Starting phenix.real_space_refine on Sat May 10 20:07:59 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vz6_43682/05_2025/8vz6_43682.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vz6_43682/05_2025/8vz6_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_43682/05_2025/8vz6_43682.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vz6_43682/05_2025/8vz6_43682.map" model { file = "/net/cci-nas-00/data/ceres_data/8vz6_43682/05_2025/8vz6_43682.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vz6_43682/05_2025/8vz6_43682.cif" } resolution = 3.56 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 4.91, per 1000 atoms: 0.71 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: 1.84 Conformation dependent library (CDL) restraints added in 786.4 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: 2.81 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: 2.08 Time building geometry restraints manager: 2.25 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=" CB GLN B 300 " pdb=" CG GLN B 300 " ideal model delta sigma weight residual 1.520 1.582 -0.062 3.00e-02 1.11e+03 4.27e+00 bond pdb=" C LYS B 64 " pdb=" N PRO B 65 " ideal model delta sigma weight residual 1.332 1.357 -0.025 1.26e-02 6.30e+03 3.94e+00 bond pdb=" C LYS A 64 " pdb=" N PRO A 65 " ideal model delta sigma weight residual 1.332 1.356 -0.024 1.26e-02 6.30e+03 3.59e+00 bond pdb=" CB ARG B 237 " pdb=" CG ARG B 237 " ideal model delta sigma weight residual 1.520 1.576 -0.056 3.00e-02 1.11e+03 3.54e+00 bond pdb=" CB ARG A 237 " pdb=" CG ARG A 237 " ideal model delta sigma weight residual 1.520 1.576 -0.056 3.00e-02 1.11e+03 3.43e+00 ... (remaining 7321 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.85: 10037 2.85 - 5.71: 307 5.71 - 8.56: 40 8.56 - 11.42: 2 11.42 - 14.27: 4 Bond angle restraints: 10390 Sorted by residual: angle pdb=" CB GLN B 300 " pdb=" CG GLN B 300 " pdb=" CD GLN B 300 " ideal model delta sigma weight residual 112.60 121.20 -8.60 1.70e+00 3.46e-01 2.56e+01 angle pdb=" C3' C S 40 " pdb=" O3' C S 40 " pdb=" P G S 41 " ideal model delta sigma weight residual 120.20 126.69 -6.49 1.50e+00 4.44e-01 1.87e+01 angle pdb=" C3' C R 40 " pdb=" O3' C R 40 " pdb=" P G R 41 " ideal model delta sigma weight residual 120.20 126.69 -6.49 1.50e+00 4.44e-01 1.87e+01 angle pdb=" C TRP B 238 " pdb=" N ILE B 239 " pdb=" CA ILE B 239 " ideal model delta sigma weight residual 120.35 126.32 -5.97 1.39e+00 5.18e-01 1.84e+01 angle pdb=" C TRP A 238 " pdb=" N ILE A 239 " pdb=" CA ILE A 239 " ideal model delta sigma weight residual 120.35 126.30 -5.95 1.39e+00 5.18e-01 1.83e+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: 1063 0.082 - 0.164: 143 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: 0.03 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: 0.670 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: 0.010 Extract box with map and model: 0.270 Check model and map are aligned: 0.050 Set scattering table: 0.080 Process input model: 21.890 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.030 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:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7497 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= 0.301 Angle : 1.160 14.274 10390 Z= 0.614 Chirality : 0.060 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.039 0.004 TRP A 220 HIS 0.006 0.002 HIS B 61 PHE 0.042 0.004 PHE B 289 TYR 0.054 0.004 TYR B 44 ARG 0.009 0.001 ARG A 36 Details of bonding type rmsd hydrogen bonds : bond 0.15620 ( 311) hydrogen bonds : angle 5.55665 ( 805) covalent geometry : bond 0.00601 ( 7326) covalent geometry : angle 1.15951 (10390) *********************** 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 : 0.692 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: 0.2100 time to fit residues: 27.3201 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 : 0.659 ------------------------------------------------------------------------------- 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 55 optimal weight: 4.9990 chunk 50 optimal weight: 0.5980 chunk 27 optimal weight: 7.9990 chunk 17 optimal weight: 0.2980 chunk 33 optimal weight: 5.9990 chunk 26 optimal weight: 0.9980 chunk 51 optimal weight: 3.9990 chunk 20 optimal weight: 0.7980 chunk 31 optimal weight: 9.9990 chunk 38 optimal weight: 3.9990 chunk 59 optimal weight: 0.5980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3981 r_free = 0.3981 target = 0.170247 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.143897 restraints weight = 10463.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.146682 restraints weight = 6392.062| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.148494 restraints weight = 4678.082| |-----------------------------------------------------------------------------| r_work (final): 0.3704 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7507 moved from start: 0.1733 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= 0.117 Angle : 0.570 7.868 10390 Z= 0.293 Chirality : 0.037 0.173 1230 Planarity : 0.005 0.038 954 Dihedral : 22.829 174.573 2182 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 1.50 % Allowed : 11.42 % Favored : 87.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.49 (0.34), residues: 590 helix: 0.25 (0.27), residues: 350 sheet: None (None), residues: 0 loop : 0.75 (0.42), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 220 HIS 0.002 0.001 HIS B 216 PHE 0.008 0.001 PHE B 199 TYR 0.011 0.002 TYR A 44 ARG 0.004 0.001 ARG A 98 Details of bonding type rmsd hydrogen bonds : bond 0.05095 ( 311) hydrogen bonds : angle 3.53151 ( 805) covalent geometry : bond 0.00247 ( 7326) covalent geometry : angle 0.57003 (10390) *********************** 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 103 residues out of total 534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 95 time to evaluate : 0.594 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 120 ASN cc_start: 0.7811 (OUTLIER) cc_final: 0.7342 (t0) REVERT: B 120 ASN cc_start: 0.7817 (OUTLIER) cc_final: 0.7358 (t0) outliers start: 8 outliers final: 5 residues processed: 102 average time/residue: 0.1739 time to fit residues: 23.9745 Evaluate side-chains 89 residues out of total 534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 82 time to evaluate : 0.601 ------------------------------------------------------------------------------- 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 284 ILE Chi-restraints excluded: chain B residue 18 VAL Chi-restraints excluded: chain B residue 120 ASN Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 284 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 38 optimal weight: 4.9990 chunk 62 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 51 optimal weight: 1.9990 chunk 35 optimal weight: 10.0000 chunk 16 optimal weight: 3.9990 chunk 57 optimal weight: 0.9990 chunk 40 optimal weight: 4.9990 chunk 27 optimal weight: 8.9990 chunk 29 optimal weight: 9.9990 chunk 58 optimal weight: 0.8980 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 151 GLN A 232 ASN B 151 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.164873 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.136837 restraints weight = 10176.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.139569 restraints weight = 6242.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.141308 restraints weight = 4591.034| |-----------------------------------------------------------------------------| r_work (final): 0.3610 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7622 moved from start: 0.2039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 7326 Z= 0.174 Angle : 0.601 7.639 10390 Z= 0.310 Chirality : 0.039 0.202 1230 Planarity : 0.006 0.054 954 Dihedral : 23.045 173.863 2182 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 2.81 % Allowed : 12.17 % Favored : 85.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.53 (0.34), residues: 590 helix: 0.41 (0.27), residues: 352 sheet: None (None), residues: 0 loop : 0.54 (0.41), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 299 HIS 0.002 0.001 HIS A 216 PHE 0.019 0.002 PHE B 289 TYR 0.010 0.001 TYR A 37 ARG 0.004 0.000 ARG B 36 Details of bonding type rmsd hydrogen bonds : bond 0.05981 ( 311) hydrogen bonds : angle 3.57455 ( 805) covalent geometry : bond 0.00399 ( 7326) covalent geometry : angle 0.60052 (10390) *********************** 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 89 residues out of total 534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 74 time to evaluate : 0.648 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 15 outliers final: 8 residues processed: 88 average time/residue: 0.1522 time to fit residues: 19.2122 Evaluate side-chains 75 residues out of total 534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 67 time to evaluate : 0.651 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 THR 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 181 THR Chi-restraints excluded: chain B residue 239 ILE 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 38 optimal weight: 8.9990 chunk 64 optimal weight: 9.9990 chunk 43 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 52 optimal weight: 3.9990 chunk 14 optimal weight: 10.0000 chunk 42 optimal weight: 0.9980 chunk 17 optimal weight: 10.0000 chunk 62 optimal weight: 10.0000 chunk 27 optimal weight: 6.9990 chunk 11 optimal weight: 3.9990 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 285 ASN B 285 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.161132 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.133593 restraints weight = 10209.612| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.136010 restraints weight = 6466.275| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.137706 restraints weight = 4864.226| |-----------------------------------------------------------------------------| r_work (final): 0.3568 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7681 moved from start: 0.2484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 7326 Z= 0.237 Angle : 0.661 7.040 10390 Z= 0.340 Chirality : 0.041 0.203 1230 Planarity : 0.006 0.057 954 Dihedral : 22.969 174.778 2178 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 3.56 % Allowed : 14.23 % Favored : 82.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.11 (0.33), residues: 590 helix: 0.26 (0.26), residues: 344 sheet: None (None), residues: 0 loop : 0.01 (0.41), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 299 HIS 0.003 0.001 HIS A 216 PHE 0.021 0.002 PHE B 289 TYR 0.010 0.002 TYR B 11 ARG 0.003 0.000 ARG A 36 Details of bonding type rmsd hydrogen bonds : bond 0.06806 ( 311) hydrogen bonds : angle 3.77233 ( 805) covalent geometry : bond 0.00551 ( 7326) covalent geometry : angle 0.66118 (10390) *********************** 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 84 residues out of total 534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 65 time to evaluate : 0.638 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 19 outliers final: 15 residues processed: 80 average time/residue: 0.1425 time to fit residues: 16.7728 Evaluate side-chains 79 residues out of total 534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 64 time to evaluate : 0.648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain A residue 90 ILE Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 181 THR Chi-restraints excluded: chain A residue 212 SER Chi-restraints excluded: chain A residue 219 VAL 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 90 ILE Chi-restraints excluded: chain B residue 109 ILE Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 219 VAL 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 8 optimal weight: 2.9990 chunk 2 optimal weight: 0.9990 chunk 3 optimal weight: 0.8980 chunk 47 optimal weight: 2.9990 chunk 5 optimal weight: 4.9990 chunk 42 optimal weight: 0.7980 chunk 14 optimal weight: 8.9990 chunk 31 optimal weight: 9.9990 chunk 10 optimal weight: 3.9990 chunk 19 optimal weight: 0.8980 chunk 28 optimal weight: 6.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.166718 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.139243 restraints weight = 10055.087| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.141985 restraints weight = 6184.946| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.143798 restraints weight = 4550.653| |-----------------------------------------------------------------------------| r_work (final): 0.3649 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7584 moved from start: 0.2647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 7326 Z= 0.118 Angle : 0.537 8.006 10390 Z= 0.267 Chirality : 0.035 0.190 1230 Planarity : 0.005 0.054 954 Dihedral : 22.765 177.593 2178 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 1.12 % Allowed : 16.48 % Favored : 82.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.64 (0.35), residues: 590 helix: 0.74 (0.28), residues: 346 sheet: None (None), residues: 0 loop : 0.14 (0.42), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 299 HIS 0.002 0.001 HIS A 216 PHE 0.010 0.001 PHE A 289 TYR 0.008 0.001 TYR A 249 ARG 0.003 0.000 ARG B 36 Details of bonding type rmsd hydrogen bonds : bond 0.04713 ( 311) hydrogen bonds : angle 3.34317 ( 805) covalent geometry : bond 0.00260 ( 7326) covalent geometry : angle 0.53653 (10390) *********************** 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 75 residues out of total 534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 69 time to evaluate : 0.596 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 4 residues processed: 74 average time/residue: 0.1515 time to fit residues: 16.2013 Evaluate side-chains 68 residues out of total 534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 64 time to evaluate : 0.656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 284 ILE Chi-restraints excluded: chain B residue 18 VAL Chi-restraints excluded: chain B residue 239 ILE 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 18 optimal weight: 5.9990 chunk 40 optimal weight: 5.9990 chunk 36 optimal weight: 0.9980 chunk 64 optimal weight: 10.0000 chunk 15 optimal weight: 4.9990 chunk 60 optimal weight: 5.9990 chunk 45 optimal weight: 4.9990 chunk 59 optimal weight: 4.9990 chunk 46 optimal weight: 8.9990 chunk 34 optimal weight: 0.9990 chunk 54 optimal weight: 0.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.159698 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.131982 restraints weight = 10271.074| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.134698 restraints weight = 6263.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.136418 restraints weight = 4581.676| |-----------------------------------------------------------------------------| r_work (final): 0.3581 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7639 moved from start: 0.2741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 7326 Z= 0.175 Angle : 0.578 7.530 10390 Z= 0.294 Chirality : 0.038 0.199 1230 Planarity : 0.006 0.057 954 Dihedral : 22.642 178.129 2178 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 2.25 % Allowed : 16.10 % Favored : 81.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.44 (0.34), residues: 590 helix: 0.65 (0.27), residues: 346 sheet: None (None), residues: 0 loop : -0.05 (0.42), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 220 HIS 0.002 0.001 HIS A 216 PHE 0.016 0.002 PHE A 289 TYR 0.008 0.001 TYR B 11 ARG 0.003 0.000 ARG A 36 Details of bonding type rmsd hydrogen bonds : bond 0.05789 ( 311) hydrogen bonds : angle 3.47859 ( 805) covalent geometry : bond 0.00406 ( 7326) covalent geometry : angle 0.57833 (10390) *********************** 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 73 residues out of total 534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 61 time to evaluate : 0.652 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 9 residues processed: 71 average time/residue: 0.1489 time to fit residues: 15.4262 Evaluate side-chains 69 residues out of total 534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 60 time to evaluate : 0.649 ------------------------------------------------------------------------------- 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 219 VAL Chi-restraints excluded: chain B residue 239 ILE 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 35 optimal weight: 9.9990 chunk 23 optimal weight: 5.9990 chunk 29 optimal weight: 10.0000 chunk 7 optimal weight: 1.9990 chunk 64 optimal weight: 10.0000 chunk 51 optimal weight: 0.8980 chunk 4 optimal weight: 4.9990 chunk 44 optimal weight: 7.9990 chunk 40 optimal weight: 3.9990 chunk 62 optimal weight: 10.0000 chunk 25 optimal weight: 0.4980 overall best weight: 2.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.159730 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.132045 restraints weight = 10274.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.134737 restraints weight = 6256.482| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.136471 restraints weight = 4597.432| |-----------------------------------------------------------------------------| r_work (final): 0.3581 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7637 moved from start: 0.2778 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= 0.168 Angle : 0.572 7.508 10390 Z= 0.290 Chirality : 0.037 0.196 1230 Planarity : 0.006 0.058 954 Dihedral : 22.627 178.046 2178 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 2.43 % Allowed : 15.92 % Favored : 81.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.48 (0.35), residues: 590 helix: 0.67 (0.27), residues: 346 sheet: None (None), residues: 0 loop : -0.02 (0.42), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 299 HIS 0.002 0.001 HIS A 216 PHE 0.016 0.002 PHE B 289 TYR 0.007 0.001 TYR B 11 ARG 0.003 0.000 ARG A 36 Details of bonding type rmsd hydrogen bonds : bond 0.05661 ( 311) hydrogen bonds : angle 3.45139 ( 805) covalent geometry : bond 0.00389 ( 7326) covalent geometry : angle 0.57161 (10390) *********************** 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 75 residues out of total 534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 62 time to evaluate : 0.650 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 276 LEU cc_start: 0.7887 (OUTLIER) cc_final: 0.7395 (mp) outliers start: 13 outliers final: 10 residues processed: 72 average time/residue: 0.1595 time to fit residues: 16.3147 Evaluate side-chains 72 residues out of total 534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 61 time to evaluate : 0.603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 239 ILE 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 219 VAL Chi-restraints excluded: chain B residue 239 ILE 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 52 optimal weight: 0.9990 chunk 49 optimal weight: 2.9990 chunk 3 optimal weight: 1.9990 chunk 8 optimal weight: 2.9990 chunk 30 optimal weight: 10.0000 chunk 56 optimal weight: 0.9990 chunk 17 optimal weight: 4.9990 chunk 39 optimal weight: 2.9990 chunk 35 optimal weight: 6.9990 chunk 25 optimal weight: 0.7980 chunk 15 optimal weight: 4.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.161900 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.134549 restraints weight = 10267.505| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.137212 restraints weight = 6279.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.139031 restraints weight = 4606.675| |-----------------------------------------------------------------------------| r_work (final): 0.3613 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7595 moved from start: 0.2943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 7326 Z= 0.127 Angle : 0.528 7.664 10390 Z= 0.265 Chirality : 0.035 0.194 1230 Planarity : 0.005 0.058 954 Dihedral : 22.515 178.810 2178 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 1.50 % Allowed : 17.23 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.74 (0.35), residues: 590 helix: 0.93 (0.28), residues: 346 sheet: None (None), residues: 0 loop : 0.01 (0.43), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 220 HIS 0.002 0.001 HIS B 216 PHE 0.011 0.001 PHE B 289 TYR 0.006 0.001 TYR B 249 ARG 0.002 0.000 ARG B 36 Details of bonding type rmsd hydrogen bonds : bond 0.04877 ( 311) hydrogen bonds : angle 3.31617 ( 805) covalent geometry : bond 0.00288 ( 7326) covalent geometry : angle 0.52762 (10390) *********************** 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 75 residues out of total 534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 67 time to evaluate : 0.628 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 6 residues processed: 74 average time/residue: 0.1511 time to fit residues: 16.2037 Evaluate side-chains 70 residues out of total 534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 64 time to evaluate : 0.682 ------------------------------------------------------------------------------- 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 239 ILE 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 5 optimal weight: 10.0000 chunk 27 optimal weight: 5.9990 chunk 44 optimal weight: 6.9990 chunk 45 optimal weight: 2.9990 chunk 18 optimal weight: 4.9990 chunk 23 optimal weight: 0.9980 chunk 19 optimal weight: 0.9990 chunk 12 optimal weight: 4.9990 chunk 47 optimal weight: 4.9990 chunk 37 optimal weight: 0.9990 chunk 46 optimal weight: 5.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.160478 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.132877 restraints weight = 10341.065| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.135592 restraints weight = 6274.877| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.137394 restraints weight = 4592.534| |-----------------------------------------------------------------------------| r_work (final): 0.3593 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7625 moved from start: 0.2989 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= 0.156 Angle : 0.555 7.662 10390 Z= 0.280 Chirality : 0.037 0.196 1230 Planarity : 0.006 0.061 954 Dihedral : 22.490 178.962 2178 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 1.87 % Allowed : 17.42 % Favored : 80.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.35), residues: 590 helix: 0.81 (0.27), residues: 346 sheet: None (None), residues: 0 loop : -0.02 (0.43), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 299 HIS 0.002 0.001 HIS B 216 PHE 0.014 0.001 PHE B 289 TYR 0.007 0.001 TYR B 11 ARG 0.003 0.000 ARG B 36 Details of bonding type rmsd hydrogen bonds : bond 0.05459 ( 311) hydrogen bonds : angle 3.39804 ( 805) covalent geometry : bond 0.00362 ( 7326) covalent geometry : angle 0.55487 (10390) *********************** 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 73 residues out of total 534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 63 time to evaluate : 0.682 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 276 LEU cc_start: 0.7847 (OUTLIER) cc_final: 0.7322 (mp) outliers start: 10 outliers final: 8 residues processed: 71 average time/residue: 0.1685 time to fit residues: 17.0220 Evaluate side-chains 72 residues out of total 534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 63 time to evaluate : 0.679 ------------------------------------------------------------------------------- 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 219 VAL Chi-restraints excluded: chain B residue 239 ILE Chi-restraints excluded: chain B residue 276 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 22 optimal weight: 0.9980 chunk 23 optimal weight: 0.0040 chunk 2 optimal weight: 3.9990 chunk 65 optimal weight: 10.0000 chunk 55 optimal weight: 0.4980 chunk 43 optimal weight: 4.9990 chunk 38 optimal weight: 10.0000 chunk 50 optimal weight: 8.9990 chunk 41 optimal weight: 0.9990 chunk 25 optimal weight: 1.9990 chunk 62 optimal weight: 8.9990 overall best weight: 0.8996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.165048 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.137468 restraints weight = 10583.427| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.140284 restraints weight = 6374.588| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.142143 restraints weight = 4627.361| |-----------------------------------------------------------------------------| r_work (final): 0.3648 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7546 moved from start: 0.3202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 7326 Z= 0.106 Angle : 0.499 7.776 10390 Z= 0.249 Chirality : 0.034 0.190 1230 Planarity : 0.005 0.060 954 Dihedral : 22.352 179.622 2178 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 1.87 % Allowed : 17.60 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.97 (0.35), residues: 590 helix: 1.11 (0.28), residues: 346 sheet: None (None), residues: 0 loop : 0.11 (0.42), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 114 HIS 0.001 0.000 HIS A 148 PHE 0.009 0.001 PHE B 289 TYR 0.006 0.001 TYR B 249 ARG 0.003 0.000 ARG B 36 Details of bonding type rmsd hydrogen bonds : bond 0.04265 ( 311) hydrogen bonds : angle 3.20774 ( 805) covalent geometry : bond 0.00237 ( 7326) covalent geometry : angle 0.49918 (10390) ********************** 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 82 residues out of total 534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 72 time to evaluate : 0.642 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 7 residues processed: 82 average time/residue: 0.1568 time to fit residues: 18.2180 Evaluate side-chains 70 residues out of total 534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 63 time to evaluate : 0.640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 181 THR Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 284 ILE Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 208 LEU Chi-restraints excluded: chain B residue 239 ILE 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 11 optimal weight: 4.9990 chunk 40 optimal weight: 4.9990 chunk 45 optimal weight: 4.9990 chunk 64 optimal weight: 10.0000 chunk 27 optimal weight: 0.8980 chunk 25 optimal weight: 0.9980 chunk 3 optimal weight: 5.9990 chunk 63 optimal weight: 10.0000 chunk 2 optimal weight: 7.9990 chunk 55 optimal weight: 4.9990 chunk 17 optimal weight: 0.3980 overall best weight: 2.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.160660 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.132758 restraints weight = 10270.896| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.135428 restraints weight = 6306.522| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.137173 restraints weight = 4648.571| |-----------------------------------------------------------------------------| r_work (final): 0.3590 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7628 moved from start: 0.3139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 7326 Z= 0.169 Angle : 0.577 7.701 10390 Z= 0.291 Chirality : 0.037 0.197 1230 Planarity : 0.006 0.061 954 Dihedral : 22.397 179.455 2178 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 1.50 % Allowed : 18.54 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.68 (0.35), residues: 590 helix: 0.92 (0.27), residues: 348 sheet: None (None), residues: 0 loop : -0.10 (0.42), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 220 HIS 0.003 0.001 HIS A 15 PHE 0.014 0.002 PHE B 289 TYR 0.006 0.001 TYR B 11 ARG 0.002 0.000 ARG B 36 Details of bonding type rmsd hydrogen bonds : bond 0.05604 ( 311) hydrogen bonds : angle 3.41106 ( 805) covalent geometry : bond 0.00399 ( 7326) covalent geometry : angle 0.57742 (10390) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1951.78 seconds wall clock time: 35 minutes 5.68 seconds (2105.68 seconds total)