Starting phenix.real_space_refine on Wed Jul 1 21:02:45 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9iua_60895/07_2026/9iua_60895.cif Found real_map, /net/cci-nas-00/data/ceres_data/9iua_60895/07_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_60895/07_2026/9iua_60895.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9iua_60895/07_2026/9iua_60895.map" model { file = "/net/cci-nas-00/data/ceres_data/9iua_60895/07_2026/9iua_60895.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9iua_60895/07_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-dev-6108/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: 0.82, per 1000 atoms: 0.38 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: 0.31 Conformation dependent library (CDL) restraints added in 44.1 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: 0.26 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: 0.20 Time building geometry restraints manager: 0.29 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: 2792 2.41 - 4.81: 332 4.81 - 7.21: 64 7.21 - 9.62: 21 9.62 - 12.02: 6 Bond angle restraints: 3215 Sorted by residual: 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 1.50e+00 4.44e-01 6.43e+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 1.50e+00 4.44e-01 6.09e+01 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=" O3' DTH1 33 " pdb=" P DCH1 34 " pdb=" O5' DCH1 34 " ideal model delta sigma weight residual 104.00 93.14 10.86 1.50e+00 4.44e-01 5.24e+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: 0.740 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: 0.040 Check model and map are aligned: 0.010 Set scattering table: 0.000 Process input model: 3.490 Find NCS groups from input model: 0.000 Set up NCS constraints: 0.000 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 5.170 ------------------------------------------------------------------------------- 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= 0.706 Angle : 1.892 21.763 3221 Z= 1.219 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 / 0.70 ( 2270) covalent geometry : angle 1.83887 / 1.22 ( 3215) hydrogen bonds : bond 0.16210 / 16.68 ( 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 : 0.037 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: 0.6855 (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: 0.7055 (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: 0.0387 time to fit residues: 2.4474 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 : 0.036 ------------------------------------------------------------------------------- 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: 0.9980 chunk 13 optimal weight: 0.3980 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: 0.3980 chunk 11 optimal weight: 0.7980 chunk 18 optimal weight: 3.9990 chunk 6 optimal weight: 0.3980 chunk 4 optimal weight: 0.7980 overall best weight: 0.4980 ------------------------------------------------------------------------------- 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 = 0.3832 r_free = 0.3832 target = 0.163016 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.130166 restraints weight = 3100.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.135264 restraints weight = 1795.498| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.138765 restraints weight = 1245.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.141209 restraints weight = 963.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.142991 restraints weight = 795.371| |-----------------------------------------------------------------------------| r_work (final): 0.3440 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7662 moved from start: 0.1973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 2274 Z= 0.190 Angle : 0.839 14.021 3221 Z= 0.448 Chirality : 0.052 0.265 355 Planarity : 0.005 0.028 286 Dihedral : 27.897 82.339 590 Min Nonbonded Distance : 2.455 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: 0.83 (0.62), residues: 169 helix: 2.04 (0.53), residues: 82 sheet: -1.00 (0.74), residues: 33 loop : -0.70 (0.83), residues: 54 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 323 TYR 0.028 0.003 TYR C 216 PHE 0.009 0.002 PHE C 464 TRP 0.009 0.002 TRP C 345 HIS 0.011 0.002 HIS C 203 Details of bonding type rmsd/Z covalent geometry : bond 0.00346 / 0.19 ( 2270) covalent geometry : angle 0.78963 / 0.45 ( 3215) hydrogen bonds : bond 0.06532 / 7.55 ( 117) hydrogen bonds : angle 3.54521 / 4.95 ( 288) metal coordination : bond 0.01077 / 0.92 ( 4) metal coordination : angle 6.59148 / 11.56 ( 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 : 0.035 Fit side-chains REVERT: C 183 ARG cc_start: 0.6425 (mmt180) cc_final: 0.5470 (ttp80) outliers start: 6 outliers final: 4 residues processed: 46 average time/residue: 0.0423 time to fit residues: 2.2370 Evaluate side-chains 38 residues out of total 150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 34 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: 0.0040 chunk 18 optimal weight: 4.9990 chunk 13 optimal weight: 0.5980 chunk 17 optimal weight: 0.6980 chunk 8 optimal weight: 2.9990 chunk 7 optimal weight: 0.5980 chunk 3 optimal weight: 0.6980 chunk 9 optimal weight: 0.7980 chunk 4 optimal weight: 0.7980 overall best weight: 0.5192 ------------------------------------------------------------------------------- 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 = 0.3663 r_free = 0.3663 target = 0.151187 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.118230 restraints weight = 2955.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.122470 restraints weight = 1776.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.125534 restraints weight = 1268.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.127378 restraints weight = 999.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.129006 restraints weight = 851.438| |-----------------------------------------------------------------------------| r_work (final): 0.3535 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7741 moved from start: 0.2681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 2274 Z= 0.173 Angle : 0.688 9.664 3221 Z= 0.380 Chirality : 0.042 0.155 355 Planarity : 0.004 0.029 286 Dihedral : 27.824 62.063 577 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 4.00 % Allowed : 14.00 % Favored : 82.00 % 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: 0.91 (0.63), residues: 169 helix: 2.23 (0.55), residues: 82 sheet: -1.37 (0.75), residues: 33 loop : -0.57 (0.84), residues: 54 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG C 279 TYR 0.017 0.003 TYR C 216 PHE 0.012 0.002 PHE C 464 TRP 0.009 0.002 TRP C 345 HIS 0.006 0.001 HIS C 203 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.17 ( 2270) covalent geometry : angle 0.65429 / 0.38 ( 3215) hydrogen bonds : bond 0.05261 / 5.65 ( 117) hydrogen bonds : angle 3.45312 / 4.91 ( 288) metal coordination : bond 0.00747 / 0.69 ( 4) metal coordination : angle 4.98381 / 8.91 ( 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: 6 poor density : 33 time to evaluate : 0.037 Fit side-chains REVERT: C 183 ARG cc_start: 0.6388 (mmt180) cc_final: 0.5278 (ptt90) REVERT: C 216 TYR cc_start: 0.6840 (OUTLIER) cc_final: 0.6375 (t80) REVERT: C 274 GLN cc_start: 0.5338 (pm20) cc_final: 0.5056 (pm20) outliers start: 6 outliers final: 3 residues processed: 37 average time/residue: 0.0549 time to fit residues: 2.3962 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 : 0.058 ------------------------------------------------------------------------------- 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 480 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 19 random chunks: chunk 13 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 8 optimal weight: 0.8980 chunk 7 optimal weight: 0.6980 chunk 5 optimal weight: 0.0470 chunk 11 optimal weight: 0.6980 chunk 16 optimal weight: 0.4980 chunk 3 optimal weight: 0.9990 chunk 15 optimal weight: 1.9990 chunk 6 optimal weight: 0.5980 chunk 18 optimal weight: 5.9990 overall best weight: 0.5078 ------------------------------------------------------------------------------- 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 = 0.3752 r_free = 0.3752 target = 0.156713 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.123051 restraints weight = 3061.588| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.127845 restraints weight = 1762.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.131107 restraints weight = 1241.893| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.133443 restraints weight = 978.137| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.134846 restraints weight = 821.166| |-----------------------------------------------------------------------------| r_work (final): 0.3518 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7763 moved from start: 0.2972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.082 2274 Z= 0.178 Angle : 0.666 8.144 3221 Z= 0.367 Chirality : 0.040 0.144 355 Planarity : 0.004 0.024 286 Dihedral : 27.762 61.659 575 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 2.67 % Allowed : 15.33 % Favored : 82.00 % 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: 0.95 (0.64), residues: 169 helix: 2.27 (0.55), residues: 82 sheet: -1.57 (0.74), residues: 33 loop : -0.39 (0.88), 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 0.010 0.001 PHE C 464 TRP 0.009 0.001 TRP C 345 HIS 0.007 0.001 HIS C 203 Details of bonding type rmsd/Z covalent geometry : bond 0.00350 / 0.18 ( 2270) covalent geometry : angle 0.64012 / 0.37 ( 3215) hydrogen bonds : bond 0.05032 / 5.37 ( 117) hydrogen bonds : angle 3.39332 / 4.87 ( 288) metal coordination : bond 0.00698 / 0.63 ( 4) metal coordination : angle 4.32044 / 7.76 ( 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 36 residues out of total 150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 32 time to evaluate : 0.054 Fit side-chains REVERT: C 183 ARG cc_start: 0.6311 (mmt180) cc_final: 0.5237 (ptt90) REVERT: C 193 ASP cc_start: 0.8521 (m-30) cc_final: 0.8177 (m-30) REVERT: C 216 TYR cc_start: 0.6789 (OUTLIER) cc_final: 0.6336 (t80) outliers start: 4 outliers final: 2 residues processed: 35 average time/residue: 0.0372 time to fit residues: 1.5828 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 : 0.052 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 19 random chunks: chunk 8 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 chunk 1 optimal weight: 4.9990 chunk 13 optimal weight: 0.0370 chunk 14 optimal weight: 0.7980 chunk 15 optimal weight: 0.9980 chunk 5 optimal weight: 0.4980 chunk 6 optimal weight: 0.4980 chunk 3 optimal weight: 0.6980 chunk 17 optimal weight: 0.7980 chunk 16 optimal weight: 0.8980 overall best weight: 0.5058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.150246 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.117237 restraints weight = 2998.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.121500 restraints weight = 1793.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.124363 restraints weight = 1285.300| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.126490 restraints weight = 1020.690| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.127703 restraints weight = 862.495| |-----------------------------------------------------------------------------| r_work (final): 0.3401 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7685 moved from start: 0.3147 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= 0.155 Angle : 0.623 8.070 3221 Z= 0.346 Chirality : 0.038 0.128 355 Planarity : 0.004 0.025 286 Dihedral : 27.715 60.147 575 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 2.67 % Allowed : 16.00 % 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: 1.00 (0.65), residues: 169 helix: 2.32 (0.55), residues: 82 sheet: -1.64 (0.75), residues: 33 loop : -0.30 (0.90), residues: 54 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 279 TYR 0.011 0.001 TYR C 216 PHE 0.010 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 0.00277 / 0.16 ( 2270) covalent geometry : angle 0.60056 / 0.35 ( 3215) hydrogen bonds : bond 0.04782 / 5.03 ( 117) hydrogen bonds : angle 3.36306 / 4.85 ( 288) metal coordination : bond 0.00653 / 0.60 ( 4) metal coordination : angle 3.88211 / 7.00 ( 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 38 residues out of total 150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 34 time to evaluate : 0.035 Fit side-chains REVERT: C 183 ARG cc_start: 0.6262 (mmt180) cc_final: 0.5195 (ptt90) REVERT: C 193 ASP cc_start: 0.8707 (m-30) cc_final: 0.8342 (m-30) REVERT: C 216 TYR cc_start: 0.6741 (OUTLIER) cc_final: 0.6314 (t80) REVERT: C 356 LEU cc_start: 0.8391 (tp) cc_final: 0.8178 (tt) outliers start: 4 outliers final: 2 residues processed: 37 average time/residue: 0.0497 time to fit residues: 2.1092 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 : 0.035 ------------------------------------------------------------------------------- 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 448 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 19 random chunks: chunk 17 optimal weight: 1.9990 chunk 10 optimal weight: 0.4980 chunk 6 optimal weight: 0.0970 chunk 4 optimal weight: 0.9980 chunk 9 optimal weight: 0.7980 chunk 2 optimal weight: 0.9980 chunk 1 optimal weight: 3.9990 chunk 16 optimal weight: 0.4980 chunk 3 optimal weight: 0.9980 chunk 12 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 overall best weight: 0.5578 ------------------------------------------------------------------------------- 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 = 0.3654 r_free = 0.3654 target = 0.150600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.117380 restraints weight = 2939.819| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.121464 restraints weight = 1777.853| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.124240 restraints weight = 1286.543| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.126416 restraints weight = 1033.654| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.127642 restraints weight = 878.495| |-----------------------------------------------------------------------------| r_work (final): 0.3573 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7781 moved from start: 0.3339 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= 0.161 Angle : 0.612 6.710 3221 Z= 0.347 Chirality : 0.038 0.116 355 Planarity : 0.005 0.044 286 Dihedral : 27.674 59.734 573 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 2.67 % Allowed : 17.33 % Favored : 80.00 % 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 (0.66), residues: 169 helix: 2.34 (0.55), residues: 82 sheet: -1.74 (0.75), residues: 33 loop : -0.29 (0.91), residues: 54 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 461 TYR 0.014 0.002 TYR C 188 PHE 0.010 0.002 PHE C 464 TRP 0.010 0.001 TRP C 345 HIS 0.007 0.001 HIS C 203 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.16 ( 2270) covalent geometry : angle 0.59085 / 0.35 ( 3215) hydrogen bonds : bond 0.04771 / 5.01 ( 117) hydrogen bonds : angle 3.26593 / 4.78 ( 288) metal coordination : bond 0.00698 / 0.64 ( 4) metal coordination : angle 3.70315 / 6.69 ( 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 38 residues out of total 150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 34 time to evaluate : 0.034 Fit side-chains REVERT: C 183 ARG cc_start: 0.6282 (mmt180) cc_final: 0.5300 (ptt90) REVERT: C 193 ASP cc_start: 0.8593 (m-30) cc_final: 0.8320 (m-30) REVERT: C 216 TYR cc_start: 0.6747 (OUTLIER) cc_final: 0.6322 (t80) REVERT: C 356 LEU cc_start: 0.8394 (tp) cc_final: 0.8161 (tt) outliers start: 4 outliers final: 2 residues processed: 36 average time/residue: 0.0575 time to fit residues: 2.3732 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 : 0.035 ------------------------------------------------------------------------------- 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 448 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 19 random chunks: chunk 11 optimal weight: 0.9990 chunk 8 optimal weight: 0.0870 chunk 13 optimal weight: 2.9990 chunk 14 optimal weight: 0.9990 chunk 3 optimal weight: 0.9990 chunk 4 optimal weight: 0.9990 chunk 17 optimal weight: 0.8980 chunk 16 optimal weight: 0.8980 chunk 18 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 10 optimal weight: 0.7980 overall best weight: 0.7360 ------------------------------------------------------------------------------- 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 = 0.3764 r_free = 0.3764 target = 0.157681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.124053 restraints weight = 3081.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.128703 restraints weight = 1826.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.131583 restraints weight = 1299.836| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.134069 restraints weight = 1038.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.135515 restraints weight = 875.631| |-----------------------------------------------------------------------------| r_work (final): 0.3420 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7796 moved from start: 0.3599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 2274 Z= 0.175 Angle : 0.620 6.474 3221 Z= 0.350 Chirality : 0.039 0.131 355 Planarity : 0.004 0.027 286 Dihedral : 27.701 59.832 573 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 2.67 % Allowed : 17.33 % Favored : 80.00 % 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: 1.27 (0.66), residues: 169 helix: 2.38 (0.56), residues: 82 sheet: -1.93 (0.78), residues: 26 loop : 0.09 (0.88), residues: 61 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 461 TYR 0.008 0.002 TYR C 216 PHE 0.008 0.002 PHE C 464 TRP 0.010 0.002 TRP C 345 HIS 0.007 0.002 HIS C 203 Details of bonding type rmsd/Z covalent geometry : bond 0.00347 / 0.18 ( 2270) covalent geometry : angle 0.60238 / 0.35 ( 3215) hydrogen bonds : bond 0.05021 / 5.29 ( 117) hydrogen bonds : angle 3.26695 / 4.55 ( 288) metal coordination : bond 0.00729 / 0.68 ( 4) metal coordination : angle 3.45722 / 6.22 ( 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 36 residues out of total 150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 32 time to evaluate : 0.059 Fit side-chains REVERT: C 183 ARG cc_start: 0.6334 (mmt180) cc_final: 0.5274 (ptt90) REVERT: C 193 ASP cc_start: 0.8677 (m-30) cc_final: 0.8370 (m-30) REVERT: C 216 TYR cc_start: 0.6780 (OUTLIER) cc_final: 0.6343 (t80) outliers start: 4 outliers final: 2 residues processed: 34 average time/residue: 0.0604 time to fit residues: 2.4202 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 : 0.062 ------------------------------------------------------------------------------- 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 448 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 19 random chunks: chunk 15 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 13 optimal weight: 1.9990 chunk 3 optimal weight: 0.9990 chunk 5 optimal weight: 0.6980 chunk 7 optimal weight: 0.8980 chunk 17 optimal weight: 0.8980 chunk 11 optimal weight: 0.9980 chunk 16 optimal weight: 0.8980 chunk 18 optimal weight: 2.9990 chunk 14 optimal weight: 0.4980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.160049 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.127669 restraints weight = 3103.158| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.132320 restraints weight = 1777.928| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.135411 restraints weight = 1241.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.137666 restraints weight = 972.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.138992 restraints weight = 817.100| |-----------------------------------------------------------------------------| r_work (final): 0.3420 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7774 moved from start: 0.3704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 2274 Z= 0.180 Angle : 0.629 6.863 3221 Z= 0.353 Chirality : 0.039 0.134 355 Planarity : 0.004 0.028 286 Dihedral : 27.685 59.890 573 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 1.33 % Allowed : 18.00 % 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: 1.27 (0.68), residues: 169 helix: 2.27 (0.56), residues: 82 sheet: -2.05 (0.82), residues: 26 loop : 0.33 (0.94), residues: 61 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 461 TYR 0.016 0.003 TYR C 188 PHE 0.010 0.002 PHE C 464 TRP 0.011 0.002 TRP C 345 HIS 0.007 0.002 HIS C 203 Details of bonding type rmsd/Z covalent geometry : bond 0.00359 / 0.18 ( 2270) covalent geometry : angle 0.60832 / 0.35 ( 3215) hydrogen bonds : bond 0.04899 / 5.14 ( 117) hydrogen bonds : angle 3.27671 / 4.61 ( 288) metal coordination : bond 0.00865 / 0.80 ( 4) metal coordination : angle 3.76393 / 6.80 ( 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 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 Fit side-chains REVERT: C 183 ARG cc_start: 0.6359 (mmt180) cc_final: 0.5260 (ptt90) REVERT: C 216 TYR cc_start: 0.6833 (OUTLIER) cc_final: 0.6346 (t80) REVERT: C 352 GLN cc_start: 0.8539 (mm110) cc_final: 0.8249 (mm110) outliers start: 2 outliers final: 1 residues processed: 34 average time/residue: 0.0592 time to fit residues: 2.3741 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 : 0.058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 199 HIS Chi-restraints excluded: chain C residue 216 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 19 random chunks: chunk 0 optimal weight: 10.0000 chunk 9 optimal weight: 2.9990 chunk 5 optimal weight: 0.7980 chunk 13 optimal weight: 0.9990 chunk 18 optimal weight: 0.8980 chunk 8 optimal weight: 0.9990 chunk 7 optimal weight: 0.7980 chunk 14 optimal weight: 0.0770 chunk 1 optimal weight: 3.9990 chunk 12 optimal weight: 0.6980 chunk 17 optimal weight: 0.6980 overall best weight: 0.6138 ------------------------------------------------------------------------------- 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 = 0.3725 r_free = 0.3725 target = 0.154538 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.120839 restraints weight = 3105.202| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.125497 restraints weight = 1790.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.128863 restraints weight = 1256.568| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.131109 restraints weight = 981.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.132701 restraints weight = 826.257| |-----------------------------------------------------------------------------| r_work (final): 0.3400 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7762 moved from start: 0.3863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 2274 Z= 0.163 Angle : 0.604 5.902 3221 Z= 0.345 Chirality : 0.039 0.173 355 Planarity : 0.004 0.028 286 Dihedral : 27.645 59.935 573 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 4.04 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: 1.44 (0.69), residues: 169 helix: 2.43 (0.56), residues: 82 sheet: -1.96 (0.84), residues: 26 loop : 0.39 (0.94), residues: 61 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 461 TYR 0.007 0.001 TYR C 216 PHE 0.009 0.001 PHE C 464 TRP 0.012 0.002 TRP C 345 HIS 0.007 0.002 HIS C 203 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.16 ( 2270) covalent geometry : angle 0.58846 / 0.34 ( 3215) hydrogen bonds : bond 0.04765 / 4.98 ( 117) hydrogen bonds : angle 3.17171 / 4.54 ( 288) metal coordination : bond 0.00708 / 0.64 ( 4) metal coordination : angle 3.20569 / 5.77 ( 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 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: 0.6359 (mmt180) cc_final: 0.5251 (ptt90) REVERT: C 216 TYR cc_start: 0.6870 (OUTLIER) cc_final: 0.6402 (t80) REVERT: C 352 GLN cc_start: 0.8542 (mm110) cc_final: 0.8241 (mm110) outliers start: 2 outliers final: 1 residues processed: 32 average time/residue: 0.0660 time to fit residues: 2.4657 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 : 0.069 ------------------------------------------------------------------------------- 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: 0.3980 chunk 3 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 8 optimal weight: 0.9980 chunk 15 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 chunk 4 optimal weight: 0.9990 chunk 1 optimal weight: 3.9990 chunk 6 optimal weight: 0.5980 chunk 5 optimal weight: 0.7980 chunk 2 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.159678 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.126821 restraints weight = 3205.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.131572 restraints weight = 1848.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.134726 restraints weight = 1292.311| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.137081 restraints weight = 1013.219| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.138325 restraints weight = 850.481| |-----------------------------------------------------------------------------| r_work (final): 0.3504 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7818 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 0.042 2274 Z= 0.177 Angle : 0.619 6.150 3221 Z= 0.352 Chirality : 0.039 0.173 355 Planarity : 0.004 0.029 286 Dihedral : 27.645 59.966 573 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % 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: 1.47 (0.69), residues: 169 helix: 2.47 (0.56), residues: 82 sheet: -2.05 (0.85), residues: 26 loop : 0.44 (0.95), residues: 61 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 461 TYR 0.012 0.002 TYR C 188 PHE 0.008 0.001 PHE C 464 TRP 0.011 0.002 TRP C 345 HIS 0.007 0.002 HIS C 203 Details of bonding type rmsd/Z covalent geometry : bond 0.00354 / 0.18 ( 2270) covalent geometry : angle 0.60427 / 0.35 ( 3215) hydrogen bonds : bond 0.04810 / 5.03 ( 117) hydrogen bonds : angle 3.23191 / 4.61 ( 288) metal coordination : bond 0.00807 / 0.74 ( 4) metal coordination : angle 3.16687 / 5.72 ( 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: 3 poor density : 29 time to evaluate : 0.058 Fit side-chains REVERT: C 183 ARG cc_start: 0.6329 (mmt180) cc_final: 0.5252 (ptt90) REVERT: C 216 TYR cc_start: 0.6930 (OUTLIER) cc_final: 0.6475 (t80) REVERT: C 352 GLN cc_start: 0.8535 (mm110) cc_final: 0.8229 (mm110) outliers start: 3 outliers final: 1 residues processed: 32 average time/residue: 0.0597 time to fit residues: 2.2238 Evaluate side-chains 31 residues out of total 150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 29 time to evaluate : 0.045 ------------------------------------------------------------------------------- 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: 3.9990 chunk 12 optimal weight: 1.9990 chunk 10 optimal weight: 0.5980 chunk 6 optimal weight: 0.5980 chunk 14 optimal weight: 0.9980 chunk 4 optimal weight: 0.7980 chunk 2 optimal weight: 1.9990 chunk 17 optimal weight: 0.8980 chunk 7 optimal weight: 0.4980 chunk 5 optimal weight: 0.3980 chunk 13 optimal weight: 0.8980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.157969 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.125294 restraints weight = 3137.385| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.130041 restraints weight = 1744.312| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.133298 restraints weight = 1206.247| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.135620 restraints weight = 934.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.137139 restraints weight = 776.586| |-----------------------------------------------------------------------------| r_work (final): 0.3513 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7774 moved from start: 0.4039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 2274 Z= 0.160 Angle : 0.592 6.033 3221 Z= 0.342 Chirality : 0.038 0.163 355 Planarity : 0.004 0.028 286 Dihedral : 27.559 59.699 573 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 1.33 % Allowed : 20.67 % Favored : 78.00 % 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: 1.64 (0.69), residues: 169 helix: 2.53 (0.56), residues: 82 sheet: -1.64 (0.89), residues: 24 loop : 0.38 (0.93), residues: 63 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 461 TYR 0.006 0.001 TYR C 216 PHE 0.010 0.001 PHE C 464 TRP 0.012 0.001 TRP C 345 HIS 0.007 0.001 HIS C 203 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.16 ( 2270) covalent geometry : angle 0.57894 / 0.34 ( 3215) hydrogen bonds : bond 0.04560 / 4.75 ( 117) hydrogen bonds : angle 3.15461 / 4.56 ( 288) metal coordination : bond 0.00662 / 0.60 ( 4) metal coordination : angle 2.96308 / 5.37 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 506.92 seconds wall clock time: 9 minutes 22.37 seconds (562.37 seconds total)