Starting phenix.real_space_refine on Tue Aug 4 21:50:57 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9b0l_44046/08_2026/9b0l_44046.cif Found real_map, /net/cci-nas-00/data/ceres_data/9b0l_44046/08_2026/9b0l_44046.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.99 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9b0l_44046/08_2026/9b0l_44046.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9b0l_44046/08_2026/9b0l_44046.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9b0l_44046/08_2026/9b0l_44046.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9b0l_44046/08_2026/9b0l_44046.map" } resolution = 2.99 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= 0.001 sd= 0.025 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: 7 Type Number sf(0) Gaussians Zn 1 6.06 5 P 155 5.49 5 Mg 1 5.21 5 S 21 5.16 5 C 3903 2.51 5 N 1242 2.21 5 O 1728 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 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: 7051 Number of models: 1 Model: "" Number of chains: 6 Chain: "B" Number of atoms: 230 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 230 Classifications: {'DNA': 11} Link IDs: {'rna3p': 10} Chain: "P" Number of atoms: 3814 Number of conformers: 1 Conformer: "" Number of residues, atoms: 466, 3814 Classifications: {'peptide': 466} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 444} Chain: "D" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 78 Classifications: {'DNA': 4} Link IDs: {'rna3p': 3} Chain: "A" Number of atoms: 473 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 473 Classifications: {'DNA': 23} Link IDs: {'rna3p': 22} Chain: "C" Number of atoms: 2454 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 2454 Classifications: {'RNA': 117} Modifications used: {'rna2p_pur': 6, 'rna2p_pyr': 4, 'rna3p_pur': 51, 'rna3p_pyr': 56} Link IDs: {'rna2p': 10, 'rna3p': 106} Chain breaks: 3 Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 47 Unresolved non-hydrogen dihedrals: 28 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {' U%rna3p_pyr:plan': 1, ' A%rna3p_pur:plan': 1, ' A%rna3p_pur:plan2': 1, ' C%rna3p_pyr:plan': 1, ' C%rna3p_pyr:plan2': 1} Unresolved non-hydrogen planarities: 30 Chain: "P" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 1, ' ZN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 3703 SG CYS P 474 23.862 13.480 65.651 1.00152.90 S ATOM 3723 SG CYS P 477 23.450 10.070 67.087 1.00180.84 S ATOM 3828 SG CYS P 491 25.287 10.437 63.786 1.00167.19 S ATOM 3849 SG CYS P 494 21.568 11.179 63.853 1.00161.64 S Time building chain proxies: 1.57, per 1000 atoms: 0.22 Number of scatterers: 7051 At special positions: 0 Unit cell: (97.092, 104.4, 105.444, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 1 29.99 S 21 16.00 P 155 15.00 Mg 1 11.99 O 1728 8.00 N 1242 7.00 C 3903 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: 0.57 Conformation dependent library (CDL) restraints added in 231.7 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN P 601 " pdb="ZN ZN P 601 " - pdb=" SG CYS P 474 " pdb="ZN ZN P 601 " - pdb=" SG CYS P 494 " pdb="ZN ZN P 601 " - pdb=" SG CYS P 477 " pdb="ZN ZN P 601 " - pdb=" SG CYS P 491 " Number of angles added : 6 928 Ramachandran restraints generated. 464 Oldfield, 0 Emsley, 464 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 906 Finding SS restraints... Secondary structure from input PDB file: 14 helices and 6 sheets defined 47.0% alpha, 12.9% beta 66 base pairs and 92 stacking pairs defined. Time for finding SS restraints: 1.13 Creating SS restraints... Processing helix chain 'P' and resid 59 through 63 Processing helix chain 'P' and resid 109 through 122 removed outlier: 3.701A pdb=" N ARG P 122 " --> pdb=" O LEU P 118 " (cutoff:3.500A) Processing helix chain 'P' and resid 142 through 171 Processing helix chain 'P' and resid 180 through 188 Processing helix chain 'P' and resid 189 through 197 Processing helix chain 'P' and resid 197 through 206 Processing helix chain 'P' and resid 213 through 237 Processing helix chain 'P' and resid 260 through 262 No H-bonds generated for 'chain 'P' and resid 260 through 262' Processing helix chain 'P' and resid 344 through 369 removed outlier: 4.702A pdb=" N ASN P 354 " --> pdb=" O ASN P 350 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N GLU P 355 " --> pdb=" O THR P 351 " (cutoff:3.500A) Processing helix chain 'P' and resid 373 through 410 Processing helix chain 'P' and resid 419 through 425 Processing helix chain 'P' and resid 432 through 443 removed outlier: 3.915A pdb=" N LYS P 438 " --> pdb=" O ALA P 434 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N SER P 443 " --> pdb=" O LEU P 439 " (cutoff:3.500A) Processing helix chain 'P' and resid 443 through 458 Processing helix chain 'P' and resid 500 through 514 Processing sheet with id=AA1, first strand: chain 'P' and resid 77 through 79 removed outlier: 4.277A pdb=" N HIS P 87 " --> pdb=" O ILE P 79 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N ILE P 413 " --> pdb=" O VAL P 463 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N VAL P 465 " --> pdb=" O ILE P 413 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N ILE P 415 " --> pdb=" O VAL P 465 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'P' and resid 101 through 105 Processing sheet with id=AA3, first strand: chain 'P' and resid 132 through 133 Processing sheet with id=AA4, first strand: chain 'P' and resid 136 through 139 removed outlier: 4.477A pdb=" N TYR P 301 " --> pdb=" O ILE P 139 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LYS P 300 " --> pdb=" O ASP P 295 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N THR P 291 " --> pdb=" O PHE P 304 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'P' and resid 264 through 265 Processing sheet with id=AA6, first strand: chain 'P' and resid 488 through 490 206 hydrogen bonds defined for protein. 588 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 166 hydrogen bonds 308 hydrogen bond angles 0 basepair planarities 66 basepair parallelities 92 stacking parallelities Total time for adding SS restraints: 1.31 Time building geometry restraints manager: 0.66 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 1583 1.33 - 1.45: 2222 1.45 - 1.57: 3363 1.57 - 1.69: 303 1.69 - 1.81: 30 Bond restraints: 7501 Sorted by residual: bond pdb=" CG HIS P 215 " pdb=" CD2 HIS P 215 " ideal model delta sigma weight residual 1.354 1.323 0.031 1.10e-02 8.26e+03 7.74e+00 bond pdb=" C3' DG A -5 " pdb=" C2' DG A -5 " ideal model delta sigma weight residual 1.516 1.537 -0.021 8.00e-03 1.56e+04 6.93e+00 bond pdb=" N TYR P 387 " pdb=" CA TYR P 387 " ideal model delta sigma weight residual 1.458 1.492 -0.034 1.30e-02 5.92e+03 6.81e+00 bond pdb=" P C C-175 " pdb=" O5' C C-175 " ideal model delta sigma weight residual 1.593 1.617 -0.024 1.00e-02 1.00e+04 5.56e+00 bond pdb=" C3' DG B -5 " pdb=" C2' DG B -5 " ideal model delta sigma weight residual 1.516 1.535 -0.019 8.00e-03 1.56e+04 5.46e+00 ... (remaining 7496 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.91: 10405 1.91 - 3.82: 403 3.82 - 5.72: 13 5.72 - 7.63: 7 7.63 - 9.54: 1 Bond angle restraints: 10829 Sorted by residual: angle pdb=" CA HIS P 215 " pdb=" C HIS P 215 " pdb=" O HIS P 215 " ideal model delta sigma weight residual 119.79 113.94 5.85 1.18e+00 7.18e-01 2.46e+01 angle pdb=" CB LYS P 61 " pdb=" CG LYS P 61 " pdb=" CD LYS P 61 " ideal model delta sigma weight residual 111.30 120.84 -9.54 2.30e+00 1.89e-01 1.72e+01 angle pdb=" N3 DT B -4 " pdb=" C4 DT B -4 " pdb=" O4 DT B -4 " ideal model delta sigma weight residual 119.90 122.37 -2.47 6.00e-01 2.78e+00 1.70e+01 angle pdb=" N3 DT A -3 " pdb=" C4 DT A -3 " pdb=" O4 DT A -3 " ideal model delta sigma weight residual 119.90 122.25 -2.35 6.00e-01 2.78e+00 1.53e+01 angle pdb=" N3 DT A -7 " pdb=" C4 DT A -7 " pdb=" O4 DT A -7 " ideal model delta sigma weight residual 119.90 122.22 -2.32 6.00e-01 2.78e+00 1.49e+01 ... (remaining 10824 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.27: 4025 29.27 - 58.54: 461 58.54 - 87.80: 112 87.80 - 117.07: 7 117.07 - 146.34: 2 Dihedral angle restraints: 4607 sinusoidal: 3213 harmonic: 1394 Sorted by residual: dihedral pdb=" O4' C C-166 " pdb=" C1' C C-166 " pdb=" N1 C C-166 " pdb=" C2 C C-166 " ideal model delta sinusoidal sigma weight residual -128.00 18.34 -146.34 1 1.70e+01 3.46e-03 6.09e+01 dihedral pdb=" O4' A C-197 " pdb=" C1' A C-197 " pdb=" N9 A C-197 " pdb=" C4 A C-197 " ideal model delta sinusoidal sigma weight residual 70.00 4.34 65.66 1 2.00e+01 2.50e-03 1.41e+01 dihedral pdb=" C4' G C-173 " pdb=" O4' G C-173 " pdb=" C1' G C-173 " pdb=" C2' G C-173 " ideal model delta sinusoidal sigma weight residual 3.00 24.79 -21.79 1 8.00e+00 1.56e-02 1.07e+01 ... (remaining 4604 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.093: 1145 0.093 - 0.187: 174 0.187 - 0.280: 1 0.280 - 0.373: 0 0.373 - 0.466: 3 Chirality restraints: 1323 Sorted by residual: chirality pdb=" P G C-174 " pdb=" OP1 G C-174 " pdb=" OP2 G C-174 " pdb=" O5' G C-174 " both_signs ideal model delta sigma weight residual True 2.41 -2.88 -0.47 2.00e-01 2.50e+01 5.43e+00 chirality pdb=" P G C-173 " pdb=" OP1 G C-173 " pdb=" OP2 G C-173 " pdb=" O5' G C-173 " both_signs ideal model delta sigma weight residual True 2.41 -2.87 -0.46 2.00e-01 2.50e+01 5.36e+00 chirality pdb=" P C C-175 " pdb=" OP1 C C-175 " pdb=" OP2 C C-175 " pdb=" O5' C C-175 " both_signs ideal model delta sigma weight residual True 2.41 -2.87 -0.46 2.00e-01 2.50e+01 5.28e+00 ... (remaining 1320 not shown) Planarity restraints: 799 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' C C 11 " -0.034 2.00e-02 2.50e+03 1.69e-02 6.46e+00 pdb=" N1 C C 11 " 0.034 2.00e-02 2.50e+03 pdb=" C2 C C 11 " 0.004 2.00e-02 2.50e+03 pdb=" O2 C C 11 " 0.005 2.00e-02 2.50e+03 pdb=" N3 C C 11 " -0.003 2.00e-02 2.50e+03 pdb=" C4 C C 11 " -0.006 2.00e-02 2.50e+03 pdb=" N4 C C 11 " -0.010 2.00e-02 2.50e+03 pdb=" C5 C C 11 " 0.001 2.00e-02 2.50e+03 pdb=" C6 C C 11 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DT A -7 " 0.021 2.00e-02 2.50e+03 1.01e-02 2.54e+00 pdb=" N1 DT A -7 " -0.022 2.00e-02 2.50e+03 pdb=" C2 DT A -7 " -0.002 2.00e-02 2.50e+03 pdb=" O2 DT A -7 " -0.004 2.00e-02 2.50e+03 pdb=" N3 DT A -7 " 0.001 2.00e-02 2.50e+03 pdb=" C4 DT A -7 " 0.004 2.00e-02 2.50e+03 pdb=" O4 DT A -7 " 0.007 2.00e-02 2.50e+03 pdb=" C5 DT A -7 " 0.001 2.00e-02 2.50e+03 pdb=" C7 DT A -7 " -0.003 2.00e-02 2.50e+03 pdb=" C6 DT A -7 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G C -3 " 0.020 2.00e-02 2.50e+03 8.81e-03 2.33e+00 pdb=" N9 G C -3 " -0.020 2.00e-02 2.50e+03 pdb=" C8 G C -3 " -0.003 2.00e-02 2.50e+03 pdb=" N7 G C -3 " 0.001 2.00e-02 2.50e+03 pdb=" C5 G C -3 " -0.001 2.00e-02 2.50e+03 pdb=" C6 G C -3 " 0.007 2.00e-02 2.50e+03 pdb=" O6 G C -3 " 0.002 2.00e-02 2.50e+03 pdb=" N1 G C -3 " 0.002 2.00e-02 2.50e+03 pdb=" C2 G C -3 " 0.001 2.00e-02 2.50e+03 pdb=" N2 G C -3 " -0.003 2.00e-02 2.50e+03 pdb=" N3 G C -3 " -0.003 2.00e-02 2.50e+03 pdb=" C4 G C -3 " -0.006 2.00e-02 2.50e+03 ... (remaining 796 not shown) Histogram of nonbonded interaction distances: 1.89 - 2.49: 54 2.49 - 3.09: 5098 3.09 - 3.70: 12750 3.70 - 4.30: 18307 4.30 - 4.90: 26647 Nonbonded interactions: 62856 Sorted by model distance: nonbonded pdb=" OD1 ASP P 324 " pdb="MG MG P 602 " model vdw 1.888 2.170 nonbonded pdb=" OP1 DC D 3 " pdb="MG MG P 602 " model vdw 1.924 2.170 nonbonded pdb=" N2 DG B -9 " pdb=" O2 DC A 9 " model vdw 2.064 2.496 nonbonded pdb=" O2' U C-162 " pdb=" OP1 G C-161 " model vdw 2.097 3.040 nonbonded pdb=" N GLU P 492 " pdb=" OE1 GLU P 492 " model vdw 2.103 3.120 ... (remaining 62851 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.780 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: 0.100 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 9.360 Find NCS groups from input model: 0.030 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:7.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6602 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 : 0.004 0.038 7505 Z= 0.339 Angle : 0.715 9.541 10835 Z= 0.574 Chirality : 0.055 0.466 1323 Planarity : 0.004 0.031 799 Dihedral : 21.936 146.341 3701 Min Nonbonded Distance : 1.888 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 0.23 % Allowed : 7.76 % Favored : 92.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 1.24 (0.41), residues: 464 helix: 2.08 (0.35), residues: 219 sheet: -0.59 (0.82), residues: 58 loop : -0.16 (0.47), residues: 187 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG P 446 TYR 0.013 0.001 TYR P 387 PHE 0.011 0.001 PHE P 444 TRP 0.003 0.001 TRP P 84 HIS 0.003 0.001 HIS P 215 Details of bonding type rmsd/Z covalent geometry : bond 0.00425 / 0.34 ( 7501) covalent geometry : angle 0.71213 / 0.57 (10829) hydrogen bonds : bond 0.12816 / 12.49 ( 372) hydrogen bonds : angle 5.83987 / 5.53 ( 896) metal coordination : bond 0.00571 / 0.30 ( 4) metal coordination : angle 2.77286 / 5.16 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 928 Ramachandran restraints generated. 464 Oldfield, 0 Emsley, 464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 928 Ramachandran restraints generated. 464 Oldfield, 0 Emsley, 464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 75 time to evaluate : 0.206 Fit side-chains REVERT: P 67 LYS cc_start: 0.7933 (pttp) cc_final: 0.7581 (ptmt) REVERT: P 276 LYS cc_start: 0.8130 (ttpp) cc_final: 0.7580 (mttt) REVERT: P 298 THR cc_start: 0.7076 (m) cc_final: 0.6725 (p) REVERT: P 382 ARG cc_start: 0.6917 (ttp80) cc_final: 0.6399 (ttt-90) REVERT: P 502 GLU cc_start: 0.6641 (mm-30) cc_final: 0.6413 (mt-10) outliers start: 1 outliers final: 0 residues processed: 76 average time/residue: 0.5651 time to fit residues: 45.1880 Evaluate side-chains 50 residues out of total 438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 50 time to evaluate : 0.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 54 optimal weight: 30.0000 chunk 24 optimal weight: 0.5980 chunk 48 optimal weight: 3.9990 chunk 56 optimal weight: 10.0000 chunk 26 optimal weight: 0.5980 chunk 2 optimal weight: 0.9990 chunk 16 optimal weight: 1.9990 chunk 32 optimal weight: 0.8980 chunk 31 optimal weight: 0.0970 chunk 25 optimal weight: 0.8980 chunk 58 optimal weight: 10.0000 overall best weight: 0.6178 ------------------------------------------------------------------------------- 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 = 0.4083 r_free = 0.4083 target = 0.172829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.129810 restraints weight = 8432.460| |-----------------------------------------------------------------------------| r_work (start): 0.3581 rms_B_bonded: 1.20 r_work: 0.3346 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3225 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3225 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 moved from start: 0.1130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 7505 Z= 0.204 Angle : 0.601 6.879 10835 Z= 0.342 Chirality : 0.041 0.208 1323 Planarity : 0.005 0.054 799 Dihedral : 23.534 160.396 2683 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 3.20 % Allowed : 13.70 % Favored : 83.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 1.02 (0.39), residues: 464 helix: 1.88 (0.34), residues: 218 sheet: -0.30 (0.78), residues: 58 loop : -0.39 (0.43), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG P 299 TYR 0.016 0.002 TYR P 387 PHE 0.017 0.003 PHE P 304 TRP 0.004 0.001 TRP P 84 HIS 0.002 0.001 HIS P 453 Details of bonding type rmsd/Z covalent geometry : bond 0.00430 / 0.20 ( 7501) covalent geometry : angle 0.59799 / 0.34 (10829) hydrogen bonds : bond 0.06275 / 5.45 ( 372) hydrogen bonds : angle 4.54085 / 4.40 ( 896) metal coordination : bond 0.00750 / 0.40 ( 4) metal coordination : angle 2.65825 / 4.93 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 928 Ramachandran restraints generated. 464 Oldfield, 0 Emsley, 464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 928 Ramachandran restraints generated. 464 Oldfield, 0 Emsley, 464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 57 time to evaluate : 0.195 Fit side-chains REVERT: P 382 ARG cc_start: 0.8492 (ttp80) cc_final: 0.8019 (ttt-90) outliers start: 14 outliers final: 3 residues processed: 67 average time/residue: 0.5345 time to fit residues: 37.9544 Evaluate side-chains 47 residues out of total 438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 44 time to evaluate : 0.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 96 SER Chi-restraints excluded: chain P residue 272 THR Chi-restraints excluded: chain P residue 339 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 6 optimal weight: 0.8980 chunk 20 optimal weight: 0.5980 chunk 24 optimal weight: 0.8980 chunk 27 optimal weight: 0.9980 chunk 23 optimal weight: 0.3980 chunk 15 optimal weight: 0.7980 chunk 8 optimal weight: 0.7980 chunk 54 optimal weight: 30.0000 chunk 56 optimal weight: 10.0000 chunk 59 optimal weight: 2.9990 chunk 45 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.171287 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.127389 restraints weight = 8351.034| |-----------------------------------------------------------------------------| r_work (start): 0.3544 rms_B_bonded: 1.19 r_work: 0.3317 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3197 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3197 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.1530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 7505 Z= 0.208 Angle : 0.587 6.188 10835 Z= 0.332 Chirality : 0.041 0.206 1323 Planarity : 0.005 0.050 799 Dihedral : 23.520 164.782 2683 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 10.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 2.97 % Allowed : 17.12 % Favored : 79.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.77 (0.38), residues: 464 helix: 1.75 (0.34), residues: 218 sheet: -0.44 (0.76), residues: 58 loop : -0.62 (0.41), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG P 88 TYR 0.019 0.002 TYR P 387 PHE 0.014 0.003 PHE P 444 TRP 0.008 0.001 TRP P 516 HIS 0.002 0.001 HIS P 399 Details of bonding type rmsd/Z covalent geometry : bond 0.00439 / 0.21 ( 7501) covalent geometry : angle 0.58267 / 0.33 (10829) hydrogen bonds : bond 0.05889 / 5.12 ( 372) hydrogen bonds : angle 4.29597 / 4.27 ( 896) metal coordination : bond 0.01931 / 1.29 ( 4) metal coordination : angle 3.22298 / 5.57 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 928 Ramachandran restraints generated. 464 Oldfield, 0 Emsley, 464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 928 Ramachandran restraints generated. 464 Oldfield, 0 Emsley, 464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 47 time to evaluate : 0.194 Fit side-chains REVERT: P 328 ARG cc_start: 0.7288 (OUTLIER) cc_final: 0.5905 (ttm110) REVERT: P 382 ARG cc_start: 0.8395 (ttp80) cc_final: 0.7912 (ttt-90) outliers start: 13 outliers final: 4 residues processed: 56 average time/residue: 0.5584 time to fit residues: 33.1179 Evaluate side-chains 45 residues out of total 438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 40 time to evaluate : 0.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 96 SER Chi-restraints excluded: chain P residue 186 LYS Chi-restraints excluded: chain P residue 272 THR Chi-restraints excluded: chain P residue 291 THR Chi-restraints excluded: chain P residue 328 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 42 optimal weight: 1.9990 chunk 40 optimal weight: 0.3980 chunk 23 optimal weight: 0.9980 chunk 45 optimal weight: 2.9990 chunk 0 optimal weight: 6.9990 chunk 47 optimal weight: 2.9990 chunk 1 optimal weight: 0.9980 chunk 4 optimal weight: 0.9990 chunk 38 optimal weight: 0.9990 chunk 49 optimal weight: 4.9990 chunk 17 optimal weight: 0.6980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... P 145 GLN P 404 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.171010 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.127169 restraints weight = 8457.145| |-----------------------------------------------------------------------------| r_work (start): 0.3536 rms_B_bonded: 1.19 r_work: 0.3303 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3183 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3183 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.1830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 7505 Z= 0.231 Angle : 0.611 6.609 10835 Z= 0.343 Chirality : 0.042 0.201 1323 Planarity : 0.005 0.038 799 Dihedral : 23.496 164.001 2683 Min Nonbonded Distance : 1.887 Molprobity Statistics. All-atom Clashscore : 11.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 3.65 % Allowed : 18.72 % Favored : 77.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 0.51 (0.38), residues: 464 helix: 1.54 (0.34), residues: 218 sheet: -0.60 (0.74), residues: 58 loop : -0.74 (0.42), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG P 299 TYR 0.020 0.002 TYR P 387 PHE 0.015 0.003 PHE P 304 TRP 0.007 0.001 TRP P 68 HIS 0.003 0.001 HIS P 215 Details of bonding type rmsd/Z covalent geometry : bond 0.00496 / 0.23 ( 7501) covalent geometry : angle 0.60629 / 0.34 (10829) hydrogen bonds : bond 0.05982 / 5.27 ( 372) hydrogen bonds : angle 4.28732 / 4.38 ( 896) metal coordination : bond 0.00757 / 0.39 ( 4) metal coordination : angle 3.32383 / 5.77 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 928 Ramachandran restraints generated. 464 Oldfield, 0 Emsley, 464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 928 Ramachandran restraints generated. 464 Oldfield, 0 Emsley, 464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 46 time to evaluate : 0.203 Fit side-chains REVERT: P 382 ARG cc_start: 0.8514 (ttp80) cc_final: 0.8058 (ttt-90) outliers start: 16 outliers final: 8 residues processed: 57 average time/residue: 0.4867 time to fit residues: 29.4265 Evaluate side-chains 53 residues out of total 438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 45 time to evaluate : 0.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 77 THR Chi-restraints excluded: chain P residue 96 SER Chi-restraints excluded: chain P residue 272 THR Chi-restraints excluded: chain P residue 291 THR Chi-restraints excluded: chain P residue 308 VAL Chi-restraints excluded: chain P residue 339 THR Chi-restraints excluded: chain P residue 421 LYS Chi-restraints excluded: chain P residue 430 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 36 optimal weight: 0.5980 chunk 25 optimal weight: 0.9980 chunk 3 optimal weight: 0.9980 chunk 0 optimal weight: 5.9990 chunk 58 optimal weight: 10.0000 chunk 22 optimal weight: 0.0670 chunk 59 optimal weight: 2.9990 chunk 24 optimal weight: 0.2980 chunk 34 optimal weight: 0.2980 chunk 50 optimal weight: 2.9990 chunk 2 optimal weight: 0.7980 overall best weight: 0.4118 ------------------------------------------------------------------------------- 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 = 0.4092 r_free = 0.4092 target = 0.173975 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.130782 restraints weight = 8364.432| |-----------------------------------------------------------------------------| r_work (start): 0.3582 rms_B_bonded: 1.18 r_work: 0.3348 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3227 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3227 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8089 moved from start: 0.1894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7505 Z= 0.155 Angle : 0.539 5.976 10835 Z= 0.310 Chirality : 0.038 0.208 1323 Planarity : 0.004 0.040 799 Dihedral : 23.439 167.645 2683 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 10.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 2.74 % Allowed : 21.00 % Favored : 76.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 0.64 (0.38), residues: 464 helix: 1.69 (0.34), residues: 218 sheet: -0.61 (0.74), residues: 58 loop : -0.70 (0.42), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG P 88 TYR 0.013 0.001 TYR P 387 PHE 0.013 0.002 PHE P 156 TRP 0.004 0.001 TRP P 68 HIS 0.002 0.001 HIS P 399 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.16 ( 7501) covalent geometry : angle 0.53433 / 0.31 (10829) hydrogen bonds : bond 0.05472 / 4.68 ( 372) hydrogen bonds : angle 4.11366 / 4.21 ( 896) metal coordination : bond 0.00622 / 0.35 ( 4) metal coordination : angle 2.98864 / 5.09 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 928 Ramachandran restraints generated. 464 Oldfield, 0 Emsley, 464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 928 Ramachandran restraints generated. 464 Oldfield, 0 Emsley, 464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 54 time to evaluate : 0.194 Fit side-chains REVERT: P 346 GLU cc_start: 0.8312 (OUTLIER) cc_final: 0.7956 (mp0) REVERT: P 382 ARG cc_start: 0.8506 (ttp80) cc_final: 0.8006 (ttt-90) outliers start: 12 outliers final: 6 residues processed: 64 average time/residue: 0.5117 time to fit residues: 34.7398 Evaluate side-chains 54 residues out of total 438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 47 time to evaluate : 0.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 77 THR Chi-restraints excluded: chain P residue 272 THR Chi-restraints excluded: chain P residue 291 THR Chi-restraints excluded: chain P residue 308 VAL Chi-restraints excluded: chain P residue 339 THR Chi-restraints excluded: chain P residue 346 GLU Chi-restraints excluded: chain P residue 430 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 33 optimal weight: 0.7980 chunk 32 optimal weight: 0.5980 chunk 19 optimal weight: 0.8980 chunk 11 optimal weight: 0.0870 chunk 16 optimal weight: 0.5980 chunk 34 optimal weight: 0.6980 chunk 54 optimal weight: 30.0000 chunk 59 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 44 optimal weight: 3.9990 chunk 57 optimal weight: 30.0000 overall best weight: 0.5558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... P 388 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4087 r_free = 0.4087 target = 0.173182 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.129609 restraints weight = 8480.164| |-----------------------------------------------------------------------------| r_work (start): 0.3569 rms_B_bonded: 1.17 r_work: 0.3323 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.3201 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3201 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 moved from start: 0.2028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 7505 Z= 0.180 Angle : 0.560 9.088 10835 Z= 0.317 Chirality : 0.039 0.195 1323 Planarity : 0.004 0.036 799 Dihedral : 23.405 166.597 2683 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 11.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 3.42 % Allowed : 19.63 % Favored : 76.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 0.65 (0.39), residues: 464 helix: 1.72 (0.34), residues: 218 sheet: -0.61 (0.75), residues: 58 loop : -0.74 (0.42), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG P 390 TYR 0.018 0.001 TYR P 387 PHE 0.014 0.002 PHE P 444 TRP 0.005 0.001 TRP P 68 HIS 0.003 0.001 HIS P 215 Details of bonding type rmsd/Z covalent geometry : bond 0.00377 / 0.18 ( 7501) covalent geometry : angle 0.55602 / 0.32 (10829) hydrogen bonds : bond 0.05563 / 4.81 ( 372) hydrogen bonds : angle 4.05124 / 4.20 ( 896) metal coordination : bond 0.00727 / 0.38 ( 4) metal coordination : angle 2.72476 / 4.66 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 928 Ramachandran restraints generated. 464 Oldfield, 0 Emsley, 464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 928 Ramachandran restraints generated. 464 Oldfield, 0 Emsley, 464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 49 time to evaluate : 0.118 Fit side-chains REVERT: P 382 ARG cc_start: 0.8560 (ttp80) cc_final: 0.8114 (ttt-90) outliers start: 15 outliers final: 10 residues processed: 62 average time/residue: 0.5021 time to fit residues: 33.0507 Evaluate side-chains 58 residues out of total 438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 48 time to evaluate : 0.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 77 THR Chi-restraints excluded: chain P residue 96 SER Chi-restraints excluded: chain P residue 272 THR Chi-restraints excluded: chain P residue 291 THR Chi-restraints excluded: chain P residue 308 VAL Chi-restraints excluded: chain P residue 329 ASP Chi-restraints excluded: chain P residue 339 THR Chi-restraints excluded: chain P residue 346 GLU Chi-restraints excluded: chain P residue 421 LYS Chi-restraints excluded: chain P residue 430 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 1 optimal weight: 0.0770 chunk 26 optimal weight: 0.3980 chunk 42 optimal weight: 0.0980 chunk 47 optimal weight: 2.9990 chunk 55 optimal weight: 10.0000 chunk 46 optimal weight: 0.7980 chunk 22 optimal weight: 0.0670 chunk 20 optimal weight: 0.2980 chunk 0 optimal weight: 5.9990 chunk 35 optimal weight: 0.1980 chunk 38 optimal weight: 0.9990 overall best weight: 0.1476 ------------------------------------------------------------------------------- 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 = 0.4135 r_free = 0.4135 target = 0.178037 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.134970 restraints weight = 8474.736| |-----------------------------------------------------------------------------| r_work (start): 0.3637 rms_B_bonded: 1.18 r_work: 0.3407 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.3285 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3285 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 moved from start: 0.2125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 7505 Z= 0.118 Angle : 0.506 7.096 10835 Z= 0.296 Chirality : 0.036 0.198 1323 Planarity : 0.004 0.039 799 Dihedral : 23.361 171.679 2683 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 11.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 1.37 % Allowed : 22.83 % Favored : 75.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 0.90 (0.39), residues: 464 helix: 1.95 (0.34), residues: 218 sheet: -0.53 (0.74), residues: 58 loop : -0.61 (0.43), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG P 390 TYR 0.009 0.001 TYR P 400 PHE 0.013 0.002 PHE P 156 TRP 0.003 0.001 TRP P 152 HIS 0.002 0.001 HIS P 399 Details of bonding type rmsd/Z covalent geometry : bond 0.00218 / 0.12 ( 7501) covalent geometry : angle 0.50263 / 0.30 (10829) hydrogen bonds : bond 0.05212 / 4.41 ( 372) hydrogen bonds : angle 3.89244 / 4.04 ( 896) metal coordination : bond 0.00376 / 0.19 ( 4) metal coordination : angle 2.62385 / 4.52 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 928 Ramachandran restraints generated. 464 Oldfield, 0 Emsley, 464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 928 Ramachandran restraints generated. 464 Oldfield, 0 Emsley, 464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 54 time to evaluate : 0.214 Fit side-chains REVERT: P 382 ARG cc_start: 0.8527 (ttp80) cc_final: 0.8073 (ttt-90) REVERT: P 421 LYS cc_start: 0.7804 (OUTLIER) cc_final: 0.7507 (mttp) outliers start: 6 outliers final: 3 residues processed: 59 average time/residue: 0.4709 time to fit residues: 29.5887 Evaluate side-chains 53 residues out of total 438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 49 time to evaluate : 0.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 329 ASP Chi-restraints excluded: chain P residue 339 THR Chi-restraints excluded: chain P residue 421 LYS Chi-restraints excluded: chain P residue 430 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 39 optimal weight: 0.9980 chunk 54 optimal weight: 30.0000 chunk 34 optimal weight: 0.1980 chunk 42 optimal weight: 0.8980 chunk 56 optimal weight: 9.9990 chunk 15 optimal weight: 0.7980 chunk 2 optimal weight: 0.8980 chunk 32 optimal weight: 0.7980 chunk 25 optimal weight: 0.0980 chunk 24 optimal weight: 0.9990 chunk 23 optimal weight: 0.6980 overall best weight: 0.5180 ------------------------------------------------------------------------------- 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 = 0.4101 r_free = 0.4101 target = 0.174554 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.131246 restraints weight = 8450.634| |-----------------------------------------------------------------------------| r_work (start): 0.3590 rms_B_bonded: 1.16 r_work: 0.3355 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3233 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3233 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8087 moved from start: 0.2137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 7505 Z= 0.171 Angle : 0.543 6.239 10835 Z= 0.310 Chirality : 0.038 0.196 1323 Planarity : 0.004 0.037 799 Dihedral : 23.325 168.015 2683 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 10.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 2.05 % Allowed : 23.29 % Favored : 74.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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 (0.39), residues: 464 helix: 1.89 (0.34), residues: 218 sheet: -0.52 (0.75), residues: 58 loop : -0.68 (0.43), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG P 390 TYR 0.015 0.001 TYR P 387 PHE 0.015 0.002 PHE P 444 TRP 0.004 0.001 TRP P 68 HIS 0.004 0.001 HIS P 215 Details of bonding type rmsd/Z covalent geometry : bond 0.00360 / 0.17 ( 7501) covalent geometry : angle 0.53973 / 0.31 (10829) hydrogen bonds : bond 0.05415 / 4.66 ( 372) hydrogen bonds : angle 3.89171 / 4.03 ( 896) metal coordination : bond 0.00640 / 0.34 ( 4) metal coordination : angle 2.43395 / 4.16 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 928 Ramachandran restraints generated. 464 Oldfield, 0 Emsley, 464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 928 Ramachandran restraints generated. 464 Oldfield, 0 Emsley, 464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 46 time to evaluate : 0.160 Fit side-chains REVERT: P 346 GLU cc_start: 0.8313 (OUTLIER) cc_final: 0.7967 (mp0) REVERT: P 382 ARG cc_start: 0.8544 (ttp80) cc_final: 0.8083 (ttt-90) outliers start: 9 outliers final: 7 residues processed: 54 average time/residue: 0.4250 time to fit residues: 24.4054 Evaluate side-chains 54 residues out of total 438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 46 time to evaluate : 0.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 77 THR Chi-restraints excluded: chain P residue 96 SER Chi-restraints excluded: chain P residue 329 ASP Chi-restraints excluded: chain P residue 339 THR Chi-restraints excluded: chain P residue 346 GLU Chi-restraints excluded: chain P residue 398 MET Chi-restraints excluded: chain P residue 421 LYS Chi-restraints excluded: chain P residue 430 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 15 optimal weight: 0.9980 chunk 6 optimal weight: 0.5980 chunk 51 optimal weight: 4.9990 chunk 2 optimal weight: 0.4980 chunk 59 optimal weight: 2.9990 chunk 24 optimal weight: 0.1980 chunk 18 optimal weight: 0.2980 chunk 25 optimal weight: 0.3980 chunk 32 optimal weight: 0.3980 chunk 11 optimal weight: 0.0970 chunk 36 optimal weight: 0.4980 overall best weight: 0.2778 ------------------------------------------------------------------------------- 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 = 0.4127 r_free = 0.4127 target = 0.177128 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.133890 restraints weight = 8447.655| |-----------------------------------------------------------------------------| r_work (start): 0.3621 rms_B_bonded: 1.17 r_work: 0.3384 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.3263 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3263 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.2200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 7505 Z= 0.131 Angle : 0.515 7.309 10835 Z= 0.298 Chirality : 0.036 0.183 1323 Planarity : 0.004 0.036 799 Dihedral : 23.321 170.063 2683 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 11.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 1.83 % Allowed : 23.52 % Favored : 74.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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 (0.39), residues: 464 helix: 1.92 (0.34), residues: 218 sheet: -0.44 (0.75), residues: 58 loop : -0.73 (0.42), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG P 390 TYR 0.010 0.001 TYR P 387 PHE 0.013 0.002 PHE P 156 TRP 0.003 0.001 TRP P 84 HIS 0.002 0.000 HIS P 399 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.13 ( 7501) covalent geometry : angle 0.51172 / 0.30 (10829) hydrogen bonds : bond 0.05158 / 4.38 ( 372) hydrogen bonds : angle 3.83053 / 3.98 ( 896) metal coordination : bond 0.00443 / 0.22 ( 4) metal coordination : angle 2.51953 / 4.31 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 928 Ramachandran restraints generated. 464 Oldfield, 0 Emsley, 464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 928 Ramachandran restraints generated. 464 Oldfield, 0 Emsley, 464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 51 time to evaluate : 0.193 Fit side-chains REVERT: P 346 GLU cc_start: 0.8319 (OUTLIER) cc_final: 0.7985 (mp0) REVERT: P 382 ARG cc_start: 0.8546 (ttp80) cc_final: 0.8096 (ttt-90) REVERT: P 421 LYS cc_start: 0.7810 (OUTLIER) cc_final: 0.7512 (mttp) outliers start: 8 outliers final: 5 residues processed: 58 average time/residue: 0.4780 time to fit residues: 29.3015 Evaluate side-chains 55 residues out of total 438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 48 time to evaluate : 0.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 77 THR Chi-restraints excluded: chain P residue 291 THR Chi-restraints excluded: chain P residue 329 ASP Chi-restraints excluded: chain P residue 339 THR Chi-restraints excluded: chain P residue 346 GLU Chi-restraints excluded: chain P residue 421 LYS Chi-restraints excluded: chain P residue 430 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 28 optimal weight: 0.9980 chunk 52 optimal weight: 10.0000 chunk 18 optimal weight: 0.7980 chunk 44 optimal weight: 0.5980 chunk 42 optimal weight: 0.6980 chunk 11 optimal weight: 0.4980 chunk 21 optimal weight: 0.5980 chunk 2 optimal weight: 0.8980 chunk 59 optimal weight: 2.9990 chunk 54 optimal weight: 30.0000 chunk 35 optimal weight: 0.0980 overall best weight: 0.4980 ------------------------------------------------------------------------------- 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 = 0.4107 r_free = 0.4107 target = 0.175168 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.131283 restraints weight = 8369.003| |-----------------------------------------------------------------------------| r_work (start): 0.3589 rms_B_bonded: 1.13 r_work: 0.3368 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3248 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3248 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 moved from start: 0.2246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7505 Z= 0.164 Angle : 0.538 7.264 10835 Z= 0.307 Chirality : 0.038 0.200 1323 Planarity : 0.004 0.037 799 Dihedral : 23.310 167.975 2683 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 10.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 1.83 % Allowed : 23.52 % Favored : 74.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.78 (0.39), residues: 464 helix: 1.86 (0.34), residues: 218 sheet: -0.45 (0.76), residues: 58 loop : -0.76 (0.43), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG P 299 TYR 0.014 0.001 TYR P 387 PHE 0.014 0.002 PHE P 444 TRP 0.008 0.001 TRP P 516 HIS 0.002 0.001 HIS P 215 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.16 ( 7501) covalent geometry : angle 0.53449 / 0.31 (10829) hydrogen bonds : bond 0.05327 / 4.59 ( 372) hydrogen bonds : angle 3.86526 / 4.00 ( 896) metal coordination : bond 0.00606 / 0.31 ( 4) metal coordination : angle 2.48813 / 4.23 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 928 Ramachandran restraints generated. 464 Oldfield, 0 Emsley, 464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 928 Ramachandran restraints generated. 464 Oldfield, 0 Emsley, 464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 49 time to evaluate : 0.196 Fit side-chains REVERT: P 346 GLU cc_start: 0.8298 (OUTLIER) cc_final: 0.7955 (mp0) REVERT: P 382 ARG cc_start: 0.8541 (ttp80) cc_final: 0.8098 (ttt-90) outliers start: 8 outliers final: 6 residues processed: 56 average time/residue: 0.4743 time to fit residues: 28.1147 Evaluate side-chains 53 residues out of total 438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 46 time to evaluate : 0.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 77 THR Chi-restraints excluded: chain P residue 291 THR Chi-restraints excluded: chain P residue 329 ASP Chi-restraints excluded: chain P residue 339 THR Chi-restraints excluded: chain P residue 346 GLU Chi-restraints excluded: chain P residue 421 LYS Chi-restraints excluded: chain P residue 430 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 24 optimal weight: 0.6980 chunk 25 optimal weight: 0.4980 chunk 31 optimal weight: 0.0770 chunk 51 optimal weight: 4.9990 chunk 8 optimal weight: 0.1980 chunk 53 optimal weight: 3.9990 chunk 37 optimal weight: 0.9980 chunk 46 optimal weight: 0.9990 chunk 56 optimal weight: 10.0000 chunk 19 optimal weight: 0.7980 chunk 23 optimal weight: 1.9990 overall best weight: 0.4538 ------------------------------------------------------------------------------- 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 = 0.4112 r_free = 0.4112 target = 0.175597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.131804 restraints weight = 8364.035| |-----------------------------------------------------------------------------| r_work (start): 0.3594 rms_B_bonded: 1.14 r_work: 0.3379 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3256 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3256 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8044 moved from start: 0.2277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7505 Z= 0.158 Angle : 0.540 7.260 10835 Z= 0.308 Chirality : 0.037 0.193 1323 Planarity : 0.004 0.037 799 Dihedral : 23.313 168.118 2683 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 10.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 2.05 % Allowed : 23.74 % Favored : 74.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 0.73 (0.39), residues: 464 helix: 1.83 (0.34), residues: 218 sheet: -0.49 (0.75), residues: 56 loop : -0.80 (0.42), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG P 299 TYR 0.014 0.001 TYR P 387 PHE 0.013 0.002 PHE P 156 TRP 0.006 0.001 TRP P 516 HIS 0.003 0.001 HIS P 215 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.16 ( 7501) covalent geometry : angle 0.53551 / 0.31 (10829) hydrogen bonds : bond 0.05275 / 4.54 ( 372) hydrogen bonds : angle 3.88406 / 4.04 ( 896) metal coordination : bond 0.00755 / 0.36 ( 4) metal coordination : angle 3.05328 / 5.35 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2262.61 seconds wall clock time: 39 minutes 25.70 seconds (2365.70 seconds total)