Starting phenix.real_space_refine on Mon Apr 28 02:00:12 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vz6_43682/04_2025/8vz6_43682.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vz6_43682/04_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_43682/04_2025/8vz6_43682.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vz6_43682/04_2025/8vz6_43682.map" model { file = "/net/cci-nas-00/data/ceres_data/8vz6_43682/04_2025/8vz6_43682.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vz6_43682/04_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-5669/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: 4.76, per 1000 atoms: 0.68 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: 1.65 Conformation dependent library (CDL) restraints added in 732.6 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: 2.43 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: 1.92 Time building geometry restraints manager: 1.99 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: 1.000 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: 0.250 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 20.940 Find NCS groups from input model: 0.110 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:2.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.390 ------------------------------------------------------------------------------- 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 : 0.619 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: 0.2000 time to fit residues: 26.1177 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 : 0.625 ------------------------------------------------------------------------------- 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 = 39)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.143883 restraints weight = 10463.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.146679 restraints weight = 6378.763| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.148500 restraints weight = 4678.192| |-----------------------------------------------------------------------------| 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 : 0.574 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: 0.7818 (OUTLIER) cc_final: 0.7359 (t0) outliers start: 8 outliers final: 5 residues processed: 102 average time/residue: 0.1739 time to fit residues: 24.0744 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 : 0.572 ------------------------------------------------------------------------------- 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: 0.9980 chunk 35 optimal weight: 9.9990 chunk 16 optimal weight: 3.9990 chunk 57 optimal weight: 0.9980 chunk 40 optimal weight: 4.9990 chunk 27 optimal weight: 8.9990 chunk 29 optimal weight: 9.9990 chunk 58 optimal weight: 0.9980 overall best weight: 2.3984 ------------------------------------------------------------------------------- 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 B 285 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.164942 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.136844 restraints weight = 10165.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.139539 restraints weight = 6229.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.141238 restraints weight = 4597.060| |-----------------------------------------------------------------------------| r_work (final): 0.3614 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7621 moved from start: 0.2092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 7326 Z= 0.168 Angle : 0.595 7.560 10390 Z= 0.307 Chirality : 0.039 0.203 1230 Planarity : 0.006 0.053 954 Dihedral : 23.046 173.877 2182 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 2.81 % Allowed : 11.99 % Favored : 85.21 % 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: 0.56 (0.34), residues: 590 helix: 0.43 (0.28), residues: 352 sheet: None (None), residues: 0 loop : 0.55 (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 A 36 Details of bonding type rmsd hydrogen bonds : bond 0.05914 ( 311) hydrogen bonds : angle 3.54916 ( 805) covalent geometry : bond 0.00383 ( 7326) covalent geometry : angle 0.59482 (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 : 0.572 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 15 outliers final: 7 residues processed: 88 average time/residue: 0.1405 time to fit residues: 17.9028 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 : 0.569 ------------------------------------------------------------------------------- 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 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: 10.0000 chunk 43 optimal weight: 0.3980 chunk 0 optimal weight: 10.0000 chunk 52 optimal weight: 0.9980 chunk 14 optimal weight: 9.9990 chunk 42 optimal weight: 1.9990 chunk 17 optimal weight: 9.9990 chunk 62 optimal weight: 10.0000 chunk 27 optimal weight: 6.9990 chunk 11 optimal weight: 5.9990 overall best weight: 3.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 285 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.162306 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.134632 restraints weight = 10212.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.137101 restraints weight = 6530.842| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.138723 restraints weight = 4939.982| |-----------------------------------------------------------------------------| r_work (final): 0.3580 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7667 moved from start: 0.2503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 7326 Z= 0.209 Angle : 0.630 7.189 10390 Z= 0.324 Chirality : 0.040 0.196 1230 Planarity : 0.006 0.055 954 Dihedral : 22.924 175.537 2178 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 3.18 % Allowed : 14.61 % 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: 0.23 (0.34), residues: 590 helix: 0.34 (0.27), residues: 344 sheet: None (None), residues: 0 loop : 0.10 (0.41), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 299 HIS 0.003 0.001 HIS A 216 PHE 0.020 0.002 PHE A 289 TYR 0.010 0.002 TYR B 37 ARG 0.004 0.000 ARG A 36 Details of bonding type rmsd hydrogen bonds : bond 0.06435 ( 311) hydrogen bonds : angle 3.68297 ( 805) covalent geometry : bond 0.00484 ( 7326) covalent geometry : angle 0.63032 (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 79 residues out of total 534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 62 time to evaluate : 0.610 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 17 outliers final: 13 residues processed: 77 average time/residue: 0.1381 time to fit residues: 15.7087 Evaluate side-chains 73 residues out of total 534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 60 time to evaluate : 0.580 ------------------------------------------------------------------------------- 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 209 THR Chi-restraints excluded: chain A residue 212 SER 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 209 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: 1.9990 chunk 2 optimal weight: 0.9990 chunk 3 optimal weight: 0.6980 chunk 47 optimal weight: 2.9990 chunk 5 optimal weight: 7.9990 chunk 42 optimal weight: 0.5980 chunk 14 optimal weight: 8.9990 chunk 31 optimal weight: 10.0000 chunk 10 optimal weight: 6.9990 chunk 19 optimal weight: 2.9990 chunk 28 optimal weight: 3.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- 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 = 0.3920 r_free = 0.3920 target = 0.166401 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.138556 restraints weight = 10139.178| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.141296 restraints weight = 6284.538| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.143057 restraints weight = 4639.400| |-----------------------------------------------------------------------------| r_work (final): 0.3638 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7591 moved from start: 0.2684 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= 0.126 Angle : 0.534 7.657 10390 Z= 0.268 Chirality : 0.036 0.192 1230 Planarity : 0.005 0.055 954 Dihedral : 22.735 177.767 2178 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 1.12 % Allowed : 16.29 % Favored : 82.58 % 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: 0.76 (0.28), residues: 346 sheet: None (None), residues: 0 loop : 0.19 (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 B 289 TYR 0.008 0.001 TYR B 249 ARG 0.003 0.000 ARG B 36 Details of bonding type rmsd hydrogen bonds : bond 0.04778 ( 311) hydrogen bonds : angle 3.34232 ( 805) covalent geometry : bond 0.00284 ( 7326) covalent geometry : angle 0.53392 (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 76 residues out of total 534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 70 time to evaluate : 0.565 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 4 residues processed: 74 average time/residue: 0.1423 time to fit residues: 15.3532 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 : 0.565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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: 3.9990 chunk 64 optimal weight: 10.9990 chunk 15 optimal weight: 3.9990 chunk 60 optimal weight: 7.9990 chunk 45 optimal weight: 5.9990 chunk 59 optimal weight: 1.9990 chunk 46 optimal weight: 9.9990 chunk 34 optimal weight: 1.9990 chunk 54 optimal weight: 6.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- 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 = 0.3841 r_free = 0.3841 target = 0.157112 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.129553 restraints weight = 10238.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.132151 restraints weight = 6248.795| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.133882 restraints weight = 4586.479| |-----------------------------------------------------------------------------| r_work (final): 0.3554 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7672 moved from start: 0.2763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 7326 Z= 0.226 Angle : 0.632 7.358 10390 Z= 0.322 Chirality : 0.040 0.204 1230 Planarity : 0.006 0.058 954 Dihedral : 22.683 177.524 2178 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 3.37 % Allowed : 15.36 % 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: 0.25 (0.34), residues: 590 helix: 0.47 (0.27), residues: 346 sheet: None (None), residues: 0 loop : -0.10 (0.42), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP B 220 HIS 0.003 0.001 HIS A 148 PHE 0.019 0.002 PHE A 289 TYR 0.008 0.002 TYR B 11 ARG 0.002 0.000 ARG A 36 Details of bonding type rmsd hydrogen bonds : bond 0.06481 ( 311) hydrogen bonds : angle 3.64314 ( 805) covalent geometry : bond 0.00529 ( 7326) covalent geometry : angle 0.63225 (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 79 residues out of total 534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 61 time to evaluate : 0.671 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 276 LEU cc_start: 0.7926 (OUTLIER) cc_final: 0.7403 (mp) outliers start: 18 outliers final: 12 residues processed: 76 average time/residue: 0.1518 time to fit residues: 17.0615 Evaluate side-chains 73 residues out of total 534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 60 time to evaluate : 0.583 ------------------------------------------------------------------------------- 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 212 SER Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 276 LEU 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 212 SER Chi-restraints excluded: chain B residue 219 VAL 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: 3.9990 chunk 29 optimal weight: 10.0000 chunk 7 optimal weight: 0.9980 chunk 64 optimal weight: 9.9990 chunk 51 optimal weight: 0.0060 chunk 4 optimal weight: 3.9990 chunk 44 optimal weight: 7.9990 chunk 40 optimal weight: 0.9990 chunk 62 optimal weight: 10.0000 chunk 25 optimal weight: 0.9980 overall best weight: 1.4000 ------------------------------------------------------------------------------- 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 = 0.3901 r_free = 0.3901 target = 0.162334 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.134850 restraints weight = 10262.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.137600 restraints weight = 6204.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.139432 restraints weight = 4531.495| |-----------------------------------------------------------------------------| r_work (final): 0.3615 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7591 moved from start: 0.2897 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= 0.122 Angle : 0.531 7.607 10390 Z= 0.266 Chirality : 0.035 0.191 1230 Planarity : 0.005 0.057 954 Dihedral : 22.560 178.273 2178 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 2.06 % Allowed : 16.67 % 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: 0.73 (0.35), residues: 590 helix: 0.89 (0.28), residues: 346 sheet: None (None), residues: 0 loop : 0.05 (0.42), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 114 HIS 0.002 0.001 HIS B 216 PHE 0.011 0.001 PHE A 289 TYR 0.007 0.001 TYR A 249 ARG 0.003 0.000 ARG A 36 Details of bonding type rmsd hydrogen bonds : bond 0.04829 ( 311) hydrogen bonds : angle 3.33369 ( 805) covalent geometry : bond 0.00275 ( 7326) covalent geometry : angle 0.53079 (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 76 residues out of total 534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 65 time to evaluate : 0.668 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 7 residues processed: 74 average time/residue: 0.1674 time to fit residues: 17.5537 Evaluate side-chains 69 residues out of total 534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 62 time to evaluate : 0.658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 208 LEU 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 208 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: 2.9990 chunk 49 optimal weight: 0.4980 chunk 3 optimal weight: 0.9990 chunk 8 optimal weight: 1.9990 chunk 30 optimal weight: 10.0000 chunk 56 optimal weight: 0.0270 chunk 17 optimal weight: 0.8980 chunk 39 optimal weight: 0.7980 chunk 35 optimal weight: 6.9990 chunk 25 optimal weight: 0.9990 chunk 15 optimal weight: 4.9990 overall best weight: 0.6440 ------------------------------------------------------------------------------- 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 = 0.3964 r_free = 0.3964 target = 0.168001 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.140821 restraints weight = 10461.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.143650 restraints weight = 6333.832| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.145505 restraints weight = 4608.850| |-----------------------------------------------------------------------------| r_work (final): 0.3679 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7500 moved from start: 0.3344 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= 0.098 Angle : 0.487 7.908 10390 Z= 0.242 Chirality : 0.033 0.190 1230 Planarity : 0.005 0.055 954 Dihedral : 22.283 179.080 2178 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % 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 (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: 1.10 (0.28), residues: 352 sheet: None (None), residues: 0 loop : 0.09 (0.42), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 114 HIS 0.002 0.000 HIS A 216 PHE 0.007 0.001 PHE B 289 TYR 0.008 0.001 TYR B 51 ARG 0.003 0.000 ARG B 36 Details of bonding type rmsd hydrogen bonds : bond 0.03909 ( 311) hydrogen bonds : angle 3.15664 ( 805) covalent geometry : bond 0.00218 ( 7326) covalent geometry : angle 0.48729 (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 88 residues out of total 534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 78 time to evaluate : 0.608 Fit side-chains REVERT: A 91 GLU cc_start: 0.8233 (tt0) cc_final: 0.8014 (tt0) outliers start: 10 outliers final: 5 residues processed: 88 average time/residue: 0.1441 time to fit residues: 18.5647 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 : 0.632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 212 SER Chi-restraints excluded: chain A residue 284 ILE Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 212 SER 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: 9.9990 chunk 27 optimal weight: 0.8980 chunk 44 optimal weight: 7.9990 chunk 45 optimal weight: 5.9990 chunk 18 optimal weight: 0.9980 chunk 23 optimal weight: 4.9990 chunk 19 optimal weight: 0.7980 chunk 12 optimal weight: 6.9990 chunk 47 optimal weight: 2.9990 chunk 37 optimal weight: 3.9990 chunk 46 optimal weight: 7.9990 overall best weight: 1.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 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 = 0.3907 r_free = 0.3907 target = 0.162801 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.134800 restraints weight = 10347.536| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.137631 restraints weight = 6248.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.139489 restraints weight = 4529.608| |-----------------------------------------------------------------------------| r_work (final): 0.3614 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7584 moved from start: 0.3216 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= 0.149 Angle : 0.557 7.809 10390 Z= 0.281 Chirality : 0.036 0.195 1230 Planarity : 0.005 0.059 954 Dihedral : 22.313 179.290 2178 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % 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: 0.88 (0.35), residues: 590 helix: 1.08 (0.28), residues: 348 sheet: None (None), residues: 0 loop : 0.00 (0.41), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 220 HIS 0.002 0.001 HIS B 216 PHE 0.013 0.001 PHE B 289 TYR 0.006 0.001 TYR B 51 ARG 0.003 0.000 ARG A 36 Details of bonding type rmsd hydrogen bonds : bond 0.05109 ( 311) hydrogen bonds : angle 3.32524 ( 805) covalent geometry : bond 0.00351 ( 7326) covalent geometry : angle 0.55738 (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 75 residues out of total 534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 65 time to evaluate : 0.635 Fit side-chains outliers start: 10 outliers final: 8 residues processed: 74 average time/residue: 0.1532 time to fit residues: 16.6361 Evaluate side-chains 72 residues out of total 534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 64 time to evaluate : 0.634 ------------------------------------------------------------------------------- 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 239 ILE 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 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 22 optimal weight: 5.9990 chunk 23 optimal weight: 6.9990 chunk 2 optimal weight: 0.0670 chunk 65 optimal weight: 10.0000 chunk 55 optimal weight: 5.9990 chunk 43 optimal weight: 9.9990 chunk 38 optimal weight: 9.9990 chunk 50 optimal weight: 3.9990 chunk 41 optimal weight: 8.9990 chunk 25 optimal weight: 0.9990 chunk 62 optimal weight: 6.9990 overall best weight: 3.4126 ------------------------------------------------------------------------------- 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 = 0.3846 r_free = 0.3846 target = 0.157688 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.130102 restraints weight = 10489.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.132792 restraints weight = 6377.618| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.134574 restraints weight = 4653.412| |-----------------------------------------------------------------------------| r_work (final): 0.3557 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7663 moved from start: 0.3106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 7326 Z= 0.218 Angle : 0.634 7.583 10390 Z= 0.323 Chirality : 0.040 0.201 1230 Planarity : 0.006 0.065 954 Dihedral : 22.487 178.755 2178 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 1.50 % Allowed : 18.35 % 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 (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: 0.36 (0.34), residues: 590 helix: 0.67 (0.27), residues: 348 sheet: None (None), residues: 0 loop : -0.25 (0.41), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 220 HIS 0.003 0.001 HIS B 216 PHE 0.018 0.002 PHE A 289 TYR 0.008 0.002 TYR B 11 ARG 0.002 0.000 ARG B 77 Details of bonding type rmsd hydrogen bonds : bond 0.06241 ( 311) hydrogen bonds : angle 3.56603 ( 805) covalent geometry : bond 0.00517 ( 7326) covalent geometry : angle 0.63437 (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 69 residues out of total 534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 61 time to evaluate : 0.566 Fit side-chains outliers start: 8 outliers final: 8 residues processed: 69 average time/residue: 0.1457 time to fit residues: 14.6524 Evaluate side-chains 68 residues out of total 534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 60 time to evaluate : 0.634 ------------------------------------------------------------------------------- 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 239 ILE 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 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: 5.9990 chunk 40 optimal weight: 0.8980 chunk 45 optimal weight: 2.9990 chunk 64 optimal weight: 10.0000 chunk 27 optimal weight: 4.9990 chunk 25 optimal weight: 0.8980 chunk 3 optimal weight: 4.9990 chunk 63 optimal weight: 10.0000 chunk 2 optimal weight: 7.9990 chunk 55 optimal weight: 0.9990 chunk 17 optimal weight: 1.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- 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 = 0.3893 r_free = 0.3893 target = 0.161709 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.134174 restraints weight = 10302.080| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.137032 restraints weight = 6138.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.138889 restraints weight = 4424.593| |-----------------------------------------------------------------------------| r_work (final): 0.3610 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7586 moved from start: 0.3168 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= 0.132 Angle : 0.555 7.502 10390 Z= 0.277 Chirality : 0.036 0.189 1230 Planarity : 0.005 0.064 954 Dihedral : 22.393 177.919 2178 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 1.31 % Allowed : 19.10 % Favored : 79.59 % 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: 0.81 (0.35), residues: 590 helix: 0.96 (0.27), residues: 346 sheet: None (None), residues: 0 loop : 0.08 (0.42), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 220 HIS 0.002 0.001 HIS B 216 PHE 0.011 0.001 PHE B 289 TYR 0.006 0.001 TYR B 11 ARG 0.002 0.000 ARG A 36 Details of bonding type rmsd hydrogen bonds : bond 0.04871 ( 311) hydrogen bonds : angle 3.32302 ( 805) covalent geometry : bond 0.00308 ( 7326) covalent geometry : angle 0.55485 (10390) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2017.55 seconds wall clock time: 35 minutes 46.90 seconds (2146.90 seconds total)