Starting phenix.real_space_refine on Tue Aug 4 21:08:21 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vz6_43682/08_2026/8vz6_43682.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vz6_43682/08_2026/8vz6_43682.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.56 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8vz6_43682/08_2026/8vz6_43682.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vz6_43682/08_2026/8vz6_43682.map" model { file = "/net/cci-nas-00/data/ceres_data/8vz6_43682/08_2026/8vz6_43682.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vz6_43682/08_2026/8vz6_43682.cif" } resolution = 3.56 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 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: 5 Type Number sf(0) Gaussians P 98 5.49 5 S 28 5.16 5 C 4098 2.51 5 N 1194 2.21 5 O 1536 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 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: 6954 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 2442 Number of conformers: 1 Conformer: "" Number of residues, atoms: 297, 2442 Classifications: {'peptide': 297} Link IDs: {'PTRANS': 18, 'TRANS': 278} Chain: "R" Number of atoms: 1035 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 1035 Classifications: {'RNA': 49} Modifications used: {'rna2p_pur': 7, 'rna2p_pyr': 7, 'rna3p_pur': 15, 'rna3p_pyr': 20} Link IDs: {'rna2p': 14, 'rna3p': 34} Chain: "B" Number of atoms: 2442 Number of conformers: 1 Conformer: "" Number of residues, atoms: 297, 2442 Classifications: {'peptide': 297} Link IDs: {'PTRANS': 18, 'TRANS': 278} Chain: "S" Number of atoms: 1035 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 1035 Classifications: {'RNA': 49} Modifications used: {'rna2p_pur': 7, 'rna2p_pyr': 7, 'rna3p_pur': 15, 'rna3p_pyr': 20} Link IDs: {'rna2p': 14, 'rna3p': 34} Time building chain proxies: 1.70, per 1000 atoms: 0.24 Number of scatterers: 6954 At special positions: 0 Unit cell: (92.4885, 138.235, 64.6425, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 28 16.00 P 98 15.00 O 1536 8.00 N 1194 7.00 C 4098 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: 0.56 Conformation dependent library (CDL) restraints added in 283.7 milliseconds 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1144 Finding SS restraints... Secondary structure from input PDB file: 34 helices and 0 sheets defined 71.0% alpha, 0.0% beta 26 base pairs and 48 stacking pairs defined. Time for finding SS restraints: 0.56 Creating SS restraints... Processing helix chain 'A' and resid 13 through 24 removed outlier: 3.713A pdb=" N VAL A 18 " --> pdb=" O ALA A 14 " (cutoff:3.500A) Processing helix chain 'A' and resid 30 through 41 removed outlier: 3.538A pdb=" N THR A 34 " --> pdb=" O ASP A 30 " (cutoff:3.500A) Processing helix chain 'A' and resid 42 through 51 removed outlier: 4.027A pdb=" N ALA A 48 " --> pdb=" O TYR A 44 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N TYR A 49 " --> pdb=" O ARG A 45 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 54 No H-bonds generated for 'chain 'A' and resid 52 through 54' Processing helix chain 'A' and resid 57 through 61 Processing helix chain 'A' and resid 68 through 110 removed outlier: 4.003A pdb=" N VAL A 72 " --> pdb=" O THR A 68 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N LEU A 84 " --> pdb=" O LYS A 80 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N GLU A 89 " --> pdb=" O LEU A 85 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N LYS A 92 " --> pdb=" O ASN A 88 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N ILE A 93 " --> pdb=" O GLU A 89 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N ARG A 98 " --> pdb=" O GLU A 94 " (cutoff:3.500A) Processing helix chain 'A' and resid 113 through 121 removed outlier: 3.739A pdb=" N ASP A 117 " --> pdb=" O TRP A 114 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N GLY A 118 " --> pdb=" O MET A 115 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N SER A 119 " --> pdb=" O THR A 116 " (cutoff:3.500A) Processing helix chain 'A' and resid 123 through 139 removed outlier: 4.299A pdb=" N HIS A 129 " --> pdb=" O ARG A 125 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ASP A 132 " --> pdb=" O ARG A 128 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N LEU A 133 " --> pdb=" O HIS A 129 " (cutoff:3.500A) Processing helix chain 'A' and resid 145 through 153 Processing helix chain 'A' and resid 159 through 164 Processing helix chain 'A' and resid 168 through 177 removed outlier: 3.535A pdb=" N ASN A 174 " --> pdb=" O GLY A 170 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N SER A 177 " --> pdb=" O THR A 173 " (cutoff:3.500A) Processing helix chain 'A' and resid 181 through 192 removed outlier: 3.690A pdb=" N LYS A 185 " --> pdb=" O THR A 181 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N PHE A 192 " --> pdb=" O ILE A 188 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 215 removed outlier: 3.570A pdb=" N HIS A 215 " --> pdb=" O ASN A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 248 through 263 removed outlier: 3.527A pdb=" N LEU A 252 " --> pdb=" O ILE A 248 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ILE A 261 " --> pdb=" O TYR A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 267 through 279 Processing helix chain 'A' and resid 283 through 287 Processing helix chain 'A' and resid 292 through 300 removed outlier: 3.817A pdb=" N GLU A 296 " --> pdb=" O TRP A 293 " (cutoff:3.500A) Proline residue: A 297 - end of helix removed outlier: 3.680A pdb=" N GLN A 300 " --> pdb=" O PRO A 297 " (cutoff:3.500A) Processing helix chain 'B' and resid 15 through 24 removed outlier: 3.758A pdb=" N SER B 19 " --> pdb=" O HIS B 15 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 41 removed outlier: 3.580A pdb=" N THR B 34 " --> pdb=" O ASP B 30 " (cutoff:3.500A) Processing helix chain 'B' and resid 42 through 51 removed outlier: 4.063A pdb=" N ALA B 48 " --> pdb=" O TYR B 44 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N TYR B 49 " --> pdb=" O ARG B 45 " (cutoff:3.500A) Processing helix chain 'B' and resid 52 through 54 No H-bonds generated for 'chain 'B' and resid 52 through 54' Processing helix chain 'B' and resid 57 through 61 Processing helix chain 'B' and resid 68 through 110 removed outlier: 3.985A pdb=" N VAL B 72 " --> pdb=" O THR B 68 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N LEU B 84 " --> pdb=" O LYS B 80 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N GLU B 89 " --> pdb=" O LEU B 85 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N LYS B 92 " --> pdb=" O ASN B 88 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N ILE B 93 " --> pdb=" O GLU B 89 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N ARG B 98 " --> pdb=" O GLU B 94 " (cutoff:3.500A) Processing helix chain 'B' and resid 113 through 121 removed outlier: 3.737A pdb=" N ASP B 117 " --> pdb=" O TRP B 114 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N GLY B 118 " --> pdb=" O MET B 115 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N SER B 119 " --> pdb=" O THR B 116 " (cutoff:3.500A) Processing helix chain 'B' and resid 123 through 139 removed outlier: 4.301A pdb=" N HIS B 129 " --> pdb=" O ARG B 125 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ASP B 132 " --> pdb=" O ARG B 128 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N LEU B 133 " --> pdb=" O HIS B 129 " (cutoff:3.500A) Processing helix chain 'B' and resid 145 through 153 Processing helix chain 'B' and resid 159 through 164 Processing helix chain 'B' and resid 168 through 177 removed outlier: 3.536A pdb=" N ASN B 174 " --> pdb=" O GLY B 170 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N SER B 177 " --> pdb=" O THR B 173 " (cutoff:3.500A) Processing helix chain 'B' and resid 181 through 192 removed outlier: 3.691A pdb=" N LYS B 185 " --> pdb=" O THR B 181 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N PHE B 192 " --> pdb=" O ILE B 188 " (cutoff:3.500A) Processing helix chain 'B' and resid 195 through 215 removed outlier: 3.573A pdb=" N HIS B 215 " --> pdb=" O ASN B 211 " (cutoff:3.500A) Processing helix chain 'B' and resid 248 through 263 removed outlier: 3.528A pdb=" N LEU B 252 " --> pdb=" O ILE B 248 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ILE B 261 " --> pdb=" O TYR B 257 " (cutoff:3.500A) Processing helix chain 'B' and resid 267 through 279 removed outlier: 3.628A pdb=" N ALA B 274 " --> pdb=" O ALA B 270 " (cutoff:3.500A) Processing helix chain 'B' and resid 283 through 287 Processing helix chain 'B' and resid 292 through 300 removed outlier: 3.809A pdb=" N GLU B 296 " --> pdb=" O TRP B 293 " (cutoff:3.500A) Proline residue: B 297 - end of helix removed outlier: 3.715A pdb=" N GLN B 300 " --> pdb=" O PRO B 297 " (cutoff:3.500A) 239 hydrogen bonds defined for protein. 669 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 72 hydrogen bonds 136 hydrogen bond angles 0 basepair planarities 26 basepair parallelities 48 stacking parallelities Total time for adding SS restraints: 0.66 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: 1.21 - 1.33: 1331 1.33 - 1.45: 2242 1.45 - 1.57: 3506 1.57 - 1.69: 197 1.69 - 1.81: 50 Bond restraints: 7326 Sorted by residual: bond pdb=" N9 A S 33 " pdb=" C4 A S 33 " ideal model delta sigma weight residual 1.374 1.389 -0.015 6.00e-03 2.78e+04 6.38e+00 bond pdb=" N9 A R 33 " pdb=" C4 A R 33 " ideal model delta sigma weight residual 1.374 1.389 -0.015 6.00e-03 2.78e+04 5.89e+00 bond pdb=" N1 C R 9 " pdb=" C2 C R 9 " ideal model delta sigma weight residual 1.397 1.419 -0.022 1.00e-02 1.00e+04 4.95e+00 bond pdb=" N1 C S 12 " pdb=" C2 C S 12 " ideal model delta sigma weight residual 1.397 1.419 -0.022 1.00e-02 1.00e+04 4.89e+00 bond pdb=" N1 C R 12 " pdb=" C2 C R 12 " ideal model delta sigma weight residual 1.397 1.419 -0.022 1.00e-02 1.00e+04 4.75e+00 ... (remaining 7321 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.85: 9998 2.85 - 5.71: 346 5.71 - 8.56: 40 8.56 - 11.42: 2 11.42 - 14.27: 4 Bond angle restraints: 10390 Sorted by residual: angle pdb=" C2 C S 25 " pdb=" N1 C S 25 " pdb=" C6 C S 25 " ideal model delta sigma weight residual 120.30 116.51 3.79 4.00e-01 6.25e+00 8.98e+01 angle pdb=" C2 C R 25 " pdb=" N1 C R 25 " pdb=" C6 C R 25 " ideal model delta sigma weight residual 120.30 116.57 3.73 4.00e-01 6.25e+00 8.71e+01 angle pdb=" N1 C R 20 " pdb=" C2 C R 20 " pdb=" O2 C R 20 " ideal model delta sigma weight residual 118.90 123.49 -4.59 6.00e-01 2.78e+00 5.86e+01 angle pdb=" N1 C S 20 " pdb=" C2 C S 20 " pdb=" O2 C S 20 " ideal model delta sigma weight residual 118.90 123.45 -4.55 6.00e-01 2.78e+00 5.75e+01 angle pdb=" O2 C S 25 " pdb=" C2 C S 25 " pdb=" N3 C S 25 " ideal model delta sigma weight residual 121.90 116.84 5.06 7.00e-01 2.04e+00 5.22e+01 ... (remaining 10385 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.63: 4155 31.63 - 63.26: 302 63.26 - 94.89: 81 94.89 - 126.51: 0 126.51 - 158.14: 4 Dihedral angle restraints: 4542 sinusoidal: 2780 harmonic: 1762 Sorted by residual: dihedral pdb=" CA PRO A 159 " pdb=" C PRO A 159 " pdb=" N ALA A 160 " pdb=" CA ALA A 160 " ideal model delta harmonic sigma weight residual -180.00 -154.21 -25.79 0 5.00e+00 4.00e-02 2.66e+01 dihedral pdb=" CA PRO B 159 " pdb=" C PRO B 159 " pdb=" N ALA B 160 " pdb=" CA ALA B 160 " ideal model delta harmonic sigma weight residual 180.00 -154.25 -25.75 0 5.00e+00 4.00e-02 2.65e+01 dihedral pdb=" O4' C R 25 " pdb=" C1' C R 25 " pdb=" N1 C R 25 " pdb=" C2 C R 25 " ideal model delta sinusoidal sigma weight residual -128.00 -50.37 -77.63 1 1.70e+01 3.46e-03 2.61e+01 ... (remaining 4539 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.082: 977 0.082 - 0.164: 229 0.164 - 0.246: 19 0.246 - 0.328: 2 0.328 - 0.410: 3 Chirality restraints: 1230 Sorted by residual: chirality pdb=" CG LEU B 17 " pdb=" CB LEU B 17 " pdb=" CD1 LEU B 17 " pdb=" CD2 LEU B 17 " both_signs ideal model delta sigma weight residual False -2.59 -2.18 -0.41 2.00e-01 2.50e+01 4.21e+00 chirality pdb=" C3' C R 40 " pdb=" C4' C R 40 " pdb=" O3' C R 40 " pdb=" C2' C R 40 " both_signs ideal model delta sigma weight residual False -2.48 -2.10 -0.37 2.00e-01 2.50e+01 3.50e+00 chirality pdb=" C3' C S 40 " pdb=" C4' C S 40 " pdb=" O3' C S 40 " pdb=" C2' C S 40 " both_signs ideal model delta sigma weight residual False -2.48 -2.10 -0.37 2.00e-01 2.50e+01 3.50e+00 ... (remaining 1227 not shown) Planarity restraints: 954 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR B 44 " -0.012 2.00e-02 2.50e+03 2.34e-02 1.09e+01 pdb=" CG TYR B 44 " 0.054 2.00e-02 2.50e+03 pdb=" CD1 TYR B 44 " -0.020 2.00e-02 2.50e+03 pdb=" CD2 TYR B 44 " -0.029 2.00e-02 2.50e+03 pdb=" CE1 TYR B 44 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR B 44 " 0.006 2.00e-02 2.50e+03 pdb=" CZ TYR B 44 " 0.003 2.00e-02 2.50e+03 pdb=" OH TYR B 44 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 44 " -0.013 2.00e-02 2.50e+03 2.27e-02 1.03e+01 pdb=" CG TYR A 44 " 0.053 2.00e-02 2.50e+03 pdb=" CD1 TYR A 44 " -0.018 2.00e-02 2.50e+03 pdb=" CD2 TYR A 44 " -0.027 2.00e-02 2.50e+03 pdb=" CE1 TYR A 44 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 TYR A 44 " 0.005 2.00e-02 2.50e+03 pdb=" CZ TYR A 44 " 0.002 2.00e-02 2.50e+03 pdb=" OH TYR A 44 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 289 " 0.007 2.00e-02 2.50e+03 1.99e-02 6.91e+00 pdb=" CG PHE B 289 " -0.042 2.00e-02 2.50e+03 pdb=" CD1 PHE B 289 " 0.023 2.00e-02 2.50e+03 pdb=" CD2 PHE B 289 " 0.018 2.00e-02 2.50e+03 pdb=" CE1 PHE B 289 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE B 289 " 0.003 2.00e-02 2.50e+03 pdb=" CZ PHE B 289 " -0.008 2.00e-02 2.50e+03 ... (remaining 951 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.78: 1376 2.78 - 3.31: 5950 3.31 - 3.84: 12336 3.84 - 4.37: 14365 4.37 - 4.90: 22246 Nonbonded interactions: 56273 Sorted by model distance: nonbonded pdb=" O ASP A 273 " pdb=" OG SER A 277 " model vdw 2.255 3.040 nonbonded pdb=" O ARG B 227 " pdb=" O2' A S 7 " model vdw 2.316 3.040 nonbonded pdb=" O ARG A 227 " pdb=" O2' A R 7 " model vdw 2.325 3.040 nonbonded pdb=" O ASP B 273 " pdb=" OG SER B 277 " model vdw 2.337 3.040 nonbonded pdb=" OG1 THR B 204 " pdb=" N4 C S 2 " model vdw 2.424 3.120 ... (remaining 56268 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'R' selection = chain 'S' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.020 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: 0.110 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 6.950 Find NCS groups from input model: 0.050 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:1.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7691 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 : 0.006 0.067 7326 Z= 0.368 Angle : 1.222 14.274 10390 Z= 0.961 Chirality : 0.069 0.410 1230 Planarity : 0.008 0.046 954 Dihedral : 21.093 158.143 3398 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 1.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % Rotamer: Outliers : 0.37 % Allowed : 9.18 % Favored : 90.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.51 (0.30), residues: 590 helix: -1.38 (0.22), residues: 340 sheet: None (None), residues: 0 loop : -0.14 (0.38), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 36 TYR 0.054 0.004 TYR B 44 PHE 0.042 0.004 PHE B 289 TRP 0.039 0.004 TRP A 220 HIS 0.006 0.002 HIS B 61 Details of bonding type rmsd/Z covalent geometry : bond 0.00604 / 0.37 ( 7326) covalent geometry : angle 1.22233 / 0.96 (10390) hydrogen bonds : bond 0.15620 / 10.05 ( 311) hydrogen bonds : angle 5.55665 / 3.83 ( 805) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 97 time to evaluate : 0.214 Fit side-chains REVERT: A 120 ASN cc_start: 0.7184 (OUTLIER) cc_final: 0.6641 (t0) REVERT: B 120 ASN cc_start: 0.7188 (OUTLIER) cc_final: 0.6673 (t0) outliers start: 2 outliers final: 0 residues processed: 99 average time/residue: 0.0862 time to fit residues: 11.4194 Evaluate side-chains 67 residues out of total 534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 65 time to evaluate : 0.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 ASN Chi-restraints excluded: chain B residue 120 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 49 optimal weight: 2.9990 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 0.7980 chunk 33 optimal weight: 5.9990 chunk 65 optimal weight: 20.0000 chunk 62 optimal weight: 10.0000 chunk 51 optimal weight: 0.7980 chunk 38 optimal weight: 3.9990 chunk 61 optimal weight: 7.9990 chunk 45 optimal weight: 8.9990 chunk 27 optimal weight: 7.9990 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 151 GLN B 151 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.166462 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.138673 restraints weight = 10241.831| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.141387 restraints weight = 6258.568| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.143200 restraints weight = 4645.290| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.144341 restraints weight = 3866.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.145084 restraints weight = 3448.762| |-----------------------------------------------------------------------------| r_work (final): 0.3673 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7764 moved from start: 0.1330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 7326 Z= 0.177 Angle : 0.655 7.217 10390 Z= 0.361 Chirality : 0.043 0.264 1230 Planarity : 0.006 0.050 954 Dihedral : 22.822 167.062 2182 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 2.81 % Allowed : 11.42 % Favored : 85.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.07 (0.34), residues: 590 helix: 0.02 (0.27), residues: 350 sheet: None (None), residues: 0 loop : 0.38 (0.40), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 125 TYR 0.012 0.002 TYR A 37 PHE 0.015 0.002 PHE B 289 TRP 0.010 0.002 TRP B 220 HIS 0.002 0.001 HIS A 61 Details of bonding type rmsd/Z covalent geometry : bond 0.00395 / 0.18 ( 7326) covalent geometry : angle 0.65458 / 0.36 (10390) hydrogen bonds : bond 0.06962 / 4.61 ( 311) hydrogen bonds : angle 3.90186 / 2.69 ( 805) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 80 time to evaluate : 0.217 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 120 ASN cc_start: 0.7796 (OUTLIER) cc_final: 0.7004 (t0) outliers start: 15 outliers final: 10 residues processed: 92 average time/residue: 0.0838 time to fit residues: 10.5152 Evaluate side-chains 81 residues out of total 534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 70 time to evaluate : 0.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain A residue 109 ILE Chi-restraints excluded: chain A residue 120 ASN Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 181 THR Chi-restraints excluded: chain B residue 13 SER Chi-restraints excluded: chain B residue 18 VAL Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 109 ILE Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 181 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 40 optimal weight: 1.9990 chunk 30 optimal weight: 40.0000 chunk 2 optimal weight: 2.9990 chunk 7 optimal weight: 0.9990 chunk 4 optimal weight: 0.0170 chunk 29 optimal weight: 20.0000 chunk 41 optimal weight: 1.9990 chunk 14 optimal weight: 0.3980 chunk 11 optimal weight: 2.9990 chunk 36 optimal weight: 4.9990 chunk 32 optimal weight: 20.0000 overall best weight: 1.0824 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 151 GLN A 266 ASN B 151 GLN B 266 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.168342 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.141133 restraints weight = 10142.419| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.143923 restraints weight = 6110.786| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.145775 restraints weight = 4467.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.146855 restraints weight = 3668.120| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.147650 restraints weight = 3273.177| |-----------------------------------------------------------------------------| r_work (final): 0.3686 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7712 moved from start: 0.1697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 7326 Z= 0.121 Angle : 0.540 7.790 10390 Z= 0.293 Chirality : 0.038 0.235 1230 Planarity : 0.005 0.050 954 Dihedral : 22.784 170.596 2180 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 1.50 % Allowed : 14.42 % Favored : 84.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.56 (0.34), residues: 590 helix: 0.43 (0.27), residues: 350 sheet: None (None), residues: 0 loop : 0.56 (0.41), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 125 TYR 0.009 0.001 TYR A 249 PHE 0.010 0.001 PHE A 289 TRP 0.004 0.001 TRP A 299 HIS 0.002 0.000 HIS A 15 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.12 ( 7326) covalent geometry : angle 0.53955 / 0.29 (10390) hydrogen bonds : bond 0.05504 / 3.65 ( 311) hydrogen bonds : angle 3.48135 / 2.42 ( 805) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 79 time to evaluate : 0.208 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 120 ASN cc_start: 0.7880 (OUTLIER) cc_final: 0.7518 (t0) outliers start: 8 outliers final: 5 residues processed: 87 average time/residue: 0.0778 time to fit residues: 9.5287 Evaluate side-chains 78 residues out of total 534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 72 time to evaluate : 0.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 ASN Chi-restraints excluded: chain A residue 284 ILE Chi-restraints excluded: chain B residue 13 SER Chi-restraints excluded: chain B residue 18 VAL Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 284 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 64 optimal weight: 40.0000 chunk 36 optimal weight: 6.9990 chunk 24 optimal weight: 5.9990 chunk 8 optimal weight: 2.9990 chunk 26 optimal weight: 4.9990 chunk 33 optimal weight: 2.9990 chunk 16 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 12 optimal weight: 0.9990 chunk 61 optimal weight: 2.9990 chunk 55 optimal weight: 6.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 151 GLN B 151 GLN B 266 ASN B 285 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.163932 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.135829 restraints weight = 10240.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.138559 restraints weight = 6282.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.140276 restraints weight = 4629.862| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.141420 restraints weight = 3850.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.142054 restraints weight = 3435.992| |-----------------------------------------------------------------------------| r_work (final): 0.3618 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7805 moved from start: 0.1998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 7326 Z= 0.184 Angle : 0.611 8.980 10390 Z= 0.324 Chirality : 0.041 0.249 1230 Planarity : 0.006 0.058 954 Dihedral : 22.857 170.611 2180 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 2.62 % Allowed : 15.92 % Favored : 81.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.44 (0.33), residues: 590 helix: 0.41 (0.27), residues: 350 sheet: None (None), residues: 0 loop : 0.36 (0.40), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 77 TYR 0.012 0.002 TYR B 11 PHE 0.023 0.002 PHE A 289 TRP 0.009 0.002 TRP A 220 HIS 0.003 0.001 HIS A 216 Details of bonding type rmsd/Z covalent geometry : bond 0.00426 / 0.18 ( 7326) covalent geometry : angle 0.61112 / 0.32 (10390) hydrogen bonds : bond 0.06513 / 4.29 ( 311) hydrogen bonds : angle 3.67779 / 2.58 ( 805) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 72 time to evaluate : 0.205 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 120 ASN cc_start: 0.8054 (OUTLIER) cc_final: 0.7798 (t0) outliers start: 14 outliers final: 10 residues processed: 84 average time/residue: 0.0582 time to fit residues: 7.3272 Evaluate side-chains 77 residues out of total 534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 66 time to evaluate : 0.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain A residue 120 ASN Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 181 THR Chi-restraints excluded: chain A residue 284 ILE Chi-restraints excluded: chain B residue 13 SER Chi-restraints excluded: chain B residue 18 VAL Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 284 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 45 optimal weight: 0.9990 chunk 24 optimal weight: 0.5980 chunk 61 optimal weight: 6.9990 chunk 48 optimal weight: 0.0670 chunk 6 optimal weight: 2.9990 chunk 3 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 chunk 30 optimal weight: 40.0000 chunk 4 optimal weight: 0.8980 chunk 23 optimal weight: 1.9990 chunk 58 optimal weight: 0.7980 overall best weight: 0.6720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 151 GLN B 151 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.168152 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.140723 restraints weight = 10224.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.143514 restraints weight = 6177.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.145310 restraints weight = 4525.119| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.146388 restraints weight = 3728.780| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.147216 restraints weight = 3324.218| |-----------------------------------------------------------------------------| r_work (final): 0.3691 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7713 moved from start: 0.2175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 7326 Z= 0.110 Angle : 0.508 7.880 10390 Z= 0.271 Chirality : 0.036 0.226 1230 Planarity : 0.005 0.054 954 Dihedral : 22.868 172.015 2180 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 1.87 % Allowed : 16.85 % Favored : 81.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.85 (0.34), residues: 590 helix: 0.82 (0.28), residues: 344 sheet: None (None), residues: 0 loop : 0.40 (0.40), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 36 TYR 0.007 0.001 TYR B 249 PHE 0.010 0.001 PHE A 78 TRP 0.012 0.001 TRP A 220 HIS 0.002 0.001 HIS A 15 Details of bonding type rmsd/Z covalent geometry : bond 0.00233 / 0.11 ( 7326) covalent geometry : angle 0.50760 / 0.27 (10390) hydrogen bonds : bond 0.04914 / 3.27 ( 311) hydrogen bonds : angle 3.25845 / 2.30 ( 805) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 78 time to evaluate : 0.219 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 120 ASN cc_start: 0.8000 (OUTLIER) cc_final: 0.7689 (t0) outliers start: 10 outliers final: 6 residues processed: 88 average time/residue: 0.0610 time to fit residues: 8.0502 Evaluate side-chains 78 residues out of total 534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 71 time to evaluate : 0.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 ASN Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 181 THR Chi-restraints excluded: chain A residue 284 ILE Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 284 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 36 optimal weight: 2.9990 chunk 47 optimal weight: 0.6980 chunk 50 optimal weight: 10.0000 chunk 43 optimal weight: 2.9990 chunk 58 optimal weight: 1.9990 chunk 21 optimal weight: 6.9990 chunk 40 optimal weight: 4.9990 chunk 10 optimal weight: 4.9990 chunk 46 optimal weight: 9.9990 chunk 19 optimal weight: 1.9990 chunk 42 optimal weight: 0.6980 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 60 GLN B 151 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.166403 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.138469 restraints weight = 10266.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.141136 restraints weight = 6387.264| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.142946 restraints weight = 4737.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.144046 restraints weight = 3928.775| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.144666 restraints weight = 3509.004| |-----------------------------------------------------------------------------| r_work (final): 0.3655 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7758 moved from start: 0.2330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 7326 Z= 0.134 Angle : 0.531 7.790 10390 Z= 0.281 Chirality : 0.038 0.230 1230 Planarity : 0.006 0.056 954 Dihedral : 22.791 172.383 2180 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 2.25 % Allowed : 17.23 % Favored : 80.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.95 (0.34), residues: 590 helix: 0.94 (0.27), residues: 344 sheet: None (None), residues: 0 loop : 0.37 (0.41), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 210 TYR 0.007 0.001 TYR B 11 PHE 0.016 0.002 PHE B 289 TRP 0.017 0.001 TRP A 220 HIS 0.003 0.001 HIS A 216 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.13 ( 7326) covalent geometry : angle 0.53138 / 0.28 (10390) hydrogen bonds : bond 0.05338 / 3.54 ( 311) hydrogen bonds : angle 3.35011 / 2.37 ( 805) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 72 time to evaluate : 0.218 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 7 residues processed: 83 average time/residue: 0.0643 time to fit residues: 7.9242 Evaluate side-chains 74 residues out of total 534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 67 time to evaluate : 0.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 181 THR Chi-restraints excluded: chain A residue 284 ILE Chi-restraints excluded: chain B residue 18 VAL Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 284 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 18 optimal weight: 3.9990 chunk 50 optimal weight: 10.0000 chunk 29 optimal weight: 20.0000 chunk 10 optimal weight: 2.9990 chunk 59 optimal weight: 2.9990 chunk 30 optimal weight: 40.0000 chunk 49 optimal weight: 5.9990 chunk 43 optimal weight: 6.9990 chunk 4 optimal weight: 0.4980 chunk 57 optimal weight: 4.9990 chunk 28 optimal weight: 2.9990 overall best weight: 2.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 285 ASN B 60 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.164188 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.136919 restraints weight = 10511.589| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.139579 restraints weight = 6423.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.141312 restraints weight = 4740.238| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.142317 restraints weight = 3931.322| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.143093 restraints weight = 3516.706| |-----------------------------------------------------------------------------| r_work (final): 0.3658 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7793 moved from start: 0.2483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 7326 Z= 0.169 Angle : 0.569 7.580 10390 Z= 0.301 Chirality : 0.040 0.242 1230 Planarity : 0.006 0.060 954 Dihedral : 22.780 172.844 2178 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 2.62 % Allowed : 17.04 % Favored : 80.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.72 (0.34), residues: 590 helix: 0.80 (0.27), residues: 344 sheet: None (None), residues: 0 loop : 0.19 (0.41), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 237 TYR 0.009 0.001 TYR B 11 PHE 0.020 0.002 PHE B 289 TRP 0.019 0.002 TRP A 220 HIS 0.003 0.001 HIS A 216 Details of bonding type rmsd/Z covalent geometry : bond 0.00396 / 0.17 ( 7326) covalent geometry : angle 0.56879 / 0.30 (10390) hydrogen bonds : bond 0.05972 / 3.96 ( 311) hydrogen bonds : angle 3.46030 / 2.45 ( 805) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 63 time to evaluate : 0.225 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 276 LEU cc_start: 0.7826 (OUTLIER) cc_final: 0.7296 (mp) outliers start: 14 outliers final: 10 residues processed: 76 average time/residue: 0.0716 time to fit residues: 7.8566 Evaluate side-chains 74 residues out of total 534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 63 time to evaluate : 0.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 181 THR Chi-restraints excluded: chain A residue 284 ILE Chi-restraints excluded: chain B residue 18 VAL Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 259 LEU Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 284 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 16 optimal weight: 0.8980 chunk 51 optimal weight: 3.9990 chunk 28 optimal weight: 3.9990 chunk 55 optimal weight: 4.9990 chunk 1 optimal weight: 0.6980 chunk 26 optimal weight: 0.9980 chunk 49 optimal weight: 1.9990 chunk 64 optimal weight: 40.0000 chunk 25 optimal weight: 0.9990 chunk 47 optimal weight: 1.9990 chunk 13 optimal weight: 10.0000 overall best weight: 1.1184 ------------------------------------------------------------------------------- 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 = 0.3942 r_free = 0.3942 target = 0.166136 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.139301 restraints weight = 10822.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.141927 restraints weight = 6634.977| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.143542 restraints weight = 4928.519| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.144775 restraints weight = 4118.560| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.145402 restraints weight = 3644.729| |-----------------------------------------------------------------------------| r_work (final): 0.3681 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7747 moved from start: 0.2613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 7326 Z= 0.110 Angle : 0.505 7.827 10390 Z= 0.267 Chirality : 0.037 0.226 1230 Planarity : 0.005 0.059 954 Dihedral : 22.738 173.827 2178 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 1.50 % Allowed : 17.98 % Favored : 80.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.00 (0.35), residues: 590 helix: 1.01 (0.28), residues: 344 sheet: None (None), residues: 0 loop : 0.36 (0.42), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 4 TYR 0.007 0.001 TYR A 249 PHE 0.011 0.001 PHE B 78 TRP 0.017 0.001 TRP A 220 HIS 0.002 0.000 HIS A 15 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.11 ( 7326) covalent geometry : angle 0.50539 / 0.27 (10390) hydrogen bonds : bond 0.04982 / 3.33 ( 311) hydrogen bonds : angle 3.25507 / 2.32 ( 805) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 71 time to evaluate : 0.278 Fit side-chains outliers start: 8 outliers final: 7 residues processed: 77 average time/residue: 0.0655 time to fit residues: 7.5152 Evaluate side-chains 73 residues out of total 534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 66 time to evaluate : 0.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 181 THR Chi-restraints excluded: chain A residue 284 ILE Chi-restraints excluded: chain B residue 18 VAL Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 284 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 22 optimal weight: 5.9990 chunk 51 optimal weight: 1.9990 chunk 63 optimal weight: 40.0000 chunk 17 optimal weight: 10.0000 chunk 60 optimal weight: 0.9990 chunk 18 optimal weight: 1.9990 chunk 58 optimal weight: 0.7980 chunk 1 optimal weight: 7.9990 chunk 20 optimal weight: 1.9990 chunk 53 optimal weight: 0.8980 chunk 56 optimal weight: 0.0050 overall best weight: 0.9398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 60 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.168639 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.141765 restraints weight = 10551.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.144482 restraints weight = 6454.385| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.146270 restraints weight = 4756.437| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.147309 restraints weight = 3923.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.148054 restraints weight = 3498.652| |-----------------------------------------------------------------------------| r_work (final): 0.3717 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7715 moved from start: 0.2829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 7326 Z= 0.108 Angle : 0.493 7.780 10390 Z= 0.258 Chirality : 0.036 0.228 1230 Planarity : 0.005 0.059 954 Dihedral : 22.603 174.781 2178 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 1.12 % Allowed : 18.73 % Favored : 80.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.18 (0.35), residues: 590 helix: 1.12 (0.27), residues: 346 sheet: None (None), residues: 0 loop : 0.49 (0.42), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 36 TYR 0.007 0.001 TYR B 249 PHE 0.010 0.001 PHE B 289 TRP 0.020 0.001 TRP A 220 HIS 0.005 0.001 HIS A 216 Details of bonding type rmsd/Z covalent geometry : bond 0.00244 / 0.11 ( 7326) covalent geometry : angle 0.49250 / 0.26 (10390) hydrogen bonds : bond 0.04689 / 3.10 ( 311) hydrogen bonds : angle 3.21872 / 2.30 ( 805) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 69 time to evaluate : 0.221 Fit side-chains outliers start: 6 outliers final: 5 residues processed: 74 average time/residue: 0.0646 time to fit residues: 7.1802 Evaluate side-chains 71 residues out of total 534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 66 time to evaluate : 0.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 181 THR Chi-restraints excluded: chain A residue 284 ILE Chi-restraints excluded: chain B residue 18 VAL Chi-restraints excluded: chain B residue 259 LEU Chi-restraints excluded: chain B residue 284 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 5 optimal weight: 8.9990 chunk 62 optimal weight: 20.0000 chunk 13 optimal weight: 9.9990 chunk 28 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 1 optimal weight: 8.9990 chunk 37 optimal weight: 0.9980 chunk 54 optimal weight: 4.9990 chunk 43 optimal weight: 0.2980 chunk 8 optimal weight: 4.9990 chunk 3 optimal weight: 0.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- 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 = 0.3946 r_free = 0.3946 target = 0.166432 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.139433 restraints weight = 10712.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.142136 restraints weight = 6503.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.143834 restraints weight = 4784.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.145003 restraints weight = 3966.469| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.145718 restraints weight = 3507.797| |-----------------------------------------------------------------------------| r_work (final): 0.3693 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7730 moved from start: 0.2884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 7326 Z= 0.117 Angle : 0.497 7.796 10390 Z= 0.260 Chirality : 0.036 0.229 1230 Planarity : 0.005 0.061 954 Dihedral : 22.515 175.483 2178 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 1.31 % Allowed : 18.73 % Favored : 79.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.14 (0.35), residues: 590 helix: 1.12 (0.27), residues: 346 sheet: None (None), residues: 0 loop : 0.41 (0.42), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 227 TYR 0.007 0.001 TYR A 249 PHE 0.011 0.001 PHE A 289 TRP 0.017 0.001 TRP A 220 HIS 0.001 0.000 HIS A 216 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.12 ( 7326) covalent geometry : angle 0.49685 / 0.26 (10390) hydrogen bonds : bond 0.04915 / 3.26 ( 311) hydrogen bonds : angle 3.22662 / 2.31 ( 805) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 64 time to evaluate : 0.310 Fit side-chains outliers start: 7 outliers final: 5 residues processed: 69 average time/residue: 0.0724 time to fit residues: 7.3897 Evaluate side-chains 69 residues out of total 534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 64 time to evaluate : 0.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 181 THR Chi-restraints excluded: chain A residue 284 ILE Chi-restraints excluded: chain B residue 18 VAL Chi-restraints excluded: chain B residue 259 LEU Chi-restraints excluded: chain B residue 284 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 12 optimal weight: 5.9990 chunk 45 optimal weight: 1.9990 chunk 53 optimal weight: 4.9990 chunk 19 optimal weight: 2.9990 chunk 28 optimal weight: 0.1980 chunk 11 optimal weight: 0.9980 chunk 37 optimal weight: 0.7980 chunk 18 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 42 optimal weight: 0.8980 chunk 26 optimal weight: 5.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- 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 = 0.3961 r_free = 0.3961 target = 0.167727 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.140962 restraints weight = 10684.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.143639 restraints weight = 6463.572| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.145395 restraints weight = 4738.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.146539 restraints weight = 3909.335| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.147280 restraints weight = 3456.664| |-----------------------------------------------------------------------------| r_work (final): 0.3711 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7705 moved from start: 0.2973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 7326 Z= 0.103 Angle : 0.485 7.846 10390 Z= 0.253 Chirality : 0.035 0.226 1230 Planarity : 0.005 0.060 954 Dihedral : 22.409 175.960 2178 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 1.12 % Allowed : 18.91 % Favored : 79.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.26 (0.35), residues: 590 helix: 1.22 (0.27), residues: 346 sheet: None (None), residues: 0 loop : 0.47 (0.42), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 4 TYR 0.007 0.001 TYR B 249 PHE 0.008 0.001 PHE B 78 TRP 0.017 0.001 TRP A 220 HIS 0.002 0.000 HIS A 216 Details of bonding type rmsd/Z covalent geometry : bond 0.00233 / 0.10 ( 7326) covalent geometry : angle 0.48495 / 0.25 (10390) hydrogen bonds : bond 0.04634 / 3.09 ( 311) hydrogen bonds : angle 3.18068 / 2.28 ( 805) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1122.48 seconds wall clock time: 20 minutes 10.26 seconds (1210.26 seconds total)