Starting phenix.real_space_refine on Thu Jul 24 23:08:38 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8cth_26990/07_2025/8cth_26990.cif Found real_map, /net/cci-nas-00/data/ceres_data/8cth_26990/07_2025/8cth_26990.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8cth_26990/07_2025/8cth_26990.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8cth_26990/07_2025/8cth_26990.map" model { file = "/net/cci-nas-00/data/ceres_data/8cth_26990/07_2025/8cth_26990.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8cth_26990/07_2025/8cth_26990.cif" } resolution = 3.3 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= 0.077 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 74 5.49 5 S 22 5.16 5 C 3250 2.51 5 N 969 2.21 5 O 1229 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 5544 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 1750 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1750 Classifications: {'peptide': 216} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 16, 'TRANS': 199} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "B" Number of atoms: 2175 Number of conformers: 1 Conformer: "" Number of residues, atoms: 278, 2175 Classifications: {'peptide': 278} Link IDs: {'PTRANS': 8, 'TRANS': 269} Chain breaks: 3 Chain: "C" Number of atoms: 1593 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 1593 Classifications: {'RNA': 74} Modifications used: {'p5*END': 1, 'rna2p': 2, 'rna2p_pur': 3, 'rna2p_pyr': 4, 'rna3p': 10, 'rna3p_pur': 32, 'rna3p_pyr': 23} Link IDs: {'rna2p': 9, 'rna3p': 64} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 5 Chain: "A" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 26 Classifications: {'peptide': 1} Time building chain proxies: 4.81, per 1000 atoms: 0.87 Number of scatterers: 5544 At special positions: 0 Unit cell: (81, 100.44, 118.8, 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 22 16.00 P 74 15.00 O 1229 8.00 N 969 7.00 C 3250 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: 1.74 Conformation dependent library (CDL) restraints added in 441.3 milliseconds 964 Ramachandran restraints generated. 482 Oldfield, 0 Emsley, 482 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 926 Finding SS restraints... Secondary structure from input PDB file: 10 helices and 9 sheets defined 18.4% alpha, 31.2% beta 20 base pairs and 39 stacking pairs defined. Time for finding SS restraints: 2.40 Creating SS restraints... Processing helix chain 'A' and resid 40 through 44 Processing helix chain 'A' and resid 45 through 49 removed outlier: 3.500A pdb=" N GLU A 48 " --> pdb=" O ASP A 45 " (cutoff:3.500A) Processing helix chain 'A' and resid 88 through 95 removed outlier: 3.866A pdb=" N VAL A 92 " --> pdb=" O GLY A 88 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N GLU A 93 " --> pdb=" O GLY A 89 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 125 Processing helix chain 'A' and resid 144 through 149 removed outlier: 3.539A pdb=" N PHE A 148 " --> pdb=" O HIS A 144 " (cutoff:3.500A) Processing helix chain 'A' and resid 168 through 174 removed outlier: 3.904A pdb=" N LYS A 172 " --> pdb=" O THR A 169 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ARG A 174 " --> pdb=" O HIS A 171 " (cutoff:3.500A) Processing helix chain 'A' and resid 177 through 187 Processing helix chain 'A' and resid 200 through 214 removed outlier: 3.599A pdb=" N HIS A 210 " --> pdb=" O TRP A 206 " (cutoff:3.500A) Processing helix chain 'A' and resid 229 through 234 removed outlier: 3.514A pdb=" N GLY A 232 " --> pdb=" O PRO A 229 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N LEU A 234 " --> pdb=" O VAL A 231 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 248 Processing sheet with id=AA1, first strand: chain 'A' and resid 134 through 137 removed outlier: 6.525A pdb=" N ILE A 103 " --> pdb=" O ALA A 135 " (cutoff:3.500A) removed outlier: 7.732A pdb=" N LEU A 137 " --> pdb=" O ILE A 103 " (cutoff:3.500A) removed outlier: 5.997A pdb=" N GLY A 105 " --> pdb=" O LEU A 137 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N LEU A 102 " --> pdb=" O VAL A 78 " (cutoff:3.500A) removed outlier: 8.453A pdb=" N GLU A 79 " --> pdb=" O THR A 155 " (cutoff:3.500A) removed outlier: 5.683A pdb=" N MET A 157 " --> pdb=" O GLU A 79 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N ALA A 81 " --> pdb=" O MET A 157 " (cutoff:3.500A) removed outlier: 5.997A pdb=" N PHE A 159 " --> pdb=" O ALA A 81 " (cutoff:3.500A) removed outlier: 7.437A pdb=" N ILE A 83 " --> pdb=" O PHE A 159 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N THR A 155 " --> pdb=" O LEU A 193 " (cutoff:3.500A) removed outlier: 7.758A pdb=" N TYR A 195 " --> pdb=" O THR A 155 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N MET A 157 " --> pdb=" O TYR A 195 " (cutoff:3.500A) removed outlier: 8.065A pdb=" N ILE A 197 " --> pdb=" O MET A 157 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N PHE A 159 " --> pdb=" O ILE A 197 " (cutoff:3.500A) removed outlier: 4.992A pdb=" N ARG A 258 " --> pdb=" O GLY A 191 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N LEU A 193 " --> pdb=" O PHE A 256 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N PHE A 256 " --> pdb=" O LEU A 193 " (cutoff:3.500A) removed outlier: 4.682A pdb=" N TYR A 195 " --> pdb=" O ALA A 254 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N ALA A 254 " --> pdb=" O TYR A 195 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N ILE A 197 " --> pdb=" O PHE A 252 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N PHE A 252 " --> pdb=" O ILE A 197 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 7 through 10 Processing sheet with id=AA3, first strand: chain 'B' and resid 7 through 10 removed outlier: 3.673A pdb=" N PHE B 22 " --> pdb=" O TYR B 38 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N TYR B 38 " --> pdb=" O PHE B 22 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 66 through 69 removed outlier: 4.133A pdb=" N ALA B 66 " --> pdb=" O THR B 79 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N PHE B 76 " --> pdb=" O PHE B 88 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N SER B 97 " --> pdb=" O LEU B 87 " (cutoff:3.500A) removed outlier: 5.997A pdb=" N ARG B 89 " --> pdb=" O CYS B 95 " (cutoff:3.500A) removed outlier: 5.958A pdb=" N CYS B 95 " --> pdb=" O ARG B 89 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 107 through 110 removed outlier: 3.975A pdb=" N ALA B 107 " --> pdb=" O ALA B 120 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N THR B 109 " --> pdb=" O LEU B 118 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N VAL B 126 " --> pdb=" O GLU B 141 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 148 through 153 removed outlier: 6.588A pdb=" N ALA B 163 " --> pdb=" O LEU B 149 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N VAL B 151 " --> pdb=" O LEU B 161 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N LEU B 161 " --> pdb=" O VAL B 151 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N VAL B 153 " --> pdb=" O PHE B 159 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N PHE B 159 " --> pdb=" O VAL B 153 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N LYS B 168 " --> pdb=" O ASP B 164 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N ILE B 169 " --> pdb=" O PHE B 183 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N PHE B 183 " --> pdb=" O ILE B 169 " (cutoff:3.500A) removed outlier: 7.172A pdb=" N VAL B 171 " --> pdb=" O GLU B 181 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 191 through 196 removed outlier: 3.897A pdb=" N SER B 206 " --> pdb=" O ARG B 214 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N LEU B 215 " --> pdb=" O LEU B 224 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 248 through 252 removed outlier: 4.199A pdb=" N ARG B 248 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N VAL B 268 " --> pdb=" O GLN B 285 " (cutoff:3.500A) removed outlier: 5.018A pdb=" N GLN B 285 " --> pdb=" O VAL B 268 " (cutoff:3.500A) removed outlier: 7.568A pdb=" N ILE B 270 " --> pdb=" O ARG B 283 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ARG B 283 " --> pdb=" O ILE B 270 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 292 through 297 removed outlier: 3.606A pdb=" N ASP B 294 " --> pdb=" O LEU B 306 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LEU B 303 " --> pdb=" O TYR B 317 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N VAL B 305 " --> pdb=" O VAL B 315 " (cutoff:3.500A) 116 hydrogen bonds defined for protein. 303 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 50 hydrogen bonds 88 hydrogen bond angles 0 basepair planarities 20 basepair parallelities 39 stacking parallelities Total time for adding SS restraints: 1.90 Time building geometry restraints manager: 1.91 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: 1036 1.33 - 1.45: 1792 1.45 - 1.57: 2826 1.57 - 1.69: 147 1.69 - 1.81: 29 Bond restraints: 5830 Sorted by residual: bond pdb=" C2 SAH A 301 " pdb=" N3 SAH A 301 " ideal model delta sigma weight residual 1.322 1.380 -0.058 2.00e-02 2.50e+03 8.48e+00 bond pdb=" C8 SAH A 301 " pdb=" N7 SAH A 301 " ideal model delta sigma weight residual 1.299 1.352 -0.053 2.00e-02 2.50e+03 6.89e+00 bond pdb=" C2 SAH A 301 " pdb=" N1 SAH A 301 " ideal model delta sigma weight residual 1.330 1.377 -0.047 2.00e-02 2.50e+03 5.52e+00 bond pdb=" C6 SAH A 301 " pdb=" N1 SAH A 301 " ideal model delta sigma weight residual 1.338 1.377 -0.039 2.00e-02 2.50e+03 3.71e+00 bond pdb=" C1' SAH A 301 " pdb=" N9 SAH A 301 " ideal model delta sigma weight residual 1.440 1.473 -0.033 2.00e-02 2.50e+03 2.71e+00 ... (remaining 5825 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.50: 8161 2.50 - 5.01: 89 5.01 - 7.51: 9 7.51 - 10.01: 8 10.01 - 12.52: 1 Bond angle restraints: 8268 Sorted by residual: angle pdb=" CG SAH A 301 " pdb=" SD SAH A 301 " pdb=" C5' SAH A 301 " ideal model delta sigma weight residual 101.77 89.25 12.52 3.00e+00 1.11e-01 1.74e+01 angle pdb=" C8 7MG C 46 " pdb=" N7 7MG C 46 " pdb=" CM7 7MG C 46 " ideal model delta sigma weight residual 112.82 122.50 -9.68 3.00e+00 1.11e-01 1.04e+01 angle pdb=" C5 7MG C 46 " pdb=" N7 7MG C 46 " pdb=" CM7 7MG C 46 " ideal model delta sigma weight residual 118.03 127.67 -9.64 3.00e+00 1.11e-01 1.03e+01 angle pdb=" O SAH A 301 " pdb=" C SAH A 301 " pdb=" OXT SAH A 301 " ideal model delta sigma weight residual 126.79 117.77 9.02 3.00e+00 1.11e-01 9.03e+00 angle pdb=" C2 SAH A 301 " pdb=" N3 SAH A 301 " pdb=" C4 SAH A 301 " ideal model delta sigma weight residual 111.67 120.42 -8.75 3.00e+00 1.11e-01 8.50e+00 ... (remaining 8263 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 19.48: 3083 19.48 - 38.95: 292 38.95 - 58.42: 116 58.42 - 77.90: 72 77.90 - 97.37: 5 Dihedral angle restraints: 3568 sinusoidal: 2139 harmonic: 1429 Sorted by residual: dihedral pdb=" CA ARG B 89 " pdb=" C ARG B 89 " pdb=" N THR B 90 " pdb=" CA THR B 90 " ideal model delta harmonic sigma weight residual -180.00 -161.34 -18.66 0 5.00e+00 4.00e-02 1.39e+01 dihedral pdb=" OP2 PSU C 39 " pdb=" P PSU C 39 " pdb=" O5' PSU C 39 " pdb=" C5' PSU C 39 " ideal model delta sinusoidal sigma weight residual 86.61 -176.02 -97.37 1 3.00e+01 1.11e-03 1.20e+01 dihedral pdb=" OP2 PSU C 55 " pdb=" P PSU C 55 " pdb=" O5' PSU C 55 " pdb=" C5' PSU C 55 " ideal model delta sinusoidal sigma weight residual 86.61 179.26 -92.65 1 3.00e+01 1.11e-03 1.12e+01 ... (remaining 3565 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 746 0.040 - 0.080: 154 0.080 - 0.120: 57 0.120 - 0.160: 9 0.160 - 0.200: 1 Chirality restraints: 967 Sorted by residual: chirality pdb=" C1' U C 59 " pdb=" O4' U C 59 " pdb=" C2' U C 59 " pdb=" N1 U C 59 " both_signs ideal model delta sigma weight residual False 2.47 2.27 0.20 2.00e-01 2.50e+01 1.00e+00 chirality pdb=" CA ILE A 259 " pdb=" N ILE A 259 " pdb=" C ILE A 259 " pdb=" CB ILE A 259 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.79e-01 chirality pdb=" CA ILE B 160 " pdb=" N ILE B 160 " pdb=" C ILE B 160 " pdb=" CB ILE B 160 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.37e-01 ... (remaining 964 not shown) Planarity restraints: 776 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP A 163 " 0.066 5.00e-02 4.00e+02 1.00e-01 1.60e+01 pdb=" N PRO A 164 " -0.173 5.00e-02 4.00e+02 pdb=" CA PRO A 164 " 0.054 5.00e-02 4.00e+02 pdb=" CD PRO A 164 " 0.054 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' G C 19 " 0.026 2.00e-02 2.50e+03 1.12e-02 3.79e+00 pdb=" N9 G C 19 " -0.027 2.00e-02 2.50e+03 pdb=" C8 G C 19 " -0.002 2.00e-02 2.50e+03 pdb=" N7 G C 19 " 0.000 2.00e-02 2.50e+03 pdb=" C5 G C 19 " 0.000 2.00e-02 2.50e+03 pdb=" C6 G C 19 " 0.003 2.00e-02 2.50e+03 pdb=" O6 G C 19 " 0.007 2.00e-02 2.50e+03 pdb=" N1 G C 19 " 0.002 2.00e-02 2.50e+03 pdb=" C2 G C 19 " -0.000 2.00e-02 2.50e+03 pdb=" N2 G C 19 " -0.002 2.00e-02 2.50e+03 pdb=" N3 G C 19 " -0.004 2.00e-02 2.50e+03 pdb=" C4 G C 19 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' U C 59 " -0.022 2.00e-02 2.50e+03 1.17e-02 3.08e+00 pdb=" N1 U C 59 " 0.026 2.00e-02 2.50e+03 pdb=" C2 U C 59 " -0.000 2.00e-02 2.50e+03 pdb=" O2 U C 59 " 0.001 2.00e-02 2.50e+03 pdb=" N3 U C 59 " -0.000 2.00e-02 2.50e+03 pdb=" C4 U C 59 " -0.002 2.00e-02 2.50e+03 pdb=" O4 U C 59 " -0.006 2.00e-02 2.50e+03 pdb=" C5 U C 59 " -0.002 2.00e-02 2.50e+03 pdb=" C6 U C 59 " 0.005 2.00e-02 2.50e+03 ... (remaining 773 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 1174 2.79 - 3.31: 4868 3.31 - 3.84: 10012 3.84 - 4.37: 11726 4.37 - 4.90: 18141 Nonbonded interactions: 45921 Sorted by model distance: nonbonded pdb=" O2' 1MA C 58 " pdb=" OP2 C C 60 " model vdw 2.257 3.040 nonbonded pdb=" NZ LYS B 83 " pdb=" OP1 5MU C 54 " model vdw 2.286 3.120 nonbonded pdb=" OH TYR A 50 " pdb=" O ILE A 103 " model vdw 2.289 3.040 nonbonded pdb=" OG SER B 146 " pdb=" OD2 ASP B 166 " model vdw 2.326 3.040 nonbonded pdb=" OG SER B 146 " pdb=" OD2 ASP B 164 " model vdw 2.367 3.040 ... (remaining 45916 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.170 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: 0.230 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 20.620 Find NCS groups from input model: 0.050 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:3.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6496 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 : 0.003 0.058 5830 Z= 0.143 Angle : 0.677 12.516 8268 Z= 0.304 Chirality : 0.038 0.200 967 Planarity : 0.005 0.100 776 Dihedral : 19.263 97.372 2642 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 11.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 0.00 % Allowed : 22.93 % Favored : 77.07 % 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: -1.68 (0.34), residues: 482 helix: -0.05 (0.58), residues: 65 sheet: -0.84 (0.43), residues: 147 loop : -1.55 (0.31), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP A 206 HIS 0.003 0.001 HIS A 210 PHE 0.008 0.001 PHE A 159 TYR 0.014 0.002 TYR A 115 ARG 0.004 0.000 ARG A 124 Details of bonding type rmsd hydrogen bonds : bond 0.23086 ( 162) hydrogen bonds : angle 7.89692 ( 391) covalent geometry : bond 0.00306 ( 5830) covalent geometry : angle 0.67652 ( 8268) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 964 Ramachandran restraints generated. 482 Oldfield, 0 Emsley, 482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 964 Ramachandran restraints generated. 482 Oldfield, 0 Emsley, 482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 51 time to evaluate : 0.440 Fit side-chains REVERT: A 30 MET cc_start: 0.5957 (mpp) cc_final: 0.5019 (mtt) REVERT: B 157 ASP cc_start: 0.6945 (m-30) cc_final: 0.6048 (m-30) outliers start: 0 outliers final: 0 residues processed: 51 average time/residue: 0.1939 time to fit residues: 13.0574 Evaluate side-chains 46 residues out of total 424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 46 time to evaluate : 0.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 46 optimal weight: 0.8980 chunk 41 optimal weight: 5.9990 chunk 23 optimal weight: 0.5980 chunk 14 optimal weight: 1.9990 chunk 28 optimal weight: 0.7980 chunk 22 optimal weight: 0.7980 chunk 43 optimal weight: 0.8980 chunk 16 optimal weight: 0.5980 chunk 26 optimal weight: 0.9980 chunk 32 optimal weight: 0.0670 chunk 49 optimal weight: 8.9990 overall best weight: 0.5718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 251 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5013 r_free = 0.5013 target = 0.262242 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4655 r_free = 0.4655 target = 0.221497 restraints weight = 7045.460| |-----------------------------------------------------------------------------| r_work (start): 0.4640 rms_B_bonded: 1.78 r_work: 0.4431 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.4431 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6556 moved from start: 0.1121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 5830 Z= 0.115 Angle : 0.546 4.961 8268 Z= 0.269 Chirality : 0.038 0.207 967 Planarity : 0.004 0.064 776 Dihedral : 17.983 78.617 1728 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 3.78 % Allowed : 18.91 % Favored : 77.30 % 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: -1.15 (0.36), residues: 482 helix: 1.05 (0.64), residues: 67 sheet: -0.68 (0.42), residues: 160 loop : -1.29 (0.34), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 206 HIS 0.002 0.001 HIS A 33 PHE 0.009 0.001 PHE B 183 TYR 0.010 0.001 TYR B 218 ARG 0.004 0.000 ARG B 283 Details of bonding type rmsd hydrogen bonds : bond 0.03980 ( 162) hydrogen bonds : angle 5.22575 ( 391) covalent geometry : bond 0.00264 ( 5830) covalent geometry : angle 0.54579 ( 8268) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 964 Ramachandran restraints generated. 482 Oldfield, 0 Emsley, 482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 964 Ramachandran restraints generated. 482 Oldfield, 0 Emsley, 482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 59 time to evaluate : 0.524 Fit side-chains revert: symmetry clash REVERT: A 124 ARG cc_start: 0.6557 (OUTLIER) cc_final: 0.5616 (mpt-90) REVERT: B 117 VAL cc_start: 0.9011 (OUTLIER) cc_final: 0.8756 (p) REVERT: B 133 GLU cc_start: 0.7428 (tm-30) cc_final: 0.7017 (tm-30) REVERT: B 145 LEU cc_start: 0.6933 (OUTLIER) cc_final: 0.6616 (tt) REVERT: B 157 ASP cc_start: 0.6989 (m-30) cc_final: 0.6061 (m-30) REVERT: B 269 TYR cc_start: 0.6422 (m-10) cc_final: 0.5974 (m-10) outliers start: 16 outliers final: 9 residues processed: 71 average time/residue: 0.2026 time to fit residues: 18.6845 Evaluate side-chains 62 residues out of total 424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 50 time to evaluate : 0.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 THR Chi-restraints excluded: chain A residue 124 ARG Chi-restraints excluded: chain A residue 169 THR Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 79 THR Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 156 ASP Chi-restraints excluded: chain B residue 162 THR Chi-restraints excluded: chain B residue 207 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 44 optimal weight: 0.9980 chunk 5 optimal weight: 1.9990 chunk 42 optimal weight: 0.9990 chunk 24 optimal weight: 3.9990 chunk 46 optimal weight: 0.9980 chunk 7 optimal weight: 1.9990 chunk 16 optimal weight: 0.7980 chunk 29 optimal weight: 0.5980 chunk 35 optimal weight: 2.9990 chunk 18 optimal weight: 2.9990 chunk 37 optimal weight: 0.0570 overall best weight: 0.6898 ------------------------------------------------------------------------------- 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 = 0.4986 r_free = 0.4986 target = 0.258537 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4615 r_free = 0.4615 target = 0.216703 restraints weight = 7129.794| |-----------------------------------------------------------------------------| r_work (start): 0.4597 rms_B_bonded: 1.82 r_work: 0.4404 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.4404 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6635 moved from start: 0.1702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 5830 Z= 0.122 Angle : 0.550 6.300 8268 Z= 0.269 Chirality : 0.039 0.229 967 Planarity : 0.004 0.047 776 Dihedral : 17.899 75.613 1728 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 5.20 % Allowed : 19.39 % Favored : 75.41 % 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: -1.04 (0.37), residues: 482 helix: 1.32 (0.66), residues: 68 sheet: -0.68 (0.41), residues: 172 loop : -1.25 (0.35), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 216 HIS 0.002 0.001 HIS A 233 PHE 0.009 0.001 PHE B 183 TYR 0.012 0.001 TYR A 115 ARG 0.005 0.000 ARG B 139 Details of bonding type rmsd hydrogen bonds : bond 0.03660 ( 162) hydrogen bonds : angle 4.77835 ( 391) covalent geometry : bond 0.00282 ( 5830) covalent geometry : angle 0.55016 ( 8268) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 964 Ramachandran restraints generated. 482 Oldfield, 0 Emsley, 482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 964 Ramachandran restraints generated. 482 Oldfield, 0 Emsley, 482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 52 time to evaluate : 0.437 Fit side-chains revert: symmetry clash REVERT: A 83 ILE cc_start: 0.8786 (mm) cc_final: 0.8521 (mt) REVERT: A 124 ARG cc_start: 0.6569 (OUTLIER) cc_final: 0.5887 (mpt-90) REVERT: A 142 MET cc_start: 0.7576 (mmm) cc_final: 0.7075 (mmm) REVERT: A 211 PHE cc_start: 0.4022 (OUTLIER) cc_final: 0.3666 (m-80) REVERT: B 117 VAL cc_start: 0.9069 (OUTLIER) cc_final: 0.8864 (p) REVERT: B 133 GLU cc_start: 0.7386 (tm-30) cc_final: 0.6976 (tm-30) REVERT: B 145 LEU cc_start: 0.6890 (OUTLIER) cc_final: 0.6493 (tt) outliers start: 22 outliers final: 14 residues processed: 67 average time/residue: 0.1665 time to fit residues: 15.1266 Evaluate side-chains 67 residues out of total 424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 49 time to evaluate : 0.490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 THR Chi-restraints excluded: chain A residue 124 ARG Chi-restraints excluded: chain A residue 134 ILE Chi-restraints excluded: chain A residue 169 THR Chi-restraints excluded: chain A residue 211 PHE Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 79 THR Chi-restraints excluded: chain B residue 89 ARG Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 146 SER Chi-restraints excluded: chain B residue 156 ASP Chi-restraints excluded: chain B residue 162 THR Chi-restraints excluded: chain B residue 247 SER Chi-restraints excluded: chain B residue 258 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 21 optimal weight: 7.9990 chunk 10 optimal weight: 0.4980 chunk 25 optimal weight: 3.9990 chunk 31 optimal weight: 2.9990 chunk 4 optimal weight: 3.9990 chunk 8 optimal weight: 2.9990 chunk 29 optimal weight: 0.5980 chunk 7 optimal weight: 0.9980 chunk 22 optimal weight: 0.9990 chunk 0 optimal weight: 4.9990 chunk 36 optimal weight: 0.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 310 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4960 r_free = 0.4960 target = 0.254502 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4593 r_free = 0.4593 target = 0.213966 restraints weight = 7213.608| |-----------------------------------------------------------------------------| r_work (start): 0.4598 rms_B_bonded: 1.68 r_work: 0.4402 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.4402 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6657 moved from start: 0.2209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 5830 Z= 0.137 Angle : 0.572 5.873 8268 Z= 0.281 Chirality : 0.039 0.244 967 Planarity : 0.004 0.047 776 Dihedral : 17.900 74.945 1728 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % Rotamer: Outliers : 5.44 % Allowed : 20.33 % Favored : 74.23 % 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: -1.18 (0.36), residues: 482 helix: 1.36 (0.66), residues: 68 sheet: -0.64 (0.42), residues: 154 loop : -1.47 (0.33), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 216 HIS 0.005 0.001 HIS A 33 PHE 0.010 0.001 PHE B 183 TYR 0.011 0.001 TYR A 115 ARG 0.003 0.000 ARG A 124 Details of bonding type rmsd hydrogen bonds : bond 0.03748 ( 162) hydrogen bonds : angle 4.66008 ( 391) covalent geometry : bond 0.00318 ( 5830) covalent geometry : angle 0.57182 ( 8268) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 964 Ramachandran restraints generated. 482 Oldfield, 0 Emsley, 482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 964 Ramachandran restraints generated. 482 Oldfield, 0 Emsley, 482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 49 time to evaluate : 0.494 Fit side-chains revert: symmetry clash REVERT: A 114 ASP cc_start: 0.5987 (t0) cc_final: 0.5781 (t0) REVERT: A 124 ARG cc_start: 0.6465 (OUTLIER) cc_final: 0.5878 (mpt-90) REVERT: A 142 MET cc_start: 0.7649 (mmm) cc_final: 0.7165 (mtp) REVERT: A 169 THR cc_start: 0.7283 (OUTLIER) cc_final: 0.6947 (p) REVERT: A 211 PHE cc_start: 0.3994 (OUTLIER) cc_final: 0.3472 (m-80) REVERT: B 117 VAL cc_start: 0.9061 (OUTLIER) cc_final: 0.8855 (p) REVERT: B 145 LEU cc_start: 0.6945 (OUTLIER) cc_final: 0.6475 (tt) outliers start: 23 outliers final: 16 residues processed: 66 average time/residue: 0.1888 time to fit residues: 16.7010 Evaluate side-chains 64 residues out of total 424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 43 time to evaluate : 0.565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 THR Chi-restraints excluded: chain A residue 103 ILE Chi-restraints excluded: chain A residue 124 ARG Chi-restraints excluded: chain A residue 134 ILE Chi-restraints excluded: chain A residue 169 THR Chi-restraints excluded: chain A residue 211 PHE Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 79 THR Chi-restraints excluded: chain B residue 89 ARG Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 146 SER Chi-restraints excluded: chain B residue 156 ASP Chi-restraints excluded: chain B residue 157 ASP Chi-restraints excluded: chain B residue 162 THR Chi-restraints excluded: chain B residue 172 SER Chi-restraints excluded: chain B residue 258 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 25 optimal weight: 3.9990 chunk 50 optimal weight: 10.0000 chunk 18 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 chunk 41 optimal weight: 3.9990 chunk 43 optimal weight: 0.7980 chunk 46 optimal weight: 1.9990 chunk 8 optimal weight: 3.9990 chunk 26 optimal weight: 0.7980 chunk 7 optimal weight: 1.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- 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 = 0.4948 r_free = 0.4948 target = 0.253986 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4565 r_free = 0.4565 target = 0.211320 restraints weight = 7075.300| |-----------------------------------------------------------------------------| r_work (start): 0.4581 rms_B_bonded: 1.65 r_work: 0.4397 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.4397 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6773 moved from start: 0.2731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 5830 Z= 0.197 Angle : 0.647 5.885 8268 Z= 0.322 Chirality : 0.042 0.280 967 Planarity : 0.005 0.055 776 Dihedral : 18.053 83.157 1728 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 11.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.05 % Favored : 92.95 % Rotamer: Outliers : 5.44 % Allowed : 19.15 % Favored : 75.41 % 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: -1.62 (0.35), residues: 482 helix: 1.16 (0.67), residues: 68 sheet: -1.08 (0.43), residues: 149 loop : -1.70 (0.31), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 216 HIS 0.004 0.001 HIS A 144 PHE 0.015 0.002 PHE B 183 TYR 0.015 0.002 TYR A 115 ARG 0.004 0.001 ARG A 258 Details of bonding type rmsd hydrogen bonds : bond 0.04565 ( 162) hydrogen bonds : angle 5.07267 ( 391) covalent geometry : bond 0.00460 ( 5830) covalent geometry : angle 0.64699 ( 8268) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 964 Ramachandran restraints generated. 482 Oldfield, 0 Emsley, 482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 964 Ramachandran restraints generated. 482 Oldfield, 0 Emsley, 482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 47 time to evaluate : 0.436 Fit side-chains revert: symmetry clash REVERT: A 114 ASP cc_start: 0.5930 (t0) cc_final: 0.5709 (t0) REVERT: A 124 ARG cc_start: 0.6699 (OUTLIER) cc_final: 0.6307 (mpt-90) REVERT: A 142 MET cc_start: 0.7729 (mmm) cc_final: 0.7442 (mtp) REVERT: A 169 THR cc_start: 0.7274 (OUTLIER) cc_final: 0.7019 (p) REVERT: A 211 PHE cc_start: 0.4182 (OUTLIER) cc_final: 0.3474 (m-80) REVERT: A 257 ARG cc_start: 0.7880 (ttt180) cc_final: 0.7676 (ttm170) REVERT: B 145 LEU cc_start: 0.7243 (OUTLIER) cc_final: 0.6621 (tt) REVERT: B 164 ASP cc_start: 0.7632 (t70) cc_final: 0.7353 (t70) outliers start: 23 outliers final: 17 residues processed: 66 average time/residue: 0.1651 time to fit residues: 14.4328 Evaluate side-chains 62 residues out of total 424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 41 time to evaluate : 0.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 THR Chi-restraints excluded: chain A residue 103 ILE Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 124 ARG Chi-restraints excluded: chain A residue 134 ILE Chi-restraints excluded: chain A residue 169 THR Chi-restraints excluded: chain A residue 211 PHE Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 79 THR Chi-restraints excluded: chain B residue 89 ARG Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 146 SER Chi-restraints excluded: chain B residue 156 ASP Chi-restraints excluded: chain B residue 157 ASP Chi-restraints excluded: chain B residue 162 THR Chi-restraints excluded: chain B residue 172 SER Chi-restraints excluded: chain B residue 207 SER Chi-restraints excluded: chain B residue 258 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 4 optimal weight: 1.9990 chunk 54 optimal weight: 5.9990 chunk 12 optimal weight: 0.9980 chunk 30 optimal weight: 0.9980 chunk 29 optimal weight: 0.3980 chunk 45 optimal weight: 0.0030 chunk 7 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 chunk 37 optimal weight: 0.8980 chunk 2 optimal weight: 0.7980 chunk 43 optimal weight: 0.6980 overall best weight: 0.5590 ------------------------------------------------------------------------------- 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 = 0.4991 r_free = 0.4991 target = 0.259358 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4636 r_free = 0.4636 target = 0.218926 restraints weight = 7083.945| |-----------------------------------------------------------------------------| r_work (start): 0.4646 rms_B_bonded: 1.68 r_work: 0.4454 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.4454 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6671 moved from start: 0.2808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 5830 Z= 0.111 Angle : 0.549 5.724 8268 Z= 0.271 Chirality : 0.038 0.272 967 Planarity : 0.004 0.053 776 Dihedral : 17.853 73.976 1728 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 5.44 % Allowed : 19.86 % Favored : 74.70 % 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: -1.29 (0.36), residues: 482 helix: 1.35 (0.68), residues: 68 sheet: -0.89 (0.42), residues: 154 loop : -1.44 (0.33), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 206 HIS 0.002 0.001 HIS B 144 PHE 0.010 0.001 PHE A 159 TYR 0.016 0.001 TYR A 115 ARG 0.003 0.000 ARG A 124 Details of bonding type rmsd hydrogen bonds : bond 0.03381 ( 162) hydrogen bonds : angle 4.47282 ( 391) covalent geometry : bond 0.00256 ( 5830) covalent geometry : angle 0.54939 ( 8268) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 964 Ramachandran restraints generated. 482 Oldfield, 0 Emsley, 482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 964 Ramachandran restraints generated. 482 Oldfield, 0 Emsley, 482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 42 time to evaluate : 0.456 Fit side-chains REVERT: A 114 ASP cc_start: 0.5869 (t0) cc_final: 0.5658 (t0) REVERT: A 124 ARG cc_start: 0.6331 (OUTLIER) cc_final: 0.5714 (mpt-90) REVERT: A 142 MET cc_start: 0.7688 (mmm) cc_final: 0.7431 (mtp) REVERT: A 169 THR cc_start: 0.7242 (OUTLIER) cc_final: 0.7023 (p) REVERT: A 211 PHE cc_start: 0.4015 (OUTLIER) cc_final: 0.3526 (m-80) REVERT: B 145 LEU cc_start: 0.6941 (OUTLIER) cc_final: 0.6539 (tt) outliers start: 23 outliers final: 15 residues processed: 60 average time/residue: 0.1880 time to fit residues: 14.6880 Evaluate side-chains 59 residues out of total 424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 40 time to evaluate : 0.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 THR Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 124 ARG Chi-restraints excluded: chain A residue 134 ILE Chi-restraints excluded: chain A residue 169 THR Chi-restraints excluded: chain A residue 211 PHE Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 79 THR Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 146 SER Chi-restraints excluded: chain B residue 156 ASP Chi-restraints excluded: chain B residue 157 ASP Chi-restraints excluded: chain B residue 162 THR Chi-restraints excluded: chain B residue 195 SER Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 295 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 35 optimal weight: 0.3980 chunk 50 optimal weight: 9.9990 chunk 8 optimal weight: 0.6980 chunk 10 optimal weight: 0.9980 chunk 33 optimal weight: 0.9990 chunk 43 optimal weight: 1.9990 chunk 14 optimal weight: 0.6980 chunk 4 optimal weight: 1.9990 chunk 2 optimal weight: 0.6980 chunk 52 optimal weight: 6.9990 chunk 0 optimal weight: 4.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.4979 r_free = 0.4979 target = 0.257967 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4609 r_free = 0.4609 target = 0.216361 restraints weight = 7150.285| |-----------------------------------------------------------------------------| r_work (start): 0.4610 rms_B_bonded: 1.71 r_work: 0.4404 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.4404 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6696 moved from start: 0.3025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 5830 Z= 0.123 Angle : 0.551 5.424 8268 Z= 0.271 Chirality : 0.039 0.253 967 Planarity : 0.004 0.047 776 Dihedral : 17.850 74.608 1728 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.43 % Favored : 93.57 % Rotamer: Outliers : 4.96 % Allowed : 20.57 % Favored : 74.47 % 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: -1.28 (0.36), residues: 482 helix: 1.33 (0.68), residues: 68 sheet: -0.88 (0.42), residues: 154 loop : -1.43 (0.33), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 216 HIS 0.002 0.001 HIS B 144 PHE 0.010 0.001 PHE A 159 TYR 0.012 0.001 TYR A 115 ARG 0.003 0.000 ARG A 124 Details of bonding type rmsd hydrogen bonds : bond 0.03546 ( 162) hydrogen bonds : angle 4.49129 ( 391) covalent geometry : bond 0.00286 ( 5830) covalent geometry : angle 0.55143 ( 8268) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 964 Ramachandran restraints generated. 482 Oldfield, 0 Emsley, 482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 964 Ramachandran restraints generated. 482 Oldfield, 0 Emsley, 482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 40 time to evaluate : 0.442 Fit side-chains REVERT: A 115 TYR cc_start: 0.4857 (t80) cc_final: 0.4576 (t80) REVERT: A 124 ARG cc_start: 0.6350 (OUTLIER) cc_final: 0.5696 (mpt-90) REVERT: A 142 MET cc_start: 0.7673 (mmm) cc_final: 0.7442 (mtp) REVERT: A 169 THR cc_start: 0.7306 (OUTLIER) cc_final: 0.7057 (p) REVERT: A 211 PHE cc_start: 0.3961 (OUTLIER) cc_final: 0.3457 (m-80) REVERT: B 145 LEU cc_start: 0.6962 (OUTLIER) cc_final: 0.6354 (tt) outliers start: 21 outliers final: 15 residues processed: 56 average time/residue: 0.1640 time to fit residues: 12.4334 Evaluate side-chains 56 residues out of total 424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 37 time to evaluate : 0.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 THR Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 124 ARG Chi-restraints excluded: chain A residue 134 ILE Chi-restraints excluded: chain A residue 169 THR Chi-restraints excluded: chain A residue 211 PHE Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 79 THR Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 146 SER Chi-restraints excluded: chain B residue 156 ASP Chi-restraints excluded: chain B residue 157 ASP Chi-restraints excluded: chain B residue 162 THR Chi-restraints excluded: chain B residue 172 SER Chi-restraints excluded: chain B residue 195 SER Chi-restraints excluded: chain B residue 258 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 23 optimal weight: 7.9990 chunk 0 optimal weight: 4.9990 chunk 24 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 11 optimal weight: 0.7980 chunk 6 optimal weight: 0.9990 chunk 44 optimal weight: 0.9990 chunk 19 optimal weight: 3.9990 chunk 37 optimal weight: 2.9990 overall best weight: 1.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 254 GLN ** 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 = 0.4941 r_free = 0.4941 target = 0.252740 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4550 r_free = 0.4550 target = 0.209572 restraints weight = 7068.397| |-----------------------------------------------------------------------------| r_work (start): 0.4547 rms_B_bonded: 1.64 r_work: 0.4352 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.4352 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6789 moved from start: 0.3384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 5830 Z= 0.201 Angle : 0.652 6.601 8268 Z= 0.325 Chirality : 0.043 0.292 967 Planarity : 0.005 0.049 776 Dihedral : 18.086 84.384 1728 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 11.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.05 % Favored : 92.95 % Rotamer: Outliers : 5.44 % Allowed : 19.39 % Favored : 75.18 % 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: -1.81 (0.35), residues: 482 helix: 1.03 (0.67), residues: 68 sheet: -1.25 (0.43), residues: 139 loop : -1.79 (0.30), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 216 HIS 0.003 0.001 HIS B 144 PHE 0.015 0.002 PHE B 183 TYR 0.014 0.002 TYR A 115 ARG 0.003 0.000 ARG B 103 Details of bonding type rmsd hydrogen bonds : bond 0.04549 ( 162) hydrogen bonds : angle 5.14733 ( 391) covalent geometry : bond 0.00470 ( 5830) covalent geometry : angle 0.65239 ( 8268) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 964 Ramachandran restraints generated. 482 Oldfield, 0 Emsley, 482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 964 Ramachandran restraints generated. 482 Oldfield, 0 Emsley, 482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 42 time to evaluate : 0.459 Fit side-chains REVERT: A 124 ARG cc_start: 0.6524 (OUTLIER) cc_final: 0.6130 (mpt-90) REVERT: A 169 THR cc_start: 0.7364 (OUTLIER) cc_final: 0.7105 (p) REVERT: A 211 PHE cc_start: 0.4060 (OUTLIER) cc_final: 0.3351 (m-80) REVERT: B 145 LEU cc_start: 0.7287 (OUTLIER) cc_final: 0.6527 (tt) REVERT: B 164 ASP cc_start: 0.7647 (t70) cc_final: 0.7334 (t70) outliers start: 23 outliers final: 17 residues processed: 60 average time/residue: 0.1827 time to fit residues: 14.3072 Evaluate side-chains 61 residues out of total 424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 40 time to evaluate : 0.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 THR Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 124 ARG Chi-restraints excluded: chain A residue 134 ILE Chi-restraints excluded: chain A residue 169 THR Chi-restraints excluded: chain A residue 211 PHE Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 79 THR Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 146 SER Chi-restraints excluded: chain B residue 156 ASP Chi-restraints excluded: chain B residue 157 ASP Chi-restraints excluded: chain B residue 162 THR Chi-restraints excluded: chain B residue 172 SER Chi-restraints excluded: chain B residue 195 SER Chi-restraints excluded: chain B residue 258 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 27 optimal weight: 1.9990 chunk 46 optimal weight: 0.9980 chunk 5 optimal weight: 0.8980 chunk 0 optimal weight: 3.9990 chunk 9 optimal weight: 0.9980 chunk 26 optimal weight: 0.5980 chunk 1 optimal weight: 0.6980 chunk 17 optimal weight: 0.7980 chunk 39 optimal weight: 1.9990 chunk 16 optimal weight: 0.9990 chunk 33 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 233 HIS ** B 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4971 r_free = 0.4971 target = 0.256571 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4591 r_free = 0.4591 target = 0.214168 restraints weight = 7116.804| |-----------------------------------------------------------------------------| r_work (start): 0.4608 rms_B_bonded: 1.68 r_work: 0.4417 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.4417 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6731 moved from start: 0.3416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 5830 Z= 0.132 Angle : 0.575 5.341 8268 Z= 0.284 Chirality : 0.040 0.290 967 Planarity : 0.004 0.046 776 Dihedral : 17.931 74.013 1728 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 10.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.22 % Favored : 93.78 % Rotamer: Outliers : 4.49 % Allowed : 20.80 % Favored : 74.70 % 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: -1.57 (0.35), residues: 482 helix: 1.20 (0.67), residues: 68 sheet: -1.14 (0.42), residues: 144 loop : -1.60 (0.31), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 216 HIS 0.002 0.001 HIS B 144 PHE 0.009 0.001 PHE B 183 TYR 0.013 0.001 TYR A 115 ARG 0.007 0.000 ARG A 168 Details of bonding type rmsd hydrogen bonds : bond 0.03621 ( 162) hydrogen bonds : angle 4.58627 ( 391) covalent geometry : bond 0.00306 ( 5830) covalent geometry : angle 0.57487 ( 8268) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 964 Ramachandran restraints generated. 482 Oldfield, 0 Emsley, 482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 964 Ramachandran restraints generated. 482 Oldfield, 0 Emsley, 482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 42 time to evaluate : 0.499 Fit side-chains REVERT: A 124 ARG cc_start: 0.6340 (OUTLIER) cc_final: 0.5759 (mpt-90) REVERT: A 169 THR cc_start: 0.7368 (OUTLIER) cc_final: 0.7145 (p) REVERT: A 211 PHE cc_start: 0.3978 (OUTLIER) cc_final: 0.3467 (m-80) REVERT: B 145 LEU cc_start: 0.7027 (OUTLIER) cc_final: 0.6395 (tt) REVERT: B 164 ASP cc_start: 0.7520 (t70) cc_final: 0.7130 (t70) outliers start: 19 outliers final: 15 residues processed: 56 average time/residue: 0.1680 time to fit residues: 12.8398 Evaluate side-chains 61 residues out of total 424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 42 time to evaluate : 0.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 THR Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 124 ARG Chi-restraints excluded: chain A residue 134 ILE Chi-restraints excluded: chain A residue 169 THR Chi-restraints excluded: chain A residue 211 PHE Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 79 THR Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 156 ASP Chi-restraints excluded: chain B residue 157 ASP Chi-restraints excluded: chain B residue 162 THR Chi-restraints excluded: chain B residue 172 SER Chi-restraints excluded: chain B residue 195 SER Chi-restraints excluded: chain B residue 258 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 48 optimal weight: 7.9990 chunk 50 optimal weight: 8.9990 chunk 33 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 13 optimal weight: 0.4980 chunk 38 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 20 optimal weight: 0.5980 chunk 24 optimal weight: 0.6980 chunk 17 optimal weight: 0.7980 chunk 41 optimal weight: 4.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 291 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4947 r_free = 0.4947 target = 0.254214 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4583 r_free = 0.4583 target = 0.213608 restraints weight = 7167.660| |-----------------------------------------------------------------------------| r_work (start): 0.4599 rms_B_bonded: 1.66 r_work: 0.4410 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.4410 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6752 moved from start: 0.3547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 5830 Z= 0.150 Angle : 0.592 5.600 8268 Z= 0.293 Chirality : 0.041 0.279 967 Planarity : 0.005 0.047 776 Dihedral : 17.977 77.305 1728 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 10.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.85 % Favored : 93.15 % Rotamer: Outliers : 4.73 % Allowed : 21.28 % Favored : 74.00 % 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: -1.66 (0.35), residues: 482 helix: 1.23 (0.67), residues: 68 sheet: -1.20 (0.43), residues: 139 loop : -1.69 (0.31), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 216 HIS 0.003 0.001 HIS B 144 PHE 0.011 0.001 PHE B 183 TYR 0.011 0.001 TYR A 115 ARG 0.006 0.000 ARG A 168 Details of bonding type rmsd hydrogen bonds : bond 0.03876 ( 162) hydrogen bonds : angle 4.71921 ( 391) covalent geometry : bond 0.00351 ( 5830) covalent geometry : angle 0.59237 ( 8268) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 964 Ramachandran restraints generated. 482 Oldfield, 0 Emsley, 482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 964 Ramachandran restraints generated. 482 Oldfield, 0 Emsley, 482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 42 time to evaluate : 0.490 Fit side-chains REVERT: A 124 ARG cc_start: 0.6420 (OUTLIER) cc_final: 0.5792 (mpt-90) REVERT: A 169 THR cc_start: 0.7350 (OUTLIER) cc_final: 0.7110 (p) REVERT: A 211 PHE cc_start: 0.4028 (OUTLIER) cc_final: 0.3487 (m-80) REVERT: B 145 LEU cc_start: 0.7183 (OUTLIER) cc_final: 0.6568 (tt) REVERT: B 164 ASP cc_start: 0.7469 (t70) cc_final: 0.7156 (t70) outliers start: 20 outliers final: 15 residues processed: 58 average time/residue: 0.1686 time to fit residues: 13.2189 Evaluate side-chains 60 residues out of total 424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 41 time to evaluate : 0.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 THR Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 124 ARG Chi-restraints excluded: chain A residue 169 THR Chi-restraints excluded: chain A residue 211 PHE Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 79 THR Chi-restraints excluded: chain B residue 86 ILE Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 156 ASP Chi-restraints excluded: chain B residue 157 ASP Chi-restraints excluded: chain B residue 162 THR Chi-restraints excluded: chain B residue 172 SER Chi-restraints excluded: chain B residue 195 SER Chi-restraints excluded: chain B residue 258 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 16 optimal weight: 0.7980 chunk 13 optimal weight: 0.5980 chunk 24 optimal weight: 2.9990 chunk 48 optimal weight: 7.9990 chunk 11 optimal weight: 0.0670 chunk 38 optimal weight: 2.9990 chunk 43 optimal weight: 4.9990 chunk 14 optimal weight: 0.3980 chunk 1 optimal weight: 0.9990 chunk 52 optimal weight: 5.9990 chunk 20 optimal weight: 4.9990 overall best weight: 0.5720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 291 GLN ** 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 = 0.4971 r_free = 0.4971 target = 0.257704 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4623 r_free = 0.4623 target = 0.218509 restraints weight = 7285.461| |-----------------------------------------------------------------------------| r_work (start): 0.4637 rms_B_bonded: 1.84 r_work: 0.4407 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.4407 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6720 moved from start: 0.3615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 5830 Z= 0.113 Angle : 0.552 6.439 8268 Z= 0.271 Chirality : 0.039 0.265 967 Planarity : 0.004 0.045 776 Dihedral : 17.872 73.962 1728 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 4.49 % Allowed : 21.51 % Favored : 74.00 % 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: -1.41 (0.36), residues: 482 helix: 1.37 (0.68), residues: 68 sheet: -1.04 (0.42), residues: 144 loop : -1.50 (0.32), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 252 HIS 0.002 0.001 HIS A 33 PHE 0.008 0.001 PHE A 159 TYR 0.009 0.001 TYR A 115 ARG 0.005 0.000 ARG A 168 Details of bonding type rmsd hydrogen bonds : bond 0.03360 ( 162) hydrogen bonds : angle 4.33670 ( 391) covalent geometry : bond 0.00263 ( 5830) covalent geometry : angle 0.55202 ( 8268) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2947.64 seconds wall clock time: 51 minutes 14.01 seconds (3074.01 seconds total)