 6.563 4941 Z= 0.338 Chirality : 0.042 0.166 531 Planarity : 0.005 0.035 485 Dihedral : 26.526 86.854 810 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 4.72 % Allowed : 12.60 % 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: 0.45 (0.51), residues: 292 helix: 0.94 (0.49), residues: 120 sheet: -1.94 (0.69), residues: 44 loop : 0.78 (0.59), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 8 TYR 0.018 0.002 TYR D 482 PHE 0.014 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 0.00348 / 0.17 ( 3510) covalent geometry : angle 0.59698 / 0.34 ( 4935) hydrogen bonds : bond 0.04450 / 4.73 ( 162) hydrogen bonds : angle 4.08584 / 5.58 ( 398) metal coordination : bond 0.00885 / 0.62 ( 4) metal coordination : angle 2.67270 / 5.43 ( 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 48 residues out of total 254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 36 time to evaluate : 0.058 Fit side-chains REVERT: D 163 TYR cc_start: 0.8581 (m-80) cc_final: 0.7704 (m-80) REVERT: D 287 ARG cc_start: 0.7093 (OUTLIER) cc_final: 0.5064 (ptm160) REVERT: D 313 LYS cc_start: 0.8669 (ttpp) cc_final: 0.8437 (tttt) REVERT: D 480 GLN cc_start: 0.7582 (mt0) cc_final: 0.7270 (mp10) REVERT: D 481 GLU cc_start: 0.7288 (tt0) cc_final: 0.7052 (tt0) outliers start: 12 outliers final: 9 residues processed: 45 average time/residue: 0.0598 time to fit residues: 3.1584 Evaluate side-chains 45 residues out of total 254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 35 time to evaluate : 0.058 ------------------------------------------------------------------------------- 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: 0.5980 chunk 6 optimal weight: 1.9990 chunk 12 optimal weight: 0.5980 chunk 8 optimal weight: 0.8980 chunk 30 optimal weight: 0.9990 chunk 28 optimal weight: 0.9990 chunk 19 optimal weight: 1.9990 chunk 22 optimal weight: 0.9980 chunk 11 optimal weight: 0.3980 chunk 2 optimal weight: 9.9990 chunk 14 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.3939 r_free = 0.3939 target = 0.176059 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.143505 restraints weight = 3232.326| |-----------------------------------------------------------------------------| r_work (start): 0.3577 rms_B_bonded: 1.22 r_work: 0.3314 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3182 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3182 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8348 moved from start: 0.3256 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= 0.153 Angle : 0.571 6.055 4941 Z= 0.325 Chirality : 0.040 0.154 531 Planarity : 0.005 0.033 485 Dihedral : 26.504 86.312 809 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % 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: 0.50 (0.51), residues: 292 helix: 1.06 (0.49), residues: 119 sheet: -2.05 (0.68), residues: 44 loop : 0.78 (0.59), residues: 129 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 58 TYR 0.016 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 0.00306 / 0.15 ( 3510) covalent geometry : angle 0.56519 / 0.32 ( 4935) hydrogen bonds : bond 0.04067 / 4.29 ( 162) hydrogen bonds : angle 3.96201 / 5.44 ( 398) metal coordination : bond 0.00625 / 0.44 ( 4) metal coordination : angle 2.46933 / 4.88 ( 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 : 0.064 Fit side-chains REVERT: D 163 TYR cc_start: 0.8583 (m-80) cc_final: 0.7730 (m-80) REVERT: D 287 ARG cc_start: 0.7197 (OUTLIER) cc_final: 0.5559 (ptm160) REVERT: D 313 LYS cc_start: 0.8674 (ttpp) cc_final: 0.8469 (tttt) REVERT: D 480 GLN cc_start: 0.7625 (mt0) cc_final: 0.7304 (mp10) REVERT: D 481 GLU cc_start: 0.7475 (tt0) cc_final: 0.7222 (tt0) outliers start: 12 outliers final: 9 residues processed: 43 average time/residue: 0.0687 time to fit residues: 3.5095 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 : 0.059 ------------------------------------------------------------------------------- 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 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: 4.9990 chunk 15 optimal weight: 0.5980 chunk 20 optimal weight: 2.9990 chunk 26 optimal weight: 0.5980 chunk 3 optimal weight: 5.9990 chunk 0 optimal weight: 4.9990 chunk 14 optimal weight: 0.7980 chunk 30 optimal weight: 0.9980 chunk 21 optimal weight: 0.6980 chunk 16 optimal weight: 0.9980 chunk 19 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.3938 r_free = 0.3938 target = 0.176325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.143955 restraints weight = 3285.689| |-----------------------------------------------------------------------------| r_work (start): 0.3583 rms_B_bonded: 1.20 r_work: 0.3315 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3186 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.3186 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8337 moved from start: 0.3405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 3514 Z= 0.153 Angle : 0.571 6.445 4941 Z= 0.323 Chirality : 0.041 0.151 531 Planarity : 0.005 0.033 485 Dihedral : 26.487 85.971 809 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 4.33 % Allowed : 14.57 % 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: 0.49 (0.51), residues: 292 helix: 1.12 (0.49), residues: 120 sheet: -2.05 (0.70), residues: 44 loop : 0.68 (0.60), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 444 TYR 0.017 0.002 TYR D 482 PHE 0.013 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 0.00303 / 0.15 ( 3510) covalent geometry : angle 0.56480 / 0.32 ( 4935) hydrogen bonds : bond 0.04138 / 4.43 ( 162) hydrogen bonds : angle 3.90365 / 5.36 ( 398) metal coordination : bond 0.00772 / 0.54 ( 4) metal coordination : angle 2.42238 / 4.74 ( 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 46 residues out of total 254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 35 time to evaluate : 0.100 Fit side-chains REVERT: D 163 TYR cc_start: 0.8585 (m-80) cc_final: 0.7712 (m-80) REVERT: D 287 ARG cc_start: 0.6938 (OUTLIER) cc_final: 0.5371 (ptm160) REVERT: D 480 GLN cc_start: 0.7682 (mt0) cc_final: 0.7383 (mp10) REVERT: D 481 GLU cc_start: 0.7553 (tt0) cc_final: 0.7292 (tt0) outliers start: 11 outliers final: 9 residues processed: 44 average time/residue: 0.0842 time to fit residues: 4.3903 Evaluate side-chains 41 residues out of total 254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 31 time to evaluate : 0.096 ------------------------------------------------------------------------------- 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 34 random chunks: chunk 7 optimal weight: 2.9990 chunk 5 optimal weight: 0.0000 chunk 26 optimal weight: 0.5980 chunk 23 optimal weight: 2.9990 chunk 6 optimal weight: 0.9980 chunk 22 optimal weight: 0.8980 chunk 30 optimal weight: 0.7980 chunk 24 optimal weight: 1.9990 chunk 13 optimal weight: 0.5980 chunk 33 optimal weight: 2.9990 chunk 2 optimal weight: 9.9990 overall best weight: 0.5784 ------------------------------------------------------------------------------- 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 = 0.3946 r_free = 0.3946 target = 0.176944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.144562 restraints weight = 3280.410| |-----------------------------------------------------------------------------| r_work (start): 0.3593 rms_B_bonded: 1.14 r_work: 0.3337 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3207 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.3207 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.3514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 3514 Z= 0.140 Angle : 0.551 5.844 4941 Z= 0.315 Chirality : 0.039 0.137 531 Planarity : 0.004 0.033 485 Dihedral : 26.447 85.687 809 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 4.72 % Allowed : 14.96 % 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: 0.53 (0.51), residues: 292 helix: 1.20 (0.49), residues: 120 sheet: -2.11 (0.69), residues: 44 loop : 0.70 (0.60), residues: 128 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 345 HIS 0.005 0.001 HIS D 199 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.14 ( 3510) covalent geometry : angle 0.54485 / 0.32 ( 4935) hydrogen bonds : bond 0.03847 / 4.04 ( 162) hydrogen bonds : angle 3.85779 / 5.30 ( 398) metal coordination : bond 0.00597 / 0.42 ( 4) metal coordination : angle 2.37626 / 4.70 ( 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 44 residues out of total 254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 32 time to evaluate : 0.070 Fit side-chains REVERT: D 163 TYR cc_start: 0.8550 (m-80) cc_final: 0.7700 (m-80) REVERT: D 251 ASN cc_start: 0.8329 (m-40) cc_final: 0.8128 (m-40) REVERT: D 287 ARG cc_start: 0.6946 (OUTLIER) cc_final: 0.5524 (ptm160) REVERT: D 480 GLN cc_start: 0.7689 (mt0) cc_final: 0.7432 (mp10) REVERT: D 481 GLU cc_start: 0.7584 (tt0) cc_final: 0.7314 (tt0) outliers start: 12 outliers final: 9 residues processed: 41 average time/residue: 0.0626 time to fit residues: 3.0391 Evaluate side-chains 43 residues out of total 254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 33 time to evaluate : 0.059 ------------------------------------------------------------------------------- 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 473 THR Chi-restraints excluded: chain D residue 479 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 34 random chunks: chunk 23 optimal weight: 1.9990 chunk 10 optimal weight: 0.8980 chunk 9 optimal weight: 0.7980 chunk 24 optimal weight: 6.9990 chunk 14 optimal weight: 1.9990 chunk 3 optimal weight: 4.9990 chunk 11 optimal weight: 0.6980 chunk 17 optimal weight: 4.9990 chunk 27 optimal weight: 3.9990 chunk 2 optimal weight: 10.0000 chunk 21 optimal weight: 0.6980 overall best weight: 1.0182 ------------------------------------------------------------------------------- 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 = 0.3923 r_free = 0.3923 target = 0.174753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.142244 restraints weight = 3243.313| |-----------------------------------------------------------------------------| r_work (start): 0.3561 rms_B_bonded: 1.23 r_work: 0.3265 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3126 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3126 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8387 moved from start: 0.3562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 3514 Z= 0.187 Angle : 0.603 6.637 4941 Z= 0.337 Chirality : 0.043 0.152 531 Planarity : 0.005 0.034 485 Dihedral : 26.576 86.929 809 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 3.94 % Allowed : 15.35 % 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: 0.47 (0.51), residues: 292 helix: 1.18 (0.49), residues: 118 sheet: -2.23 (0.66), residues: 44 loop : 0.66 (0.60), residues: 130 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 444 TYR 0.018 0.002 TYR D 482 PHE 0.015 0.002 PHE D 464 TRP 0.007 0.001 TRP D 64 HIS 0.005 0.001 HIS D 199 Details of bonding type rmsd/Z covalent geometry : bond 0.00395 / 0.19 ( 3510) covalent geometry : angle 0.59585 / 0.34 ( 4935) hydrogen bonds : bond 0.04410 / 4.76 ( 162) hydrogen bonds : angle 3.97215 / 5.42 ( 398) metal coordination : bond 0.00883 / 0.62 ( 4) metal coordination : angle 2.76983 / 5.68 ( 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 40 residues out of total 254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 30 time to evaluate : 0.102 Fit side-chains REVERT: D 163 TYR cc_start: 0.8634 (m-80) cc_final: 0.7660 (m-80) REVERT: D 287 ARG cc_start: 0.6906 (OUTLIER) cc_final: 0.5489 (ptm160) REVERT: D 480 GLN cc_start: 0.7827 (mt0) cc_final: 0.7496 (mp10) REVERT: D 481 GLU cc_start: 0.7527 (tt0) cc_final: 0.7253 (tt0) outliers start: 10 outliers final: 9 residues processed: 39 average time/residue: 0.0971 time to fit residues: 4.4264 Evaluate side-chains 40 residues out of total 254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 30 time to evaluate : 0.060 ------------------------------------------------------------------------------- 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 473 THR Chi-restraints excluded: chain D residue 479 LEU 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: 0.9980 chunk 28 optimal weight: 0.6980 chunk 29 optimal weight: 5.9990 chunk 27 optimal weight: 2.9990 chunk 10 optimal weight: 0.5980 chunk 18 optimal weight: 3.9990 chunk 21 optimal weight: 0.7980 chunk 32 optimal weight: 0.8980 chunk 30 optimal weight: 0.8980 chunk 7 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.3934 r_free = 0.3934 target = 0.175731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.144900 restraints weight = 3195.870| |-----------------------------------------------------------------------------| r_work (start): 0.3619 rms_B_bonded: 1.06 r_work: 0.3341 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3218 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.3218 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8356 moved from start: 0.3626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 3514 Z= 0.154 Angle : 0.569 6.082 4941 Z= 0.322 Chirality : 0.040 0.134 531 Planarity : 0.005 0.033 485 Dihedral : 26.551 86.462 809 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 4.33 % Allowed : 14.96 % 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: 0.55 (0.52), residues: 292 helix: 1.31 (0.50), residues: 118 sheet: -2.25 (0.67), residues: 44 loop : 0.66 (0.59), residues: 130 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 444 TYR 0.016 0.002 TYR D 482 PHE 0.013 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 0.00308 / 0.15 ( 3510) covalent geometry : angle 0.56235 / 0.32 ( 4935) hydrogen bonds : bond 0.04028 / 4.27 ( 162) hydrogen bonds : angle 3.91360 / 5.34 ( 398) metal coordination : bond 0.00679 / 0.48 ( 4) metal coordination : angle 2.53525 / 5.02 ( 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 41 residues out of total 254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 30 time to evaluate : 0.111 Fit side-chains REVERT: D 163 TYR cc_start: 0.8565 (m-80) cc_final: 0.7625 (m-80) REVERT: D 287 ARG cc_start: 0.6933 (OUTLIER) cc_final: 0.5655 (ptm160) REVERT: D 480 GLN cc_start: 0.7720 (mt0) cc_final: 0.7434 (mp10) REVERT: D 481 GLU cc_start: 0.7495 (tt0) cc_final: 0.7215 (tt0) outliers start: 11 outliers final: 10 residues processed: 40 average time/residue: 0.0997 time to fit residues: 4.7011 Evaluate side-chains 40 residues out of total 254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 29 time to evaluate : 0.108 ------------------------------------------------------------------------------- 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 463 THR Chi-restraints excluded: chain D residue 473 THR Chi-restraints excluded: chain D residue 479 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 34 random chunks: chunk 30 optimal weight: 0.0570 chunk 7 optimal weight: 0.4980 chunk 25 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 6 optimal weight: 0.6980 chunk 12 optimal weight: 0.7980 chunk 17 optimal weight: 4.9990 chunk 16 optimal weight: 0.9990 chunk 9 optimal weight: 0.4980 chunk 15 optimal weight: 0.8980 overall best weight: 0.5098 ------------------------------------------------------------------------------- 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 = 0.176892 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.144644 restraints weight = 3320.807| |-----------------------------------------------------------------------------| r_work (start): 0.3593 rms_B_bonded: 1.18 r_work: 0.3351 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3222 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.3222 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8306 moved from start: 0.3723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.016 3514 Z= 0.132 Angle : 0.535 5.612 4941 Z= 0.308 Chirality : 0.038 0.119 531 Planarity : 0.004 0.033 485 Dihedral : 26.431 84.776 809 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 3.94 % Allowed : 15.35 % 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: 0.68 (0.51), residues: 292 helix: 1.62 (0.51), residues: 113 sheet: -2.14 (0.68), residues: 44 loop : 0.56 (0.58), residues: 135 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 0.010 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 0.00247 / 0.13 ( 3510) covalent geometry : angle 0.52943 / 0.31 ( 4935) hydrogen bonds : bond 0.03700 / 3.85 ( 162) hydrogen bonds : angle 3.82718 / 5.23 ( 398) metal coordination : bond 0.00517 / 0.37 ( 4) metal coordination : angle 2.17372 / 4.15 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 949.80 seconds wall clock time: 16 minutes 50.15 seconds (1010.15 seconds total)