Starting phenix.real_space_refine on Tue Aug 4 12:04:22 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9iua_60895/08_2026/9iua_60895.cif Found real_map, /net/cci-nas-00/data/ceres_data/9iua_60895/08_2026/9iua_60895.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.78 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9iua_60895/08_2026/9iua_60895.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9iua_60895/08_2026/9iua_60895.map" model { file = "/net/cci-nas-00/data/ceres_data/9iua_60895/08_2026/9iua_60895.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9iua_60895/08_2026/9iua_60895.cif" } resolution = 3.78 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= 0.030 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 36 5.49 5 S 9 5.16 5 C 1238 2.51 5 N 402 2.21 5 O 468 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 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: 2154 Number of models: 1 Model: "" Number of chains: 4 Chain: "G1" Number of atoms: 370 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 370 Classifications: {'DNA': 18} Link IDs: {'rna3p': 17} Chain: "H1" Number of atoms: 368 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 368 Classifications: {'DNA': 18} Link IDs: {'rna3p': 17} Chain: "C" Number of atoms: 1415 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1415 Classifications: {'peptide': 177} Link IDs: {'PTRANS': 8, 'TRANS': 168} Chain breaks: 3 Chain: "C" 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 1425 SG CYS C 304 33.951 42.017 16.994 1.00198.50 S ATOM 1443 SG CYS C 307 33.730 38.218 16.696 1.00196.64 S ATOM 1594 SG CYS C 326 35.896 39.210 18.793 1.00188.29 S ATOM 1666 SG CYS C 335 36.869 40.318 15.310 1.00202.76 S Time building chain proxies: 0.63, per 1000 atoms: 0.29 Number of scatterers: 2154 At special positions: 0 Unit cell: (77.6048, 74.0773, 50.5607, 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 9 16.00 P 36 15.00 O 468 8.00 N 402 7.00 C 1238 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: 0.19 Conformation dependent library (CDL) restraints added in 61.8 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN C1000 " pdb="ZN ZN C1000 " - pdb=" SG CYS C 326 " pdb="ZN ZN C1000 " - pdb=" SG CYS C 335 " pdb="ZN ZN C1000 " - pdb=" SG CYS C 307 " pdb="ZN ZN C1000 " - pdb=" SG CYS C 304 " Number of angles added : 6 338 Ramachandran restraints generated. 169 Oldfield, 0 Emsley, 169 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 330 Finding SS restraints... Secondary structure from input PDB file: 9 helices and 2 sheets defined 50.8% alpha, 9.6% beta 18 base pairs and 28 stacking pairs defined. Time for finding SS restraints: 0.24 Creating SS restraints... Processing helix chain 'C' and resid 182 through 193 Processing helix chain 'C' and resid 197 through 208 Processing helix chain 'C' and resid 212 through 217 Processing helix chain 'C' and resid 231 through 241 Processing helix chain 'C' and resid 274 through 283 Processing helix chain 'C' and resid 328 through 331 Processing helix chain 'C' and resid 342 through 357 Processing helix chain 'C' and resid 449 through 458 Processing helix chain 'C' and resid 478 through 486 Processing sheet with id=AA1, first strand: chain 'C' and resid 302 through 304 Processing sheet with id=AA2, first strand: chain 'C' and resid 311 through 314 69 hydrogen bonds defined for protein. 192 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 48 hydrogen bonds 96 hydrogen bond angles 0 basepair planarities 18 basepair parallelities 28 stacking parallelities Total time for adding SS restraints: 0.24 Time building geometry restraints manager: 0.24 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 440 1.33 - 1.45: 756 1.45 - 1.57: 991 1.57 - 1.69: 70 1.69 - 1.81: 13 Bond restraints: 2270 Sorted by residual: bond pdb=" P DGH1 29 " pdb=" O5' DGH1 29 " ideal model delta sigma weight residual 1.593 1.635 -0.042 1.00e-02 1.00e+04 1.80e+01 bond pdb=" N1 DCH1 34 " pdb=" C6 DCH1 34 " ideal model delta sigma weight residual 1.367 1.344 0.023 6.00e-03 2.78e+04 1.53e+01 bond pdb=" P DGG1 1 " pdb=" O5' DGG1 1 " ideal model delta sigma weight residual 1.593 1.628 -0.035 1.00e-02 1.00e+04 1.23e+01 bond pdb=" N1 DCH1 31 " pdb=" C6 DCH1 31 " ideal model delta sigma weight residual 1.367 1.347 0.020 6.00e-03 2.78e+04 1.07e+01 bond pdb=" CA SER C 212 " pdb=" CB SER C 212 " ideal model delta sigma weight residual 1.526 1.480 0.046 1.53e-02 4.27e+03 9.04e+00 ... (remaining 2265 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.41: 2785 2.41 - 4.81: 338 4.81 - 7.21: 65 7.21 - 9.62: 21 9.62 - 12.02: 6 Bond angle restraints: 3215 Sorted by residual: angle pdb=" C1' DGH1 29 " pdb=" N9 DGH1 29 " pdb=" C8 DGH1 29 " ideal model delta sigma weight residual 127.00 137.02 -10.02 1.30e+00 5.92e-01 5.94e+01 angle pdb=" O4' DGH1 32 " pdb=" C1' DGH1 32 " pdb=" N9 DGH1 32 " ideal model delta sigma weight residual 108.00 102.91 5.09 7.00e-01 2.04e+00 5.29e+01 angle pdb=" C1' DGH1 29 " pdb=" N9 DGH1 29 " pdb=" C4 DGH1 29 " ideal model delta sigma weight residual 126.50 117.15 9.35 1.30e+00 5.92e-01 5.17e+01 angle pdb=" O3' DGH1 32 " pdb=" P DTH1 33 " pdb=" O5' DTH1 33 " ideal model delta sigma weight residual 104.00 91.98 12.02 1.90e+00 2.77e-01 4.00e+01 angle pdb=" O3' DGH1 35 " pdb=" P DAH1 36 " pdb=" O5' DAH1 36 " ideal model delta sigma weight residual 104.00 92.30 11.70 1.90e+00 2.77e-01 3.79e+01 ... (remaining 3210 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.39: 867 15.39 - 30.77: 169 30.77 - 46.16: 104 46.16 - 61.55: 95 61.55 - 76.93: 8 Dihedral angle restraints: 1243 sinusoidal: 735 harmonic: 508 Sorted by residual: dihedral pdb=" CA LEU C 282 " pdb=" C LEU C 282 " pdb=" N VAL C 283 " pdb=" CA VAL C 283 " ideal model delta harmonic sigma weight residual -180.00 -141.68 -38.32 0 5.00e+00 4.00e-02 5.87e+01 dihedral pdb=" C TYR C 216 " pdb=" N TYR C 216 " pdb=" CA TYR C 216 " pdb=" CB TYR C 216 " ideal model delta harmonic sigma weight residual -122.60 -134.26 11.66 0 2.50e+00 1.60e-01 2.18e+01 dihedral pdb=" C HIS C 199 " pdb=" N HIS C 199 " pdb=" CA HIS C 199 " pdb=" CB HIS C 199 " ideal model delta harmonic sigma weight residual -122.60 -134.01 11.41 0 2.50e+00 1.60e-01 2.08e+01 ... (remaining 1240 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.140: 313 0.140 - 0.279: 34 0.279 - 0.419: 6 0.419 - 0.559: 0 0.559 - 0.698: 2 Chirality restraints: 355 Sorted by residual: chirality pdb=" P DGH1 29 " pdb=" OP1 DGH1 29 " pdb=" OP2 DGH1 29 " pdb=" O5' DGH1 29 " both_signs ideal model delta sigma weight residual True 2.34 -3.03 -0.70 2.00e-01 2.50e+01 1.22e+01 chirality pdb=" P DGG1 1 " pdb=" OP1 DGG1 1 " pdb=" OP2 DGG1 1 " pdb=" O5' DGG1 1 " both_signs ideal model delta sigma weight residual True 2.34 -2.99 -0.66 2.00e-01 2.50e+01 1.08e+01 chirality pdb=" P DCH1 37 " pdb=" OP1 DCH1 37 " pdb=" OP2 DCH1 37 " pdb=" O5' DCH1 37 " both_signs ideal model delta sigma weight residual True 2.34 -2.73 -0.39 2.00e-01 2.50e+01 3.81e+00 ... (remaining 352 not shown) Planarity restraints: 286 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DGH1 32 " -0.056 2.00e-02 2.50e+03 2.68e-02 2.15e+01 pdb=" N9 DGH1 32 " 0.058 2.00e-02 2.50e+03 pdb=" C8 DGH1 32 " 0.020 2.00e-02 2.50e+03 pdb=" N7 DGH1 32 " 0.004 2.00e-02 2.50e+03 pdb=" C5 DGH1 32 " -0.003 2.00e-02 2.50e+03 pdb=" C6 DGH1 32 " -0.015 2.00e-02 2.50e+03 pdb=" O6 DGH1 32 " -0.006 2.00e-02 2.50e+03 pdb=" N1 DGH1 32 " -0.019 2.00e-02 2.50e+03 pdb=" C2 DGH1 32 " 0.004 2.00e-02 2.50e+03 pdb=" N2 DGH1 32 " 0.029 2.00e-02 2.50e+03 pdb=" N3 DGH1 32 " -0.007 2.00e-02 2.50e+03 pdb=" C4 DGH1 32 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 461 " 0.364 9.50e-02 1.11e+02 1.64e-01 1.85e+01 pdb=" NE ARG C 461 " -0.031 2.00e-02 2.50e+03 pdb=" CZ ARG C 461 " 0.021 2.00e-02 2.50e+03 pdb=" NH1 ARG C 461 " -0.011 2.00e-02 2.50e+03 pdb=" NH2 ARG C 461 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DGG1 16 " 0.051 2.00e-02 2.50e+03 2.45e-02 1.81e+01 pdb=" N9 DGG1 16 " -0.047 2.00e-02 2.50e+03 pdb=" C8 DGG1 16 " -0.002 2.00e-02 2.50e+03 pdb=" N7 DGG1 16 " 0.006 2.00e-02 2.50e+03 pdb=" C5 DGG1 16 " 0.010 2.00e-02 2.50e+03 pdb=" C6 DGG1 16 " 0.019 2.00e-02 2.50e+03 pdb=" O6 DGG1 16 " -0.005 2.00e-02 2.50e+03 pdb=" N1 DGG1 16 " 0.013 2.00e-02 2.50e+03 pdb=" C2 DGG1 16 " -0.020 2.00e-02 2.50e+03 pdb=" N2 DGG1 16 " 0.018 2.00e-02 2.50e+03 pdb=" N3 DGG1 16 " -0.025 2.00e-02 2.50e+03 pdb=" C4 DGG1 16 " -0.019 2.00e-02 2.50e+03 ... (remaining 283 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 449 2.80 - 3.33: 1946 3.33 - 3.85: 4085 3.85 - 4.38: 4547 4.38 - 4.90: 6813 Nonbonded interactions: 17840 Sorted by model distance: nonbonded pdb=" NH1 ARG C 323 " pdb=" OG1 THR C 339 " model vdw 2.275 3.120 nonbonded pdb=" OP2 DCG1 12 " pdb=" NZ LYS C 236 " model vdw 2.367 3.120 nonbonded pdb=" O5' DCG1 18 " pdb=" O4' DCG1 18 " model vdw 2.451 2.432 nonbonded pdb=" OP2 DGH1 35 " pdb=" OH TYR C 312 " model vdw 2.471 3.040 nonbonded pdb=" O LEU C 297 " pdb=" ND2 ASN C 452 " model vdw 2.493 3.120 ... (remaining 17835 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 group one per residue 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: 0.960 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.020 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 3.500 Find NCS groups from input model: 0.000 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:0.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 5.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5896 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 : 0.010 0.056 2274 Z= 0.707 Angle : 1.898 21.763 3221 Z= 1.210 Chirality : 0.109 0.698 355 Planarity : 0.020 0.164 286 Dihedral : 24.967 76.932 913 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.59 % Allowed : 2.96 % Favored : 96.45 % Rotamer: Outliers : 8.67 % Allowed : 10.00 % Favored : 81.33 % Cbeta Deviations : 1.82 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.60 % 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: -0.26 (0.57), residues: 169 helix: 0.19 (0.46), residues: 88 sheet: -0.21 (1.31), residues: 19 loop : -0.48 (0.73), residues: 62 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.025 0.005 ARG C 461 TYR 0.038 0.007 TYR C 216 PHE 0.020 0.004 PHE C 331 TRP 0.011 0.004 TRP C 345 HIS 0.014 0.005 HIS C 485 Details of bonding type rmsd/Z covalent geometry : bond 0.01034 / 0.71 ( 2270) covalent geometry : angle 1.84500 / 1.21 ( 3215) hydrogen bonds : bond 0.16210 / 16.85 ( 117) hydrogen bonds : angle 7.41123 / 9.96 ( 288) metal coordination : bond 0.03706 / 2.98 ( 4) metal coordination : angle 10.50380 / 18.53 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 338 Ramachandran restraints generated. 169 Oldfield, 0 Emsley, 169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 338 Ramachandran restraints generated. 169 Oldfield, 0 Emsley, 169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 46 time to evaluate : 0.067 Fit side-chains REVERT: C 183 ARG cc_start: 0.6513 (mmt180) cc_final: 0.5566 (ptt90) REVERT: C 229 GLU cc_start: 0.7122 (OUTLIER) cc_final: 0.6854 (pt0) REVERT: C 274 GLN cc_start: 0.7631 (mt0) cc_final: 0.6663 (pm20) REVERT: C 458 MET cc_start: 0.7556 (OUTLIER) cc_final: 0.7056 (mmm) REVERT: C 480 GLN cc_start: 0.7885 (pp30) cc_final: 0.7632 (pp30) outliers start: 13 outliers final: 7 residues processed: 54 average time/residue: 0.0437 time to fit residues: 2.7840 Evaluate side-chains 43 residues out of total 150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 34 time to evaluate : 0.035 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 198 LEU Chi-restraints excluded: chain C residue 199 HIS Chi-restraints excluded: chain C residue 216 TYR Chi-restraints excluded: chain C residue 229 GLU Chi-restraints excluded: chain C residue 282 LEU Chi-restraints excluded: chain C residue 299 LEU Chi-restraints excluded: chain C residue 314 PHE Chi-restraints excluded: chain C residue 352 GLN Chi-restraints excluded: chain C residue 458 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 19 random chunks: chunk 12 optimal weight: 0.2980 chunk 13 optimal weight: 2.9990 chunk 1 optimal weight: 2.9990 chunk 8 optimal weight: 0.5980 chunk 16 optimal weight: 0.8980 chunk 15 optimal weight: 0.6980 chunk 9 optimal weight: 0.9980 chunk 11 optimal weight: 1.9990 chunk 18 optimal weight: 3.9990 chunk 6 optimal weight: 0.5980 chunk 4 optimal weight: 0.4980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 334 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.161956 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.128766 restraints weight = 3096.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.133846 restraints weight = 1800.646| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.137382 restraints weight = 1254.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.139696 restraints weight = 967.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.141497 restraints weight = 806.229| |-----------------------------------------------------------------------------| r_work (final): 0.3528 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7740 moved from start: 0.1948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 2274 Z= 0.195 Angle : 0.850 14.232 3221 Z= 0.449 Chirality : 0.052 0.264 355 Planarity : 0.005 0.028 286 Dihedral : 27.818 82.954 590 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 4.00 % Allowed : 13.33 % Favored : 82.67 % 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: 0.81 (0.62), residues: 169 helix: 2.03 (0.53), residues: 82 sheet: -1.01 (0.74), residues: 33 loop : -0.71 (0.84), residues: 54 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 323 TYR 0.030 0.003 TYR C 216 PHE 0.010 0.002 PHE C 464 TRP 0.009 0.002 TRP C 230 HIS 0.013 0.003 HIS C 203 Details of bonding type rmsd/Z covalent geometry : bond 0.00370 / 0.19 ( 2270) covalent geometry : angle 0.80022 / 0.45 ( 3215) hydrogen bonds : bond 0.06580 / 7.58 ( 117) hydrogen bonds : angle 3.55727 / 5.00 ( 288) metal coordination : bond 0.01152 / 1.02 ( 4) metal coordination : angle 6.66765 / 11.68 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 338 Ramachandran restraints generated. 169 Oldfield, 0 Emsley, 169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 338 Ramachandran restraints generated. 169 Oldfield, 0 Emsley, 169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 40 time to evaluate : 0.041 Fit side-chains REVERT: C 183 ARG cc_start: 0.6408 (mmt180) cc_final: 0.5475 (ttp-170) outliers start: 6 outliers final: 4 residues processed: 46 average time/residue: 0.0426 time to fit residues: 2.2631 Evaluate side-chains 37 residues out of total 150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 33 time to evaluate : 0.034 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 199 HIS Chi-restraints excluded: chain C residue 216 TYR Chi-restraints excluded: chain C residue 282 LEU Chi-restraints excluded: chain C residue 314 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 19 random chunks: chunk 2 optimal weight: 0.9990 chunk 15 optimal weight: 2.9990 chunk 12 optimal weight: 0.7980 chunk 18 optimal weight: 4.9990 chunk 13 optimal weight: 1.9990 chunk 17 optimal weight: 0.8980 chunk 8 optimal weight: 2.9990 chunk 7 optimal weight: 0.6980 chunk 3 optimal weight: 0.7980 chunk 9 optimal weight: 1.9990 chunk 4 optimal weight: 0.5980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 194 ASN C 480 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.154137 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.121085 restraints weight = 3100.049| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.125320 restraints weight = 1914.047| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.128225 restraints weight = 1401.445| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.130390 restraints weight = 1125.389| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.131618 restraints weight = 961.714| |-----------------------------------------------------------------------------| r_work (final): 0.3377 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7726 moved from start: 0.2844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 2274 Z= 0.191 Angle : 0.718 9.850 3221 Z= 0.388 Chirality : 0.042 0.146 355 Planarity : 0.005 0.028 286 Dihedral : 27.864 63.368 577 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 3.33 % Allowed : 15.33 % Favored : 81.33 % 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: 0.76 (0.63), residues: 169 helix: 2.15 (0.55), residues: 82 sheet: -1.56 (0.73), residues: 33 loop : -0.63 (0.83), residues: 54 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG C 279 TYR 0.016 0.003 TYR C 216 PHE 0.013 0.002 PHE C 464 TRP 0.008 0.002 TRP C 345 HIS 0.007 0.002 HIS C 203 Details of bonding type rmsd/Z covalent geometry : bond 0.00360 / 0.19 ( 2270) covalent geometry : angle 0.68389 / 0.39 ( 3215) hydrogen bonds : bond 0.05456 / 5.94 ( 117) hydrogen bonds : angle 3.58179 / 5.14 ( 288) metal coordination : bond 0.00846 / 0.79 ( 4) metal coordination : angle 5.12182 / 9.17 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 338 Ramachandran restraints generated. 169 Oldfield, 0 Emsley, 169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 338 Ramachandran restraints generated. 169 Oldfield, 0 Emsley, 169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 34 time to evaluate : 0.056 Fit side-chains REVERT: C 183 ARG cc_start: 0.6413 (mmt180) cc_final: 0.5231 (ptt90) REVERT: C 193 ASP cc_start: 0.8617 (m-30) cc_final: 0.8315 (m-30) REVERT: C 274 GLN cc_start: 0.5551 (pm20) cc_final: 0.5241 (pm20) outliers start: 5 outliers final: 5 residues processed: 37 average time/residue: 0.0452 time to fit residues: 1.9658 Evaluate side-chains 38 residues out of total 150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 33 time to evaluate : 0.037 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 199 HIS Chi-restraints excluded: chain C residue 216 TYR Chi-restraints excluded: chain C residue 314 PHE Chi-restraints excluded: chain C residue 353 VAL Chi-restraints excluded: chain C residue 480 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 19 random chunks: chunk 13 optimal weight: 0.0570 chunk 0 optimal weight: 9.9990 chunk 8 optimal weight: 0.4980 chunk 7 optimal weight: 0.7980 chunk 5 optimal weight: 1.9990 chunk 11 optimal weight: 0.9980 chunk 16 optimal weight: 0.4980 chunk 3 optimal weight: 0.0870 chunk 15 optimal weight: 0.3980 chunk 6 optimal weight: 0.1980 chunk 18 optimal weight: 4.9990 overall best weight: 0.2476 ------------------------------------------------------------------------------- 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 = 0.3651 r_free = 0.3651 target = 0.150700 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.117628 restraints weight = 2949.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.122062 restraints weight = 1735.085| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.125170 restraints weight = 1226.631| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.127347 restraints weight = 959.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.128611 restraints weight = 804.741| |-----------------------------------------------------------------------------| r_work (final): 0.3544 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7736 moved from start: 0.3110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 2274 Z= 0.172 Angle : 0.673 9.881 3221 Z= 0.375 Chirality : 0.039 0.139 355 Planarity : 0.004 0.023 286 Dihedral : 27.582 59.547 575 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 3.33 % Allowed : 16.00 % Favored : 80.67 % 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: 0.87 (0.64), residues: 169 helix: 2.19 (0.55), residues: 82 sheet: -1.65 (0.73), residues: 33 loop : -0.35 (0.87), residues: 54 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 279 TYR 0.013 0.002 TYR C 216 PHE 0.011 0.001 PHE C 464 TRP 0.011 0.001 TRP C 345 HIS 0.007 0.001 HIS C 203 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.17 ( 2270) covalent geometry : angle 0.64804 / 0.37 ( 3215) hydrogen bonds : bond 0.04853 / 5.26 ( 117) hydrogen bonds : angle 3.55439 / 5.34 ( 288) metal coordination : bond 0.00566 / 0.51 ( 4) metal coordination : angle 4.27835 / 7.72 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 338 Ramachandran restraints generated. 169 Oldfield, 0 Emsley, 169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 338 Ramachandran restraints generated. 169 Oldfield, 0 Emsley, 169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 34 time to evaluate : 0.056 Fit side-chains REVERT: C 183 ARG cc_start: 0.6326 (mmt180) cc_final: 0.5175 (ptt90) REVERT: C 216 TYR cc_start: 0.6724 (OUTLIER) cc_final: 0.6304 (t80) outliers start: 5 outliers final: 1 residues processed: 38 average time/residue: 0.0713 time to fit residues: 3.1258 Evaluate side-chains 35 residues out of total 150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 33 time to evaluate : 0.057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 199 HIS Chi-restraints excluded: chain C residue 216 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 19 random chunks: chunk 8 optimal weight: 0.6980 chunk 12 optimal weight: 0.0370 chunk 1 optimal weight: 4.9990 chunk 13 optimal weight: 3.9990 chunk 14 optimal weight: 0.5980 chunk 15 optimal weight: 0.7980 chunk 5 optimal weight: 0.5980 chunk 6 optimal weight: 0.5980 chunk 3 optimal weight: 0.0670 chunk 17 optimal weight: 0.6980 chunk 16 optimal weight: 0.7980 overall best weight: 0.3796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 194 ASN C 480 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.156364 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.123470 restraints weight = 3092.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.127925 restraints weight = 1894.252| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.131086 restraints weight = 1361.984| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.133217 restraints weight = 1076.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.134483 restraints weight = 916.778| |-----------------------------------------------------------------------------| r_work (final): 0.3548 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7729 moved from start: 0.3373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 2274 Z= 0.145 Angle : 0.598 6.000 3221 Z= 0.338 Chirality : 0.037 0.109 355 Planarity : 0.004 0.044 286 Dihedral : 27.586 59.999 573 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 2.00 % Allowed : 15.33 % Favored : 82.67 % 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: 1.07 (0.65), residues: 169 helix: 2.37 (0.56), residues: 82 sheet: -1.62 (0.75), residues: 33 loop : -0.25 (0.90), residues: 54 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 461 TYR 0.014 0.002 TYR C 188 PHE 0.011 0.001 PHE C 464 TRP 0.009 0.001 TRP C 345 HIS 0.006 0.001 HIS C 203 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.14 ( 2270) covalent geometry : angle 0.57839 / 0.34 ( 3215) hydrogen bonds : bond 0.04625 / 4.88 ( 117) hydrogen bonds : angle 3.17758 / 4.57 ( 288) metal coordination : bond 0.00526 / 0.49 ( 4) metal coordination : angle 3.52275 / 6.39 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 338 Ramachandran restraints generated. 169 Oldfield, 0 Emsley, 169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 338 Ramachandran restraints generated. 169 Oldfield, 0 Emsley, 169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 33 time to evaluate : 0.062 Fit side-chains REVERT: C 183 ARG cc_start: 0.6287 (mmt180) cc_final: 0.5259 (ptt90) REVERT: C 216 TYR cc_start: 0.6678 (OUTLIER) cc_final: 0.6256 (t80) outliers start: 3 outliers final: 1 residues processed: 35 average time/residue: 0.0612 time to fit residues: 2.5279 Evaluate side-chains 34 residues out of total 150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 32 time to evaluate : 0.059 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 199 HIS Chi-restraints excluded: chain C residue 216 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 19 random chunks: chunk 17 optimal weight: 0.8980 chunk 10 optimal weight: 0.1980 chunk 6 optimal weight: 0.8980 chunk 4 optimal weight: 0.5980 chunk 9 optimal weight: 0.9980 chunk 2 optimal weight: 1.9990 chunk 1 optimal weight: 4.9990 chunk 16 optimal weight: 0.6980 chunk 3 optimal weight: 0.0170 chunk 12 optimal weight: 0.6980 chunk 0 optimal weight: 10.0000 overall best weight: 0.4418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 194 ASN C 480 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.161534 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.129151 restraints weight = 3042.451| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.133866 restraints weight = 1747.548| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.137135 restraints weight = 1223.192| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.139125 restraints weight = 950.425| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.140841 restraints weight = 802.278| |-----------------------------------------------------------------------------| r_work (final): 0.3470 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7718 moved from start: 0.3516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 2274 Z= 0.146 Angle : 0.591 5.664 3221 Z= 0.338 Chirality : 0.038 0.135 355 Planarity : 0.004 0.025 286 Dihedral : 27.534 59.992 573 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 2.00 % Allowed : 16.67 % Favored : 81.33 % 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: 0.99 (0.65), residues: 169 helix: 2.27 (0.55), residues: 82 sheet: -1.71 (0.74), residues: 33 loop : -0.19 (0.90), residues: 54 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 461 TYR 0.008 0.001 TYR C 216 PHE 0.009 0.001 PHE C 464 TRP 0.009 0.001 TRP C 345 HIS 0.006 0.001 HIS C 203 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.15 ( 2270) covalent geometry : angle 0.57459 / 0.34 ( 3215) hydrogen bonds : bond 0.04508 / 4.75 ( 117) hydrogen bonds : angle 3.14121 / 4.49 ( 288) metal coordination : bond 0.00577 / 0.52 ( 4) metal coordination : angle 3.29149 / 5.96 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 338 Ramachandran restraints generated. 169 Oldfield, 0 Emsley, 169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 338 Ramachandran restraints generated. 169 Oldfield, 0 Emsley, 169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 33 time to evaluate : 0.060 Fit side-chains REVERT: C 183 ARG cc_start: 0.6297 (mmt180) cc_final: 0.5253 (ptt90) REVERT: C 216 TYR cc_start: 0.6669 (OUTLIER) cc_final: 0.6251 (t80) outliers start: 3 outliers final: 1 residues processed: 35 average time/residue: 0.0598 time to fit residues: 2.4675 Evaluate side-chains 34 residues out of total 150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 32 time to evaluate : 0.057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 199 HIS Chi-restraints excluded: chain C residue 216 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 19 random chunks: chunk 11 optimal weight: 0.9980 chunk 8 optimal weight: 0.0670 chunk 13 optimal weight: 0.9980 chunk 14 optimal weight: 0.6980 chunk 3 optimal weight: 0.5980 chunk 4 optimal weight: 0.9990 chunk 17 optimal weight: 1.9990 chunk 16 optimal weight: 0.8980 chunk 18 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 10 optimal weight: 0.8980 overall best weight: 0.6318 ------------------------------------------------------------------------------- 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 = 0.3817 r_free = 0.3817 target = 0.162197 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.129498 restraints weight = 3092.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.134193 restraints weight = 1793.523| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.137508 restraints weight = 1269.222| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.139724 restraints weight = 994.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.141006 restraints weight = 838.362| |-----------------------------------------------------------------------------| r_work (final): 0.3467 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7759 moved from start: 0.3616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 2274 Z= 0.165 Angle : 0.606 5.848 3221 Z= 0.345 Chirality : 0.038 0.120 355 Planarity : 0.004 0.027 286 Dihedral : 27.580 59.820 573 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 2.00 % Allowed : 17.33 % Favored : 80.67 % 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: 1.00 (0.65), residues: 169 helix: 2.31 (0.54), residues: 82 sheet: -1.77 (0.74), residues: 33 loop : -0.18 (0.92), residues: 54 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 461 TYR 0.013 0.002 TYR C 188 PHE 0.009 0.002 PHE C 464 TRP 0.009 0.001 TRP C 345 HIS 0.006 0.001 HIS C 203 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.16 ( 2270) covalent geometry : angle 0.59077 / 0.34 ( 3215) hydrogen bonds : bond 0.04743 / 5.00 ( 117) hydrogen bonds : angle 3.23192 / 4.77 ( 288) metal coordination : bond 0.00715 / 0.65 ( 4) metal coordination : angle 3.20890 / 5.79 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 338 Ramachandran restraints generated. 169 Oldfield, 0 Emsley, 169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 338 Ramachandran restraints generated. 169 Oldfield, 0 Emsley, 169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 34 time to evaluate : 0.062 Fit side-chains REVERT: C 183 ARG cc_start: 0.6297 (mmt180) cc_final: 0.5216 (ptt90) REVERT: C 216 TYR cc_start: 0.6718 (OUTLIER) cc_final: 0.6310 (t80) REVERT: C 352 GLN cc_start: 0.8167 (mm110) cc_final: 0.7950 (mm110) outliers start: 3 outliers final: 1 residues processed: 36 average time/residue: 0.0615 time to fit residues: 2.6047 Evaluate side-chains 35 residues out of total 150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 33 time to evaluate : 0.058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 199 HIS Chi-restraints excluded: chain C residue 216 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 19 random chunks: chunk 15 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 13 optimal weight: 1.9990 chunk 3 optimal weight: 0.5980 chunk 5 optimal weight: 0.5980 chunk 7 optimal weight: 0.6980 chunk 17 optimal weight: 0.0070 chunk 11 optimal weight: 0.7980 chunk 16 optimal weight: 0.9980 chunk 18 optimal weight: 1.9990 chunk 14 optimal weight: 0.7980 overall best weight: 0.5398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 194 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.164165 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.132492 restraints weight = 3065.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.137184 restraints weight = 1726.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.140437 restraints weight = 1190.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.142773 restraints weight = 915.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.144272 restraints weight = 758.918| |-----------------------------------------------------------------------------| r_work (final): 0.3509 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7754 moved from start: 0.3796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 2274 Z= 0.156 Angle : 0.599 5.695 3221 Z= 0.343 Chirality : 0.038 0.160 355 Planarity : 0.004 0.027 286 Dihedral : 27.528 59.938 573 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 2.00 % Allowed : 18.67 % Favored : 79.33 % 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: 1.39 (0.66), residues: 169 helix: 2.38 (0.54), residues: 82 sheet: -1.75 (0.84), residues: 26 loop : 0.26 (0.90), residues: 61 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 279 TYR 0.007 0.001 TYR C 216 PHE 0.007 0.001 PHE C 464 TRP 0.010 0.001 TRP C 345 HIS 0.006 0.002 HIS C 203 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.16 ( 2270) covalent geometry : angle 0.58326 / 0.34 ( 3215) hydrogen bonds : bond 0.04548 / 4.78 ( 117) hydrogen bonds : angle 3.13208 / 4.49 ( 288) metal coordination : bond 0.00684 / 0.62 ( 4) metal coordination : angle 3.18993 / 5.78 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 338 Ramachandran restraints generated. 169 Oldfield, 0 Emsley, 169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 338 Ramachandran restraints generated. 169 Oldfield, 0 Emsley, 169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 32 time to evaluate : 0.056 Fit side-chains REVERT: C 183 ARG cc_start: 0.6307 (mmt180) cc_final: 0.5264 (ptt90) REVERT: C 216 TYR cc_start: 0.6742 (OUTLIER) cc_final: 0.6315 (t80) REVERT: C 352 GLN cc_start: 0.8246 (mm110) cc_final: 0.8003 (mm110) outliers start: 3 outliers final: 2 residues processed: 34 average time/residue: 0.0608 time to fit residues: 2.4329 Evaluate side-chains 35 residues out of total 150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 32 time to evaluate : 0.056 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 199 HIS Chi-restraints excluded: chain C residue 216 TYR Chi-restraints excluded: chain C residue 329 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 19 random chunks: chunk 0 optimal weight: 10.0000 chunk 9 optimal weight: 3.9990 chunk 5 optimal weight: 0.0060 chunk 13 optimal weight: 0.0970 chunk 18 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 7 optimal weight: 0.6980 chunk 14 optimal weight: 0.7980 chunk 1 optimal weight: 3.9990 chunk 12 optimal weight: 1.9990 chunk 17 optimal weight: 0.5980 overall best weight: 0.4394 ------------------------------------------------------------------------------- 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 = 0.3832 r_free = 0.3832 target = 0.163190 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.130892 restraints weight = 3143.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.135741 restraints weight = 1819.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.139201 restraints weight = 1269.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.141515 restraints weight = 983.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.143131 restraints weight = 819.073| |-----------------------------------------------------------------------------| r_work (final): 0.3447 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7694 moved from start: 0.3867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 2274 Z= 0.148 Angle : 0.591 5.888 3221 Z= 0.341 Chirality : 0.037 0.150 355 Planarity : 0.004 0.026 286 Dihedral : 27.475 59.929 573 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 2.00 % Allowed : 18.67 % Favored : 79.33 % 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: 1.51 (0.67), residues: 169 helix: 2.50 (0.54), residues: 82 sheet: -1.85 (0.83), residues: 26 loop : 0.36 (0.91), residues: 61 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 461 TYR 0.012 0.002 TYR C 188 PHE 0.009 0.001 PHE C 464 TRP 0.011 0.001 TRP C 345 HIS 0.006 0.001 HIS C 203 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.15 ( 2270) covalent geometry : angle 0.57882 / 0.34 ( 3215) hydrogen bonds : bond 0.04434 / 4.68 ( 117) hydrogen bonds : angle 3.07785 / 4.43 ( 288) metal coordination : bond 0.00581 / 0.52 ( 4) metal coordination : angle 2.82448 / 5.12 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 338 Ramachandran restraints generated. 169 Oldfield, 0 Emsley, 169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 338 Ramachandran restraints generated. 169 Oldfield, 0 Emsley, 169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 30 time to evaluate : 0.066 Fit side-chains REVERT: C 183 ARG cc_start: 0.6307 (mmt180) cc_final: 0.5221 (ptt90) REVERT: C 216 TYR cc_start: 0.6732 (OUTLIER) cc_final: 0.6274 (t80) REVERT: C 352 GLN cc_start: 0.8274 (mm110) cc_final: 0.7983 (mm110) outliers start: 3 outliers final: 1 residues processed: 32 average time/residue: 0.0747 time to fit residues: 2.7833 Evaluate side-chains 32 residues out of total 150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 30 time to evaluate : 0.063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 199 HIS Chi-restraints excluded: chain C residue 216 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 19 random chunks: chunk 17 optimal weight: 0.9990 chunk 3 optimal weight: 0.7980 chunk 0 optimal weight: 9.9990 chunk 8 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 chunk 4 optimal weight: 0.9980 chunk 1 optimal weight: 4.9990 chunk 6 optimal weight: 0.5980 chunk 5 optimal weight: 0.0670 chunk 2 optimal weight: 0.9990 overall best weight: 0.6920 ------------------------------------------------------------------------------- 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 = 0.3707 r_free = 0.3707 target = 0.153471 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.120133 restraints weight = 3144.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.124468 restraints weight = 1941.308| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.127577 restraints weight = 1410.388| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.129736 restraints weight = 1122.132| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.131045 restraints weight = 952.312| |-----------------------------------------------------------------------------| r_work (final): 0.3532 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7817 moved from start: 0.3987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 2274 Z= 0.170 Angle : 0.608 6.066 3221 Z= 0.346 Chirality : 0.037 0.117 355 Planarity : 0.004 0.028 286 Dihedral : 27.550 59.936 573 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 1.33 % Allowed : 20.00 % Favored : 78.67 % 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: 1.49 (0.67), residues: 169 helix: 2.52 (0.55), residues: 82 sheet: -1.98 (0.83), residues: 26 loop : 0.35 (0.90), residues: 61 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 279 TYR 0.007 0.001 TYR C 324 PHE 0.007 0.001 PHE C 464 TRP 0.009 0.001 TRP C 345 HIS 0.006 0.001 HIS C 203 Details of bonding type rmsd/Z covalent geometry : bond 0.00335 / 0.17 ( 2270) covalent geometry : angle 0.59606 / 0.35 ( 3215) hydrogen bonds : bond 0.04808 / 5.09 ( 117) hydrogen bonds : angle 3.09578 / 4.40 ( 288) metal coordination : bond 0.00784 / 0.71 ( 4) metal coordination : angle 2.85676 / 5.15 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 338 Ramachandran restraints generated. 169 Oldfield, 0 Emsley, 169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 338 Ramachandran restraints generated. 169 Oldfield, 0 Emsley, 169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 32 residues out of total 150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 30 time to evaluate : 0.060 Fit side-chains REVERT: C 183 ARG cc_start: 0.6331 (mmt180) cc_final: 0.5293 (ptt90) REVERT: C 216 TYR cc_start: 0.6770 (OUTLIER) cc_final: 0.6373 (t80) REVERT: C 352 GLN cc_start: 0.8290 (mm110) cc_final: 0.8009 (mm110) outliers start: 2 outliers final: 1 residues processed: 32 average time/residue: 0.0665 time to fit residues: 2.4906 Evaluate side-chains 32 residues out of total 150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 30 time to evaluate : 0.059 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 199 HIS Chi-restraints excluded: chain C residue 216 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 19 random chunks: chunk 18 optimal weight: 5.9990 chunk 12 optimal weight: 0.7980 chunk 10 optimal weight: 0.5980 chunk 6 optimal weight: 0.7980 chunk 14 optimal weight: 0.5980 chunk 4 optimal weight: 0.7980 chunk 2 optimal weight: 0.5980 chunk 17 optimal weight: 0.9990 chunk 7 optimal weight: 0.1980 chunk 5 optimal weight: 0.6980 chunk 13 optimal weight: 7.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- 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 = 0.3785 r_free = 0.3785 target = 0.159003 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.125606 restraints weight = 3193.088| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.130454 restraints weight = 1837.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.133809 restraints weight = 1282.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.135787 restraints weight = 1000.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.137590 restraints weight = 845.552| |-----------------------------------------------------------------------------| r_work (final): 0.3541 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7782 moved from start: 0.4079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 2274 Z= 0.152 Angle : 0.586 5.942 3221 Z= 0.339 Chirality : 0.037 0.150 355 Planarity : 0.004 0.027 286 Dihedral : 27.434 59.790 573 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 1.33 % Allowed : 20.00 % Favored : 78.67 % 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: 1.65 (0.68), residues: 169 helix: 2.60 (0.55), residues: 82 sheet: -1.87 (0.85), residues: 26 loop : 0.51 (0.93), residues: 61 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 279 TYR 0.013 0.002 TYR C 188 PHE 0.009 0.001 PHE C 464 TRP 0.011 0.001 TRP C 345 HIS 0.006 0.001 HIS C 203 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.15 ( 2270) covalent geometry : angle 0.57386 / 0.34 ( 3215) hydrogen bonds : bond 0.04415 / 4.63 ( 117) hydrogen bonds : angle 3.06797 / 4.45 ( 288) metal coordination : bond 0.00668 / 0.59 ( 4) metal coordination : angle 2.82110 / 5.12 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 650.54 seconds wall clock time: 11 minutes 48.88 seconds (708.88 seconds total)