Starting phenix.real_space_refine on Sat Apr 4 21:00:00 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9iub_60896/04_2026/9iub_60896.cif Found real_map, /net/cci-nas-00/data/ceres_data/9iub_60896/04_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_60896/04_2026/9iub_60896.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9iub_60896/04_2026/9iub_60896.map" model { file = "/net/cci-nas-00/data/ceres_data/9iub_60896/04_2026/9iub_60896.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9iub_60896/04_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-2.1rc1-6017/lib/python3.9/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: 0.86, per 1000 atoms: 0.26 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: 0.34 Conformation dependent library (CDL) restraints added in 56.7 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: 0.50 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: 0.60 Time building geometry restraints manager: 0.36 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=" 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 bond pdb=" C GLU D 196 " pdb=" N PRO D 197 " ideal model delta sigma weight residual 1.331 1.362 -0.031 1.31e-02 5.83e+03 5.63e+00 bond pdb=" C LYS D 289 " pdb=" N PRO D 290 " ideal model delta sigma weight residual 1.331 1.359 -0.029 1.31e-02 5.83e+03 4.86e+00 bond pdb=" C ASP D 51 " pdb=" N PRO D 52 " ideal model delta sigma weight residual 1.333 1.365 -0.032 1.44e-02 4.82e+03 4.83e+00 ... (remaining 3505 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.11: 4618 3.11 - 6.22: 279 6.22 - 9.33: 35 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=" 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=" 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 angle pdb=" O3' DCG2 27 " pdb=" P DCG2 28 " pdb=" O5' DCG2 28 " ideal model delta sigma weight residual 104.00 95.18 8.82 1.50e+00 4.44e-01 3.46e+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 - 0.128: 471 0.128 - 0.256: 53 0.256 - 0.384: 5 0.384 - 0.511: 1 0.511 - 0.639: 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 2.35 -2.98 -0.64 2.00e-01 2.50e+01 1.02e+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 2.35 -2.81 -0.46 2.00e-01 2.50e+01 5.37e+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 2.35 2.68 -0.34 2.00e-01 2.50e+01 2.86e+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: 0.540 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: 0.000 Set scattering table: 0.010 Process input model: 5.760 Find NCS groups from input model: 0.020 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:1.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 7.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5053 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= 0.512 Angle : 1.678 21.849 4941 Z= 1.019 Chirality : 0.085 0.639 531 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 covalent geometry : bond 0.00880 ( 3510) covalent geometry : angle 1.63971 ( 4935) hydrogen bonds : bond 0.16093 ( 162) hydrogen bonds : angle 6.21066 ( 398) metal coordination : bond 0.05617 ( 4) metal coordination : angle 10.38354 ( 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 : 0.060 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: 0.0887 time to fit residues: 7.5459 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 : 0.104 ------------------------------------------------------------------------------- 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: 2.9990 chunk 16 optimal weight: 0.5980 chunk 32 optimal weight: 1.9990 chunk 31 optimal weight: 0.7980 chunk 25 optimal weight: 0.0270 chunk 19 optimal weight: 0.9980 chunk 30 optimal weight: 5.9990 chunk 22 optimal weight: 0.6980 chunk 13 optimal weight: 0.8980 overall best weight: 0.6038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3970 r_free = 0.3970 target = 0.178958 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.136829 restraints weight = 3252.723| |-----------------------------------------------------------------------------| r_work (start): 0.3503 rms_B_bonded: 1.22 r_work: 0.3346 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3211 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.3211 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8090 moved from start: 0.2271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 3514 Z= 0.184 Angle : 0.615 4.951 4941 Z= 0.342 Chirality : 0.039 0.137 531 Planarity : 0.006 0.072 485 Dihedral : 26.044 86.315 816 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.03 % Favored : 98.97 % Rotamer: Outliers : 5.12 % Allowed : 9.45 % Favored : 85.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.93 (0.50), residues: 292 helix: 1.10 (0.48), residues: 119 sheet: -0.44 (0.77), residues: 42 loop : 0.75 (0.57), residues: 131 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 323 TYR 0.017 0.002 TYR D 482 PHE 0.013 0.002 PHE D 464 TRP 0.009 0.001 TRP D 230 HIS 0.009 0.002 HIS D 199 Details of bonding type rmsd covalent geometry : bond 0.00409 ( 3510) covalent geometry : angle 0.60650 ( 4935) hydrogen bonds : bond 0.04360 ( 162) hydrogen bonds : angle 4.22569 ( 398) metal coordination : bond 0.00191 ( 4) metal coordination : angle 3.03683 ( 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 56 residues out of total 254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 43 time to evaluate : 0.161 Fit side-chains REVERT: D 163 TYR cc_start: 0.8529 (m-80) cc_final: 0.7869 (m-80) REVERT: D 287 ARG cc_start: 0.6895 (OUTLIER) cc_final: 0.4068 (ptm160) REVERT: D 458 MET cc_start: 0.8344 (mmt) cc_final: 0.8098 (mmt) REVERT: D 473 THR cc_start: 0.8165 (m) cc_final: 0.7737 (p) REVERT: D 480 GLN cc_start: 0.7504 (mt0) cc_final: 0.7212 (mp10) outliers start: 13 outliers final: 5 residues processed: 54 average time/residue: 0.0990 time to fit residues: 6.2310 Evaluate side-chains 43 residues out of total 254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 37 time to evaluate : 0.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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: 6.9990 chunk 3 optimal weight: 0.9980 chunk 7 optimal weight: 0.0870 chunk 21 optimal weight: 0.6980 chunk 10 optimal weight: 0.8980 chunk 17 optimal weight: 1.9990 chunk 28 optimal weight: 3.9990 chunk 19 optimal weight: 2.9990 chunk 26 optimal weight: 0.8980 chunk 30 optimal weight: 1.9990 chunk 23 optimal weight: 0.7980 overall best weight: 0.6758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 194 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.177102 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.134839 restraints weight = 3248.182| |-----------------------------------------------------------------------------| r_work (start): 0.3516 rms_B_bonded: 1.26 r_work: 0.3340 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3203 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3203 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 moved from start: 0.2932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 3514 Z= 0.182 Angle : 0.576 5.300 4941 Z= 0.323 Chirality : 0.038 0.125 531 Planarity : 0.005 0.047 485 Dihedral : 26.033 86.495 810 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 3.54 % Allowed : 12.60 % Favored : 83.86 % 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: 0.83 (0.51), residues: 292 helix: 1.13 (0.49), residues: 119 sheet: -1.37 (0.70), residues: 44 loop : 0.98 (0.58), residues: 129 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 58 TYR 0.017 0.002 TYR D 482 PHE 0.012 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 covalent geometry : bond 0.00409 ( 3510) covalent geometry : angle 0.57098 ( 4935) hydrogen bonds : bond 0.03871 ( 162) hydrogen bonds : angle 4.05310 ( 398) metal coordination : bond 0.00736 ( 4) metal coordination : angle 2.35083 ( 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 47 residues out of total 254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 38 time to evaluate : 0.114 Fit side-chains REVERT: D 163 TYR cc_start: 0.8617 (m-80) cc_final: 0.7800 (m-80) REVERT: D 287 ARG cc_start: 0.7037 (OUTLIER) cc_final: 0.4825 (ptm160) REVERT: D 361 GLU cc_start: 0.7905 (tt0) cc_final: 0.6734 (pm20) REVERT: D 473 THR cc_start: 0.8155 (m) cc_final: 0.7706 (p) REVERT: D 480 GLN cc_start: 0.7514 (mt0) cc_final: 0.7258 (mp10) REVERT: D 481 GLU cc_start: 0.7210 (tt0) cc_final: 0.6986 (tt0) outliers start: 9 outliers final: 7 residues processed: 44 average time/residue: 0.0999 time to fit residues: 5.1168 Evaluate side-chains 40 residues out of total 254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 32 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 328 SER Chi-restraints excluded: chain D residue 351 GLU Chi-restraints excluded: chain D residue 354 LEU Chi-restraints excluded: chain D residue 453 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 34 random chunks: chunk 5 optimal weight: 3.9990 chunk 14 optimal weight: 0.5980 chunk 25 optimal weight: 0.0570 chunk 27 optimal weight: 3.9990 chunk 1 optimal weight: 1.9990 chunk 9 optimal weight: 0.9990 chunk 18 optimal weight: 0.5980 chunk 19 optimal weight: 0.6980 chunk 2 optimal weight: 2.9990 chunk 13 optimal weight: 0.8980 chunk 31 optimal weight: 0.7980 overall best weight: 0.5498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 446 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.177889 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.136283 restraints weight = 3199.412| |-----------------------------------------------------------------------------| r_work (start): 0.3509 rms_B_bonded: 1.22 r_work: 0.3342 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3211 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.3211 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.3246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.021 3514 Z= 0.158 Angle : 0.527 5.549 4941 Z= 0.298 Chirality : 0.036 0.122 531 Planarity : 0.005 0.033 485 Dihedral : 25.986 85.213 809 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 3.54 % Allowed : 13.78 % 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: 0.79 (0.51), residues: 292 helix: 1.17 (0.50), residues: 119 sheet: -1.67 (0.68), residues: 44 loop : 0.99 (0.59), residues: 129 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 472 TYR 0.014 0.002 TYR D 482 PHE 0.012 0.001 PHE D 348 TRP 0.009 0.001 TRP D 230 HIS 0.005 0.001 HIS D 199 Details of bonding type rmsd covalent geometry : bond 0.00351 ( 3510) covalent geometry : angle 0.52208 ( 4935) hydrogen bonds : bond 0.03443 ( 162) hydrogen bonds : angle 3.82356 ( 398) metal coordination : bond 0.00559 ( 4) metal coordination : angle 2.19013 ( 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: 9 poor density : 38 time to evaluate : 0.101 Fit side-chains REVERT: D 163 TYR cc_start: 0.8565 (m-80) cc_final: 0.7736 (m-80) REVERT: D 287 ARG cc_start: 0.6911 (OUTLIER) cc_final: 0.5212 (ptm160) REVERT: D 361 GLU cc_start: 0.7790 (tt0) cc_final: 0.7555 (tt0) REVERT: D 481 GLU cc_start: 0.7206 (tt0) cc_final: 0.6938 (tt0) outliers start: 9 outliers final: 6 residues processed: 44 average time/residue: 0.0962 time to fit residues: 4.9176 Evaluate side-chains 40 residues out of total 254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 33 time to evaluate : 0.080 ------------------------------------------------------------------------------- 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 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: 0.9990 chunk 27 optimal weight: 5.9990 chunk 21 optimal weight: 0.9990 chunk 25 optimal weight: 0.9990 chunk 24 optimal weight: 0.0670 chunk 29 optimal weight: 0.5980 chunk 7 optimal weight: 0.9980 chunk 33 optimal weight: 0.8980 chunk 28 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 overall best weight: 0.7120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.175378 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.134705 restraints weight = 3234.296| |-----------------------------------------------------------------------------| r_work (start): 0.3477 rms_B_bonded: 1.22 r_work: 0.3322 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3186 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.3186 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 moved from start: 0.3435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 3514 Z= 0.182 Angle : 0.542 3.859 4941 Z= 0.307 Chirality : 0.037 0.132 531 Planarity : 0.005 0.031 485 Dihedral : 26.039 86.101 809 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 5.12 % Allowed : 12.99 % Favored : 81.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.79 (0.51), residues: 292 helix: 1.37 (0.51), residues: 113 sheet: -1.78 (0.68), residues: 44 loop : 0.84 (0.58), residues: 135 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 58 TYR 0.016 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 covalent geometry : bond 0.00409 ( 3510) covalent geometry : angle 0.53657 ( 4935) hydrogen bonds : bond 0.03672 ( 162) hydrogen bonds : angle 3.81077 ( 398) metal coordination : bond 0.00792 ( 4) metal coordination : angle 2.32221 ( 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: 13 poor density : 35 time to evaluate : 0.175 Fit side-chains REVERT: D 163 TYR cc_start: 0.8590 (m-80) cc_final: 0.7720 (m-80) REVERT: D 287 ARG cc_start: 0.6868 (OUTLIER) cc_final: 0.5413 (ptm160) REVERT: D 481 GLU cc_start: 0.7529 (tt0) cc_final: 0.7229 (tt0) outliers start: 13 outliers final: 10 residues processed: 45 average time/residue: 0.1058 time to fit residues: 5.5196 Evaluate side-chains 44 residues out of total 254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 33 time to evaluate : 0.097 ------------------------------------------------------------------------------- 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 328 SER Chi-restraints excluded: chain D residue 351 GLU Chi-restraints excluded: chain D residue 354 LEU Chi-restraints excluded: chain D residue 453 THR Chi-restraints excluded: chain D residue 458 MET Chi-restraints excluded: chain D residue 463 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 34 random chunks: chunk 26 optimal weight: 1.9990 chunk 6 optimal weight: 0.7980 chunk 12 optimal weight: 0.8980 chunk 8 optimal weight: 0.2980 chunk 30 optimal weight: 0.9990 chunk 28 optimal weight: 3.9990 chunk 19 optimal weight: 0.8980 chunk 22 optimal weight: 0.5980 chunk 11 optimal weight: 0.6980 chunk 2 optimal weight: 2.9990 chunk 14 optimal weight: 0.9980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.173944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.135474 restraints weight = 3229.290| |-----------------------------------------------------------------------------| r_work (start): 0.3500 rms_B_bonded: 1.11 r_work: 0.3351 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.3220 rms_B_bonded: 3.43 restraints_weight: 0.2500 r_work (final): 0.3220 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 moved from start: 0.3635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.021 3514 Z= 0.170 Angle : 0.522 3.774 4941 Z= 0.297 Chirality : 0.036 0.126 531 Planarity : 0.004 0.031 485 Dihedral : 25.978 86.199 809 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 5.51 % Allowed : 12.99 % Favored : 81.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.82 (0.51), residues: 292 helix: 1.48 (0.51), residues: 112 sheet: -1.83 (0.68), residues: 44 loop : 0.80 (0.57), residues: 136 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 0.012 0.001 PHE D 464 TRP 0.007 0.001 TRP D 230 HIS 0.004 0.001 HIS D 199 Details of bonding type rmsd covalent geometry : bond 0.00380 ( 3510) covalent geometry : angle 0.51685 ( 4935) hydrogen bonds : bond 0.03380 ( 162) hydrogen bonds : angle 3.74760 ( 398) metal coordination : bond 0.00669 ( 4) metal coordination : angle 2.16757 ( 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: 14 poor density : 32 time to evaluate : 0.059 Fit side-chains REVERT: D 163 TYR cc_start: 0.8570 (m-80) cc_final: 0.7606 (m-80) REVERT: D 287 ARG cc_start: 0.6812 (OUTLIER) cc_final: 0.5202 (ptm160) REVERT: D 453 THR cc_start: 0.8921 (OUTLIER) cc_final: 0.8721 (t) REVERT: D 481 GLU cc_start: 0.7485 (tt0) cc_final: 0.7188 (tt0) outliers start: 14 outliers final: 11 residues processed: 43 average time/residue: 0.0979 time to fit residues: 4.8845 Evaluate side-chains 43 residues out of total 254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 30 time to evaluate : 0.090 ------------------------------------------------------------------------------- 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 354 LEU Chi-restraints excluded: chain D residue 453 THR Chi-restraints excluded: chain D residue 458 MET Chi-restraints excluded: chain D residue 463 THR Chi-restraints excluded: chain D residue 473 THR 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: 0.7980 chunk 3 optimal weight: 1.9990 chunk 0 optimal weight: 0.9990 chunk 14 optimal weight: 0.9990 chunk 30 optimal weight: 0.9990 chunk 21 optimal weight: 0.5980 chunk 16 optimal weight: 0.9980 chunk 19 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.172834 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.143227 restraints weight = 3319.892| |-----------------------------------------------------------------------------| r_work (start): 0.3619 rms_B_bonded: 1.08 r_work: 0.3323 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3199 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.3199 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.3727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 3514 Z= 0.193 Angle : 0.545 3.994 4941 Z= 0.309 Chirality : 0.038 0.134 531 Planarity : 0.005 0.033 485 Dihedral : 26.049 86.640 809 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 5.51 % Allowed : 12.99 % Favored : 81.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.72 (0.51), residues: 292 helix: 1.44 (0.51), residues: 112 sheet: -1.91 (0.69), residues: 44 loop : 0.71 (0.58), residues: 136 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 444 TYR 0.016 0.002 TYR D 482 PHE 0.013 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 covalent geometry : bond 0.00436 ( 3510) covalent geometry : angle 0.53872 ( 4935) hydrogen bonds : bond 0.03699 ( 162) hydrogen bonds : angle 3.79639 ( 398) metal coordination : bond 0.00825 ( 4) metal coordination : angle 2.47027 ( 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: 14 poor density : 32 time to evaluate : 0.062 Fit side-chains REVERT: D 163 TYR cc_start: 0.8630 (m-80) cc_final: 0.7681 (m-80) REVERT: D 287 ARG cc_start: 0.6828 (OUTLIER) cc_final: 0.5295 (ptm160) REVERT: D 481 GLU cc_start: 0.7453 (tt0) cc_final: 0.7199 (tt0) outliers start: 14 outliers final: 11 residues processed: 43 average time/residue: 0.0937 time to fit residues: 4.6647 Evaluate side-chains 43 residues out of total 254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 31 time to evaluate : 0.097 ------------------------------------------------------------------------------- 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 354 LEU Chi-restraints excluded: chain D residue 458 MET Chi-restraints excluded: chain D residue 463 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: 1.9990 chunk 5 optimal weight: 0.8980 chunk 26 optimal weight: 0.7980 chunk 23 optimal weight: 1.9990 chunk 6 optimal weight: 0.8980 chunk 22 optimal weight: 0.8980 chunk 30 optimal weight: 0.9980 chunk 24 optimal weight: 1.9990 chunk 13 optimal weight: 0.5980 chunk 33 optimal weight: 1.9990 chunk 2 optimal weight: 2.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.172814 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.143807 restraints weight = 3321.963| |-----------------------------------------------------------------------------| r_work (start): 0.3625 rms_B_bonded: 1.06 r_work: 0.3318 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3191 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.3191 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.3824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 3514 Z= 0.193 Angle : 0.543 3.997 4941 Z= 0.307 Chirality : 0.037 0.133 531 Planarity : 0.005 0.033 485 Dihedral : 26.047 86.761 809 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 5.12 % Allowed : 13.39 % Favored : 81.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.53 (0.51), residues: 112 sheet: -1.91 (0.69), residues: 44 loop : 0.70 (0.59), residues: 136 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 444 TYR 0.016 0.002 TYR D 482 PHE 0.013 0.001 PHE D 464 TRP 0.007 0.001 TRP D 64 HIS 0.004 0.001 HIS D 199 Details of bonding type rmsd covalent geometry : bond 0.00439 ( 3510) covalent geometry : angle 0.53592 ( 4935) hydrogen bonds : bond 0.03591 ( 162) hydrogen bonds : angle 3.82453 ( 398) metal coordination : bond 0.00800 ( 4) metal coordination : angle 2.48657 ( 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: 13 poor density : 31 time to evaluate : 0.106 Fit side-chains REVERT: D 163 TYR cc_start: 0.8600 (m-80) cc_final: 0.7673 (m-80) REVERT: D 287 ARG cc_start: 0.6653 (OUTLIER) cc_final: 0.5152 (ptm160) outliers start: 13 outliers final: 11 residues processed: 41 average time/residue: 0.0966 time to fit residues: 4.6000 Evaluate side-chains 41 residues out of total 254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 29 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 354 LEU Chi-restraints excluded: chain D residue 458 MET Chi-restraints excluded: chain D residue 463 THR Chi-restraints excluded: chain D residue 473 THR 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: 0.9990 chunk 9 optimal weight: 0.7980 chunk 24 optimal weight: 3.9990 chunk 14 optimal weight: 0.5980 chunk 3 optimal weight: 0.9990 chunk 11 optimal weight: 0.6980 chunk 17 optimal weight: 0.0050 chunk 27 optimal weight: 2.9990 chunk 2 optimal weight: 2.9990 chunk 21 optimal weight: 0.8980 overall best weight: 0.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.173944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.145972 restraints weight = 3278.103| |-----------------------------------------------------------------------------| r_work (start): 0.3653 rms_B_bonded: 1.01 r_work: 0.3348 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3221 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.3221 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 moved from start: 0.3879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.021 3514 Z= 0.164 Angle : 0.518 3.811 4941 Z= 0.295 Chirality : 0.036 0.125 531 Planarity : 0.004 0.033 485 Dihedral : 25.967 86.845 809 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 4.72 % Allowed : 13.78 % Favored : 81.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.80 (0.52), residues: 292 helix: 1.58 (0.51), residues: 113 sheet: -1.82 (0.70), residues: 44 loop : 0.65 (0.59), 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 0.012 0.001 PHE D 464 TRP 0.006 0.001 TRP D 230 HIS 0.004 0.001 HIS D 199 Details of bonding type rmsd covalent geometry : bond 0.00366 ( 3510) covalent geometry : angle 0.51343 ( 4935) hydrogen bonds : bond 0.03359 ( 162) hydrogen bonds : angle 3.75800 ( 398) metal coordination : bond 0.00583 ( 4) metal coordination : angle 2.13400 ( 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: 12 poor density : 28 time to evaluate : 0.063 Fit side-chains REVERT: D 163 TYR cc_start: 0.8568 (m-80) cc_final: 0.7749 (m-80) REVERT: D 287 ARG cc_start: 0.6658 (OUTLIER) cc_final: 0.5023 (ptm160) outliers start: 12 outliers final: 11 residues processed: 38 average time/residue: 0.0880 time to fit residues: 3.9182 Evaluate side-chains 40 residues out of total 254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 28 time to evaluate : 0.097 ------------------------------------------------------------------------------- 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 354 LEU Chi-restraints excluded: chain D residue 458 MET Chi-restraints excluded: chain D residue 463 THR Chi-restraints excluded: chain D residue 473 THR 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: 0.9990 chunk 28 optimal weight: 0.3980 chunk 29 optimal weight: 2.9990 chunk 27 optimal weight: 0.9990 chunk 10 optimal weight: 0.9980 chunk 18 optimal weight: 0.9990 chunk 21 optimal weight: 0.7980 chunk 32 optimal weight: 0.9990 chunk 30 optimal weight: 0.9980 chunk 7 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.172922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.143398 restraints weight = 3238.503| |-----------------------------------------------------------------------------| r_work (start): 0.3600 rms_B_bonded: 1.07 r_work: 0.3309 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3179 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3179 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 moved from start: 0.3917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.023 3514 Z= 0.185 Angle : 0.539 4.008 4941 Z= 0.305 Chirality : 0.037 0.129 531 Planarity : 0.004 0.033 485 Dihedral : 26.017 86.846 809 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 5.12 % Allowed : 13.39 % Favored : 81.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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 (0.52), residues: 292 helix: 1.56 (0.51), residues: 113 sheet: -1.91 (0.69), residues: 44 loop : 0.62 (0.59), residues: 135 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 444 TYR 0.016 0.002 TYR D 482 PHE 0.013 0.001 PHE D 464 TRP 0.007 0.001 TRP D 230 HIS 0.004 0.001 HIS D 199 Details of bonding type rmsd covalent geometry : bond 0.00420 ( 3510) covalent geometry : angle 0.53236 ( 4935) hydrogen bonds : bond 0.03573 ( 162) hydrogen bonds : angle 3.79271 ( 398) metal coordination : bond 0.00766 ( 4) metal coordination : angle 2.47907 ( 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 43 residues out of total 254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 30 time to evaluate : 0.108 Fit side-chains REVERT: D 163 TYR cc_start: 0.8599 (m-80) cc_final: 0.7646 (m-80) REVERT: D 287 ARG cc_start: 0.6626 (OUTLIER) cc_final: 0.4931 (ptm160) outliers start: 13 outliers final: 11 residues processed: 41 average time/residue: 0.0874 time to fit residues: 4.2951 Evaluate side-chains 41 residues out of total 254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 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 354 LEU Chi-restraints excluded: chain D residue 458 MET Chi-restraints excluded: chain D residue 463 THR Chi-restraints excluded: chain D residue 473 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 34 random chunks: chunk 30 optimal weight: 0.9990 chunk 7 optimal weight: 0.8980 chunk 25 optimal weight: 0.8980 chunk 24 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 6 optimal weight: 0.7980 chunk 12 optimal weight: 0.5980 chunk 17 optimal weight: 3.9990 chunk 16 optimal weight: 0.5980 chunk 9 optimal weight: 0.4980 chunk 15 optimal weight: 0.6980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.173635 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.145677 restraints weight = 3338.185| |-----------------------------------------------------------------------------| r_work (start): 0.3655 rms_B_bonded: 1.02 r_work: 0.3335 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3206 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.3206 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 moved from start: 0.3945 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= 0.169 Angle : 0.528 3.834 4941 Z= 0.300 Chirality : 0.037 0.125 531 Planarity : 0.004 0.032 485 Dihedral : 25.977 86.679 809 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 4.72 % Allowed : 13.39 % Favored : 81.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.78 (0.52), residues: 292 helix: 1.61 (0.51), residues: 113 sheet: -1.87 (0.70), residues: 44 loop : 0.61 (0.59), 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 0.012 0.001 PHE D 464 TRP 0.006 0.001 TRP D 230 HIS 0.004 0.001 HIS D 199 Details of bonding type rmsd covalent geometry : bond 0.00378 ( 3510) covalent geometry : angle 0.52210 ( 4935) hydrogen bonds : bond 0.03413 ( 162) hydrogen bonds : angle 3.76548 ( 398) metal coordination : bond 0.00653 ( 4) metal coordination : angle 2.27536 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1157.76 seconds wall clock time: 20 minutes 20.37 seconds (1220.37 seconds total)