Starting phenix.real_space_refine on Thu Jul 2 05:43:26 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9b0l_44046/07_2026/9b0l_44046.cif Found real_map, /net/cci-nas-00/data/ceres_data/9b0l_44046/07_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9b0l_44046/07_2026/9b0l_44046.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9b0l_44046/07_2026/9b0l_44046.map" model { file = "/net/cci-nas-00/data/ceres_data/9b0l_44046/07_2026/9b0l_44046.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9b0l_44046/07_2026/9b0l_44046.cif" } 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-dev-6108/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: 1.80, per 1000 atoms: 0.26 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: 0.63 Conformation dependent library (CDL) restraints added in 302.1 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: 1.11 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: 1.52 Time building geometry restraints manager: 0.76 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=" 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 bond pdb=" C1' DC B -7 " pdb=" N1 DC B -7 " ideal model delta sigma weight residual 1.468 1.500 -0.032 1.40e-02 5.10e+03 5.26e+00 ... (remaining 7496 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.91: 10596 1.91 - 3.82: 212 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: 1239 0.093 - 0.187: 80 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: 3.200 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 10.090 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:6.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.270 ------------------------------------------------------------------------------- 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= 0.325 Angle : 0.628 9.541 10835 Z= 0.488 Chirality : 0.048 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 0.00414 / 0.33 ( 7501) covalent geometry : angle 0.62444 / 0.49 (10829) hydrogen bonds : bond 0.12816 / 12.37 ( 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 : 0.208 Fit side-chains REVERT: P 67 LYS cc_start: 0.7933 (pttp) cc_final: 0.7580 (ptmt) REVERT: P 276 LYS cc_start: 0.8130 (ttpp) cc_final: 0.7581 (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: 0.5841 time to fit residues: 46.7532 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 : 0.198 ------------------------------------------------------------------------------- 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: 20.0000 chunk 24 optimal weight: 0.5980 chunk 48 optimal weight: 2.9990 chunk 56 optimal weight: 7.9990 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: 0.6980 chunk 58 optimal weight: 9.9990 overall best weight: 0.5778 ------------------------------------------------------------------------------- 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 = 0.4088 r_free = 0.4088 target = 0.173242 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.129764 restraints weight = 8434.673| |-----------------------------------------------------------------------------| r_work (start): 0.3574 rms_B_bonded: 1.28 r_work: 0.3344 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3220 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3220 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.1140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 7505 Z= 0.200 Angle : 0.581 6.859 10835 Z= 0.338 Chirality : 0.039 0.164 1323 Planarity : 0.005 0.056 799 Dihedral : 23.584 159.588 2683 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 2.74 % Allowed : 13.93 % Favored : 83.33 % 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: 1.01 (0.39), residues: 464 helix: 1.89 (0.34), residues: 218 sheet: -0.33 (0.77), residues: 58 loop : -0.40 (0.43), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG P 299 TYR 0.016 0.002 TYR P 387 PHE 0.015 0.003 PHE P 304 TRP 0.004 0.001 TRP P 84 HIS 0.002 0.001 HIS P 399 Details of bonding type rmsd/Z covalent geometry : bond 0.00419 / 0.20 ( 7501) covalent geometry : angle 0.57796 / 0.34 (10829) hydrogen bonds : bond 0.06215 / 5.34 ( 372) hydrogen bonds : angle 4.51493 / 4.38 ( 896) metal coordination : bond 0.00706 / 0.36 ( 4) metal coordination : angle 2.75865 / 5.12 ( 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 70 residues out of total 438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 58 time to evaluate : 0.207 Fit side-chains REVERT: P 276 LYS cc_start: 0.8593 (ttpp) cc_final: 0.8387 (mttt) REVERT: P 382 ARG cc_start: 0.8426 (ttp80) cc_final: 0.7940 (ttt-90) outliers start: 12 outliers final: 3 residues processed: 66 average time/residue: 0.5187 time to fit residues: 36.2113 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 : 0.195 ------------------------------------------------------------------------------- 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: 0.0030 chunk 20 optimal weight: 0.0050 chunk 24 optimal weight: 0.0370 chunk 27 optimal weight: 1.9990 chunk 23 optimal weight: 0.7980 chunk 15 optimal weight: 0.9990 chunk 8 optimal weight: 0.8980 chunk 54 optimal weight: 20.0000 chunk 56 optimal weight: 7.9990 chunk 59 optimal weight: 1.9990 chunk 45 optimal weight: 0.0870 overall best weight: 0.1860 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... P 145 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4125 r_free = 0.4125 target = 0.177077 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.134009 restraints weight = 8443.183| |-----------------------------------------------------------------------------| r_work (start): 0.3619 rms_B_bonded: 1.15 r_work: 0.3416 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3293 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3293 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 moved from start: 0.1424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 7505 Z= 0.131 Angle : 0.505 5.011 10835 Z= 0.301 Chirality : 0.035 0.159 1323 Planarity : 0.004 0.041 799 Dihedral : 23.534 166.974 2683 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 2.51 % Allowed : 17.12 % Favored : 80.37 % 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 (0.39), residues: 464 helix: 2.04 (0.34), residues: 218 sheet: -0.13 (0.78), residues: 58 loop : -0.27 (0.43), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG P 88 TYR 0.011 0.001 TYR P 387 PHE 0.013 0.002 PHE P 156 TRP 0.009 0.001 TRP P 516 HIS 0.002 0.000 HIS P 399 Details of bonding type rmsd/Z covalent geometry : bond 0.00246 / 0.13 ( 7501) covalent geometry : angle 0.50083 / 0.30 (10829) hydrogen bonds : bond 0.05382 / 4.56 ( 372) hydrogen bonds : angle 4.13089 / 4.03 ( 896) metal coordination : bond 0.00483 / 0.25 ( 4) metal coordination : angle 2.65835 / 4.80 ( 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 62 residues out of total 438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 51 time to evaluate : 0.193 Fit side-chains REVERT: P 381 ASN cc_start: 0.8011 (OUTLIER) cc_final: 0.7766 (t0) REVERT: P 382 ARG cc_start: 0.8395 (ttp80) cc_final: 0.7934 (ttt-90) outliers start: 11 outliers final: 1 residues processed: 58 average time/residue: 0.5403 time to fit residues: 33.2188 Evaluate side-chains 44 residues out of total 438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 42 time to evaluate : 0.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 272 THR Chi-restraints excluded: chain P residue 381 ASN 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: 0.5980 chunk 23 optimal weight: 0.0030 chunk 45 optimal weight: 0.6980 chunk 0 optimal weight: 5.9990 chunk 47 optimal weight: 2.9990 chunk 1 optimal weight: 0.6980 chunk 4 optimal weight: 1.9990 chunk 38 optimal weight: 0.0980 chunk 49 optimal weight: 3.9990 chunk 17 optimal weight: 0.0980 overall best weight: 0.2990 ------------------------------------------------------------------------------- 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 = 0.4123 r_free = 0.4123 target = 0.177058 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.134808 restraints weight = 8574.364| |-----------------------------------------------------------------------------| r_work (start): 0.3631 rms_B_bonded: 1.15 r_work: 0.3407 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3287 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3287 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.1626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7505 Z= 0.142 Angle : 0.509 9.360 10835 Z= 0.297 Chirality : 0.036 0.156 1323 Planarity : 0.004 0.036 799 Dihedral : 23.447 168.591 2683 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 2.28 % Allowed : 18.49 % Favored : 79.22 % 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: 1.22 (0.39), residues: 464 helix: 2.03 (0.34), residues: 218 sheet: -0.21 (0.76), residues: 58 loop : -0.26 (0.43), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG P 88 TYR 0.016 0.001 TYR P 387 PHE 0.011 0.002 PHE P 156 TRP 0.005 0.001 TRP P 516 HIS 0.004 0.001 HIS P 388 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.14 ( 7501) covalent geometry : angle 0.50301 / 0.30 (10829) hydrogen bonds : bond 0.05283 / 4.50 ( 372) hydrogen bonds : angle 3.93362 / 3.94 ( 896) metal coordination : bond 0.01765 / 1.59 ( 4) metal coordination : angle 3.33574 / 5.75 ( 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 58 residues out of total 438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 48 time to evaluate : 0.154 Fit side-chains REVERT: P 328 ARG cc_start: 0.7322 (OUTLIER) cc_final: 0.7113 (ttm110) REVERT: P 382 ARG cc_start: 0.8532 (ttp80) cc_final: 0.8070 (ttt-90) outliers start: 10 outliers final: 3 residues processed: 56 average time/residue: 0.5014 time to fit residues: 29.8308 Evaluate side-chains 42 residues out of total 438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 38 time to evaluate : 0.116 ------------------------------------------------------------------------------- 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 291 THR Chi-restraints excluded: chain P residue 328 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 36 optimal weight: 0.7980 chunk 25 optimal weight: 0.0020 chunk 3 optimal weight: 0.2980 chunk 0 optimal weight: 6.9990 chunk 58 optimal weight: 9.9990 chunk 22 optimal weight: 0.4980 chunk 59 optimal weight: 1.9990 chunk 24 optimal weight: 0.2980 chunk 34 optimal weight: 0.6980 chunk 50 optimal weight: 2.9990 chunk 2 optimal weight: 0.5980 overall best weight: 0.3388 ------------------------------------------------------------------------------- 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 = 0.4121 r_free = 0.4121 target = 0.176874 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.133841 restraints weight = 8455.537| |-----------------------------------------------------------------------------| r_work (start): 0.3621 rms_B_bonded: 1.16 r_work: 0.3408 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3287 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3287 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.1765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7505 Z= 0.142 Angle : 0.496 5.667 10835 Z= 0.294 Chirality : 0.036 0.183 1323 Planarity : 0.004 0.036 799 Dihedral : 23.388 169.035 2683 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 2.51 % Allowed : 18.95 % Favored : 78.54 % 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: 1.25 (0.39), residues: 464 helix: 2.09 (0.34), residues: 218 sheet: -0.13 (0.76), residues: 58 loop : -0.33 (0.43), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG P 88 TYR 0.012 0.001 TYR P 387 PHE 0.011 0.002 PHE P 156 TRP 0.004 0.001 TRP P 516 HIS 0.002 0.001 HIS P 453 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.14 ( 7501) covalent geometry : angle 0.49172 / 0.29 (10829) hydrogen bonds : bond 0.05184 / 4.44 ( 372) hydrogen bonds : angle 3.84996 / 3.89 ( 896) metal coordination : bond 0.00527 / 0.28 ( 4) metal coordination : angle 2.87587 / 4.95 ( 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 58 residues out of total 438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 47 time to evaluate : 0.200 Fit side-chains REVERT: P 346 GLU cc_start: 0.8145 (OUTLIER) cc_final: 0.7846 (mp0) REVERT: P 382 ARG cc_start: 0.8532 (ttp80) cc_final: 0.8076 (ttt-90) outliers start: 11 outliers final: 6 residues processed: 57 average time/residue: 0.4961 time to fit residues: 30.0135 Evaluate side-chains 52 residues out of total 438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 45 time to evaluate : 0.116 ------------------------------------------------------------------------------- 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 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: 0.6980 chunk 11 optimal weight: 0.8980 chunk 16 optimal weight: 0.5980 chunk 34 optimal weight: 0.1980 chunk 54 optimal weight: 20.0000 chunk 59 optimal weight: 1.9990 chunk 8 optimal weight: 0.6980 chunk 44 optimal weight: 0.6980 chunk 57 optimal weight: 20.0000 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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 = 0.4096 r_free = 0.4096 target = 0.174251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.130647 restraints weight = 8509.657| |-----------------------------------------------------------------------------| r_work (start): 0.3585 rms_B_bonded: 1.18 r_work: 0.3360 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3236 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3236 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8071 moved from start: 0.1918 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= 0.181 Angle : 0.527 6.035 10835 Z= 0.310 Chirality : 0.038 0.166 1323 Planarity : 0.004 0.037 799 Dihedral : 23.345 166.075 2683 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 9.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 2.74 % Allowed : 20.32 % 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: 1.01 (0.39), residues: 464 helix: 1.94 (0.34), residues: 218 sheet: -0.28 (0.75), residues: 58 loop : -0.49 (0.43), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG P 299 TYR 0.017 0.001 TYR P 387 PHE 0.017 0.003 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 0.00382 / 0.18 ( 7501) covalent geometry : angle 0.52350 / 0.31 (10829) hydrogen bonds : bond 0.05417 / 4.70 ( 372) hydrogen bonds : angle 3.90341 / 3.96 ( 896) metal coordination : bond 0.00761 / 0.41 ( 4) metal coordination : angle 2.62632 / 4.47 ( 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 59 residues out of total 438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 47 time to evaluate : 0.195 Fit side-chains REVERT: P 382 ARG cc_start: 0.8511 (ttp80) cc_final: 0.8044 (ttt-90) REVERT: P 390 ARG cc_start: 0.8008 (OUTLIER) cc_final: 0.7465 (mmt90) outliers start: 12 outliers final: 7 residues processed: 58 average time/residue: 0.4599 time to fit residues: 28.4537 Evaluate side-chains 52 residues out of total 438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 44 time to evaluate : 0.188 ------------------------------------------------------------------------------- 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 339 THR Chi-restraints excluded: chain P residue 346 GLU Chi-restraints excluded: chain P residue 390 ARG 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: 0.5980 chunk 26 optimal weight: 0.7980 chunk 42 optimal weight: 0.6980 chunk 47 optimal weight: 2.9990 chunk 55 optimal weight: 9.9990 chunk 46 optimal weight: 0.5980 chunk 22 optimal weight: 0.0970 chunk 20 optimal weight: 0.5980 chunk 0 optimal weight: 5.9990 chunk 35 optimal weight: 0.1980 chunk 38 optimal weight: 0.6980 overall best weight: 0.4178 ------------------------------------------------------------------------------- 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 = 0.4111 r_free = 0.4111 target = 0.175915 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.132617 restraints weight = 8478.496| |-----------------------------------------------------------------------------| r_work (start): 0.3609 rms_B_bonded: 1.17 r_work: 0.3386 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3264 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3264 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 moved from start: 0.2004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7505 Z= 0.153 Angle : 0.502 5.448 10835 Z= 0.298 Chirality : 0.037 0.166 1323 Planarity : 0.004 0.037 799 Dihedral : 23.335 167.472 2683 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 10.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 2.28 % Allowed : 21.46 % 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: 1.03 (0.39), residues: 464 helix: 1.98 (0.34), residues: 218 sheet: -0.23 (0.75), residues: 58 loop : -0.55 (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 0.013 0.002 PHE P 444 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 0.00309 / 0.15 ( 7501) covalent geometry : angle 0.49882 / 0.30 (10829) hydrogen bonds : bond 0.05143 / 4.44 ( 372) hydrogen bonds : angle 3.84560 / 3.95 ( 896) metal coordination : bond 0.00602 / 0.30 ( 4) metal coordination : angle 2.54377 / 4.33 ( 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 58 residues out of total 438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 48 time to evaluate : 0.198 Fit side-chains REVERT: P 382 ARG cc_start: 0.8497 (ttp80) cc_final: 0.8035 (ttt-90) REVERT: P 390 ARG cc_start: 0.8004 (OUTLIER) cc_final: 0.7411 (mmt90) REVERT: P 421 LYS cc_start: 0.7605 (OUTLIER) cc_final: 0.7344 (tppt) outliers start: 10 outliers final: 5 residues processed: 56 average time/residue: 0.5039 time to fit residues: 29.9584 Evaluate side-chains 52 residues out of total 438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 45 time to evaluate : 0.168 ------------------------------------------------------------------------------- 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 339 THR Chi-restraints excluded: chain P residue 390 ARG 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: 0.8980 chunk 54 optimal weight: 20.0000 chunk 34 optimal weight: 0.7980 chunk 42 optimal weight: 0.5980 chunk 56 optimal weight: 7.9990 chunk 15 optimal weight: 0.9980 chunk 2 optimal weight: 0.5980 chunk 32 optimal weight: 0.6980 chunk 25 optimal weight: 0.9980 chunk 24 optimal weight: 0.9980 chunk 23 optimal weight: 0.5980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 = 0.4087 r_free = 0.4087 target = 0.173471 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.130074 restraints weight = 8447.091| |-----------------------------------------------------------------------------| r_work (start): 0.3578 rms_B_bonded: 1.18 r_work: 0.3345 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3221 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3221 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.2092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 7505 Z= 0.204 Angle : 0.544 5.405 10835 Z= 0.318 Chirality : 0.039 0.164 1323 Planarity : 0.004 0.037 799 Dihedral : 23.334 164.822 2683 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 11.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 2.74 % Allowed : 21.69 % Favored : 75.57 % 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: 0.86 (0.39), residues: 464 helix: 1.87 (0.34), residues: 218 sheet: -0.28 (0.75), residues: 58 loop : -0.70 (0.43), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG P 299 TYR 0.018 0.001 TYR P 387 PHE 0.018 0.003 PHE P 444 TRP 0.006 0.001 TRP P 68 HIS 0.003 0.001 HIS P 215 Details of bonding type rmsd/Z covalent geometry : bond 0.00435 / 0.20 ( 7501) covalent geometry : angle 0.54138 / 0.32 (10829) hydrogen bonds : bond 0.05467 / 4.78 ( 372) hydrogen bonds : angle 3.95459 / 4.04 ( 896) metal coordination : bond 0.00767 / 0.40 ( 4) metal coordination : angle 2.44385 / 4.14 ( 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 60 residues out of total 438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 48 time to evaluate : 0.130 Fit side-chains REVERT: P 346 GLU cc_start: 0.8337 (OUTLIER) cc_final: 0.8002 (mp0) REVERT: P 382 ARG cc_start: 0.8530 (ttp80) cc_final: 0.8075 (ttt-90) REVERT: P 390 ARG cc_start: 0.8085 (OUTLIER) cc_final: 0.7597 (mmt90) outliers start: 12 outliers final: 8 residues processed: 58 average time/residue: 0.4381 time to fit residues: 27.1433 Evaluate side-chains 56 residues out of total 438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 46 time to evaluate : 0.130 ------------------------------------------------------------------------------- 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 339 THR Chi-restraints excluded: chain P residue 346 GLU Chi-restraints excluded: chain P residue 390 ARG Chi-restraints excluded: chain P residue 421 LYS Chi-restraints excluded: chain P residue 430 VAL Chi-restraints excluded: chain P residue 454 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 15 optimal weight: 0.8980 chunk 6 optimal weight: 0.9980 chunk 51 optimal weight: 3.9990 chunk 2 optimal weight: 0.6980 chunk 59 optimal weight: 1.9990 chunk 24 optimal weight: 0.9990 chunk 18 optimal weight: 0.0870 chunk 25 optimal weight: 0.6980 chunk 32 optimal weight: 0.6980 chunk 11 optimal weight: 0.0970 chunk 36 optimal weight: 0.5980 overall best weight: 0.4356 ------------------------------------------------------------------------------- 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 = 0.175417 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.131367 restraints weight = 8421.083| |-----------------------------------------------------------------------------| r_work (start): 0.3592 rms_B_bonded: 1.14 r_work: 0.3387 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3268 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3268 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 moved from start: 0.2156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7505 Z= 0.158 Angle : 0.518 6.366 10835 Z= 0.304 Chirality : 0.037 0.167 1323 Planarity : 0.004 0.037 799 Dihedral : 23.339 166.594 2683 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 10.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 2.28 % Allowed : 21.92 % 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: 0.85 (0.39), residues: 464 helix: 1.89 (0.34), residues: 218 sheet: -0.24 (0.75), residues: 58 loop : -0.73 (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 0.012 0.002 PHE P 444 TRP 0.004 0.001 TRP P 68 HIS 0.002 0.001 HIS P 404 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.16 ( 7501) covalent geometry : angle 0.51481 / 0.30 (10829) hydrogen bonds : bond 0.05158 / 4.47 ( 372) hydrogen bonds : angle 3.89217 / 4.01 ( 896) metal coordination : bond 0.00593 / 0.30 ( 4) metal coordination : angle 2.53576 / 4.29 ( 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 56 residues out of total 438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 46 time to evaluate : 0.121 Fit side-chains REVERT: P 346 GLU cc_start: 0.8281 (OUTLIER) cc_final: 0.7937 (mp0) REVERT: P 382 ARG cc_start: 0.8507 (ttp80) cc_final: 0.8054 (ttt-90) REVERT: P 390 ARG cc_start: 0.8010 (OUTLIER) cc_final: 0.7472 (mmt90) REVERT: P 421 LYS cc_start: 0.7556 (OUTLIER) cc_final: 0.7290 (tppt) outliers start: 10 outliers final: 6 residues processed: 54 average time/residue: 0.4844 time to fit residues: 27.7958 Evaluate side-chains 56 residues out of total 438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 47 time to evaluate : 0.189 ------------------------------------------------------------------------------- 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 339 THR Chi-restraints excluded: chain P residue 346 GLU Chi-restraints excluded: chain P residue 390 ARG 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: 0.8980 chunk 52 optimal weight: 8.9990 chunk 18 optimal weight: 0.5980 chunk 44 optimal weight: 0.0970 chunk 42 optimal weight: 0.9990 chunk 11 optimal weight: 0.1980 chunk 21 optimal weight: 0.0980 chunk 2 optimal weight: 0.8980 chunk 59 optimal weight: 1.9990 chunk 54 optimal weight: 20.0000 chunk 35 optimal weight: 0.0980 overall best weight: 0.2178 ------------------------------------------------------------------------------- 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 = 0.4138 r_free = 0.4138 target = 0.178635 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.135636 restraints weight = 8420.538| |-----------------------------------------------------------------------------| r_work (start): 0.3643 rms_B_bonded: 1.16 r_work: 0.3424 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3303 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3303 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 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 : 0.002 0.028 7505 Z= 0.124 Angle : 0.492 6.909 10835 Z= 0.291 Chirality : 0.035 0.172 1323 Planarity : 0.004 0.036 799 Dihedral : 23.318 170.182 2683 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 10.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 2.28 % Allowed : 22.37 % Favored : 75.34 % 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: 1.07 (0.39), residues: 464 helix: 2.05 (0.34), residues: 218 sheet: -0.16 (0.75), residues: 58 loop : -0.59 (0.44), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG P 88 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 215 Details of bonding type rmsd/Z covalent geometry : bond 0.00238 / 0.12 ( 7501) covalent geometry : angle 0.48881 / 0.29 (10829) hydrogen bonds : bond 0.04960 / 4.23 ( 372) hydrogen bonds : angle 3.76576 / 3.89 ( 896) metal coordination : bond 0.00413 / 0.20 ( 4) metal coordination : angle 2.40551 / 4.11 ( 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 61 residues out of total 438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 51 time to evaluate : 0.203 Fit side-chains REVERT: P 346 GLU cc_start: 0.8254 (OUTLIER) cc_final: 0.7901 (mp0) REVERT: P 382 ARG cc_start: 0.8511 (ttp80) cc_final: 0.8062 (ttt-90) REVERT: P 421 LYS cc_start: 0.7541 (OUTLIER) cc_final: 0.7320 (tppt) outliers start: 10 outliers final: 6 residues processed: 59 average time/residue: 0.5227 time to fit residues: 32.8353 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 : 0.205 ------------------------------------------------------------------------------- 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 130 VAL Chi-restraints excluded: chain P residue 291 THR 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: 0.9990 chunk 25 optimal weight: 0.8980 chunk 31 optimal weight: 0.0980 chunk 51 optimal weight: 3.9990 chunk 8 optimal weight: 0.7980 chunk 53 optimal weight: 2.9990 chunk 37 optimal weight: 0.5980 chunk 46 optimal weight: 0.2980 chunk 56 optimal weight: 6.9990 chunk 19 optimal weight: 1.9990 chunk 23 optimal weight: 0.6980 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 = 0.4110 r_free = 0.4110 target = 0.175552 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.131730 restraints weight = 8363.964| |-----------------------------------------------------------------------------| r_work (start): 0.3595 rms_B_bonded: 1.13 r_work: 0.3383 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3262 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3262 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 moved from start: 0.2294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 7505 Z= 0.169 Angle : 0.521 6.448 10835 Z= 0.303 Chirality : 0.037 0.171 1323 Planarity : 0.004 0.037 799 Dihedral : 23.277 167.263 2683 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 10.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 1.60 % Allowed : 23.52 % Favored : 74.89 % 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: 1.00 (0.39), residues: 464 helix: 1.98 (0.34), residues: 218 sheet: -0.16 (0.75), residues: 58 loop : -0.61 (0.44), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG P 299 TYR 0.015 0.001 TYR P 387 PHE 0.015 0.002 PHE P 444 TRP 0.009 0.001 TRP P 516 HIS 0.003 0.001 HIS P 215 Details of bonding type rmsd/Z covalent geometry : bond 0.00355 / 0.17 ( 7501) covalent geometry : angle 0.51784 / 0.30 (10829) hydrogen bonds : bond 0.05209 / 4.52 ( 372) hydrogen bonds : angle 3.81145 / 3.94 ( 896) metal coordination : bond 0.00632 / 0.32 ( 4) metal coordination : angle 2.38252 / 4.03 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2354.85 seconds wall clock time: 40 minutes 59.89 seconds (2459.89 seconds total)