Starting phenix.real_space_refine on Wed Mar 4 01:38:13 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9prz_71817/03_2026/9prz_71817.cif Found real_map, /net/cci-nas-00/data/ceres_data/9prz_71817/03_2026/9prz_71817.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.95 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9prz_71817/03_2026/9prz_71817.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9prz_71817/03_2026/9prz_71817.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9prz_71817/03_2026/9prz_71817.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9prz_71817/03_2026/9prz_71817.map" } resolution = 2.95 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.048 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: 4 Type Number sf(0) Gaussians S 78 5.16 5 C 6114 2.51 5 N 1668 2.21 5 O 1830 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9690 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 1615 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1615 Classifications: {'peptide': 206} Link IDs: {'PTRANS': 13, 'TRANS': 192} Chain breaks: 2 Restraints were copied for chains: B, C, D, E, F Time building chain proxies: 1.29, per 1000 atoms: 0.13 Number of scatterers: 9690 At special positions: 0 Unit cell: (102.6, 108, 78.84, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 78 16.00 O 1830 8.00 N 1668 7.00 C 6114 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=48, symmetry=0 Number of additional bonds: simple=48, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.02 Conformation dependent library (CDL) restraints added in 384.4 milliseconds 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2328 Finding SS restraints... Secondary structure from input PDB file: 72 helices and 0 sheets defined 74.8% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.28 Creating SS restraints... Processing helix chain 'A' and resid 16 through 31 removed outlier: 3.632A pdb=" N ALA A 31 " --> pdb=" O VAL A 27 " (cutoff:3.500A) Processing helix chain 'A' and resid 35 through 44 Processing helix chain 'A' and resid 48 through 58 Processing helix chain 'A' and resid 62 through 84 Processing helix chain 'A' and resid 100 through 105 Processing helix chain 'A' and resid 110 through 120 Processing helix chain 'A' and resid 125 through 145 removed outlier: 3.688A pdb=" N LYS A 140 " --> pdb=" O LEU A 136 " (cutoff:3.500A) Processing helix chain 'A' and resid 149 through 153 removed outlier: 3.538A pdb=" N ILE A 153 " --> pdb=" O ILE A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 160 through 173 Processing helix chain 'A' and resid 178 through 193 removed outlier: 3.790A pdb=" N TRP A 184 " --> pdb=" O GLU A 180 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N LEU A 190 " --> pdb=" O THR A 186 " (cutoff:3.500A) removed outlier: 4.938A pdb=" N VAL A 191 " --> pdb=" O GLU A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 206 removed outlier: 3.621A pdb=" N THR A 200 " --> pdb=" O PRO A 196 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N ILE A 201 " --> pdb=" O ASP A 197 " (cutoff:3.500A) Processing helix chain 'A' and resid 210 through 218 Processing helix chain 'B' and resid 16 through 31 removed outlier: 3.632A pdb=" N ALA B 31 " --> pdb=" O VAL B 27 " (cutoff:3.500A) Processing helix chain 'B' and resid 35 through 44 Processing helix chain 'B' and resid 48 through 58 Processing helix chain 'B' and resid 62 through 84 Processing helix chain 'B' and resid 100 through 105 Processing helix chain 'B' and resid 110 through 120 Processing helix chain 'B' and resid 125 through 145 removed outlier: 3.688A pdb=" N LYS B 140 " --> pdb=" O LEU B 136 " (cutoff:3.500A) Processing helix chain 'B' and resid 149 through 153 removed outlier: 3.537A pdb=" N ILE B 153 " --> pdb=" O ILE B 150 " (cutoff:3.500A) Processing helix chain 'B' and resid 160 through 173 Processing helix chain 'B' and resid 178 through 193 removed outlier: 3.790A pdb=" N TRP B 184 " --> pdb=" O GLU B 180 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N LEU B 190 " --> pdb=" O THR B 186 " (cutoff:3.500A) removed outlier: 4.938A pdb=" N VAL B 191 " --> pdb=" O GLU B 187 " (cutoff:3.500A) Processing helix chain 'B' and resid 195 through 206 removed outlier: 3.621A pdb=" N THR B 200 " --> pdb=" O PRO B 196 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N ILE B 201 " --> pdb=" O ASP B 197 " (cutoff:3.500A) Processing helix chain 'B' and resid 210 through 218 Processing helix chain 'C' and resid 16 through 31 removed outlier: 3.632A pdb=" N ALA C 31 " --> pdb=" O VAL C 27 " (cutoff:3.500A) Processing helix chain 'C' and resid 35 through 44 Processing helix chain 'C' and resid 48 through 58 Processing helix chain 'C' and resid 62 through 84 Processing helix chain 'C' and resid 100 through 105 Processing helix chain 'C' and resid 110 through 120 Processing helix chain 'C' and resid 125 through 145 removed outlier: 3.688A pdb=" N LYS C 140 " --> pdb=" O LEU C 136 " (cutoff:3.500A) Processing helix chain 'C' and resid 149 through 153 removed outlier: 3.538A pdb=" N ILE C 153 " --> pdb=" O ILE C 150 " (cutoff:3.500A) Processing helix chain 'C' and resid 160 through 173 Processing helix chain 'C' and resid 178 through 193 removed outlier: 3.790A pdb=" N TRP C 184 " --> pdb=" O GLU C 180 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N LEU C 190 " --> pdb=" O THR C 186 " (cutoff:3.500A) removed outlier: 4.937A pdb=" N VAL C 191 " --> pdb=" O GLU C 187 " (cutoff:3.500A) Processing helix chain 'C' and resid 195 through 206 removed outlier: 3.621A pdb=" N THR C 200 " --> pdb=" O PRO C 196 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N ILE C 201 " --> pdb=" O ASP C 197 " (cutoff:3.500A) Processing helix chain 'C' and resid 210 through 218 Processing helix chain 'D' and resid 16 through 31 removed outlier: 3.632A pdb=" N ALA D 31 " --> pdb=" O VAL D 27 " (cutoff:3.500A) Processing helix chain 'D' and resid 35 through 44 Processing helix chain 'D' and resid 48 through 58 Processing helix chain 'D' and resid 62 through 84 Processing helix chain 'D' and resid 100 through 105 Processing helix chain 'D' and resid 110 through 120 Processing helix chain 'D' and resid 125 through 145 removed outlier: 3.688A pdb=" N LYS D 140 " --> pdb=" O LEU D 136 " (cutoff:3.500A) Processing helix chain 'D' and resid 149 through 153 removed outlier: 3.538A pdb=" N ILE D 153 " --> pdb=" O ILE D 150 " (cutoff:3.500A) Processing helix chain 'D' and resid 160 through 173 Processing helix chain 'D' and resid 178 through 193 removed outlier: 3.790A pdb=" N TRP D 184 " --> pdb=" O GLU D 180 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N LEU D 190 " --> pdb=" O THR D 186 " (cutoff:3.500A) removed outlier: 4.938A pdb=" N VAL D 191 " --> pdb=" O GLU D 187 " (cutoff:3.500A) Processing helix chain 'D' and resid 195 through 206 removed outlier: 3.621A pdb=" N THR D 200 " --> pdb=" O PRO D 196 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N ILE D 201 " --> pdb=" O ASP D 197 " (cutoff:3.500A) Processing helix chain 'D' and resid 210 through 218 Processing helix chain 'E' and resid 16 through 31 removed outlier: 3.632A pdb=" N ALA E 31 " --> pdb=" O VAL E 27 " (cutoff:3.500A) Processing helix chain 'E' and resid 35 through 44 Processing helix chain 'E' and resid 48 through 58 Processing helix chain 'E' and resid 62 through 84 Processing helix chain 'E' and resid 100 through 105 Processing helix chain 'E' and resid 110 through 120 Processing helix chain 'E' and resid 125 through 145 removed outlier: 3.688A pdb=" N LYS E 140 " --> pdb=" O LEU E 136 " (cutoff:3.500A) Processing helix chain 'E' and resid 149 through 153 removed outlier: 3.537A pdb=" N ILE E 153 " --> pdb=" O ILE E 150 " (cutoff:3.500A) Processing helix chain 'E' and resid 160 through 173 Processing helix chain 'E' and resid 178 through 193 removed outlier: 3.790A pdb=" N TRP E 184 " --> pdb=" O GLU E 180 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N LEU E 190 " --> pdb=" O THR E 186 " (cutoff:3.500A) removed outlier: 4.938A pdb=" N VAL E 191 " --> pdb=" O GLU E 187 " (cutoff:3.500A) Processing helix chain 'E' and resid 195 through 206 removed outlier: 3.621A pdb=" N THR E 200 " --> pdb=" O PRO E 196 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N ILE E 201 " --> pdb=" O ASP E 197 " (cutoff:3.500A) Processing helix chain 'E' and resid 210 through 218 Processing helix chain 'F' and resid 16 through 31 removed outlier: 3.632A pdb=" N ALA F 31 " --> pdb=" O VAL F 27 " (cutoff:3.500A) Processing helix chain 'F' and resid 35 through 44 Processing helix chain 'F' and resid 48 through 58 Processing helix chain 'F' and resid 62 through 84 Processing helix chain 'F' and resid 100 through 105 Processing helix chain 'F' and resid 110 through 120 Processing helix chain 'F' and resid 125 through 145 removed outlier: 3.688A pdb=" N LYS F 140 " --> pdb=" O LEU F 136 " (cutoff:3.500A) Processing helix chain 'F' and resid 149 through 153 removed outlier: 3.538A pdb=" N ILE F 153 " --> pdb=" O ILE F 150 " (cutoff:3.500A) Processing helix chain 'F' and resid 160 through 173 Processing helix chain 'F' and resid 178 through 193 removed outlier: 3.790A pdb=" N TRP F 184 " --> pdb=" O GLU F 180 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N LEU F 190 " --> pdb=" O THR F 186 " (cutoff:3.500A) removed outlier: 4.938A pdb=" N VAL F 191 " --> pdb=" O GLU F 187 " (cutoff:3.500A) Processing helix chain 'F' and resid 195 through 206 removed outlier: 3.621A pdb=" N THR F 200 " --> pdb=" O PRO F 196 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N ILE F 201 " --> pdb=" O ASP F 197 " (cutoff:3.500A) Processing helix chain 'F' and resid 210 through 218 594 hydrogen bonds defined for protein. 1764 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.63 Time building geometry restraints manager: 1.27 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3210 1.34 - 1.46: 1875 1.46 - 1.58: 4653 1.58 - 1.69: 0 1.69 - 1.81: 144 Bond restraints: 9882 Sorted by residual: bond pdb=" CA ASN B 121 " pdb=" C ASN B 121 " ideal model delta sigma weight residual 1.520 1.526 -0.006 1.23e-02 6.61e+03 2.16e-01 bond pdb=" CA ASN E 121 " pdb=" C ASN E 121 " ideal model delta sigma weight residual 1.520 1.526 -0.006 1.23e-02 6.61e+03 2.16e-01 bond pdb=" CB VAL C 27 " pdb=" CG2 VAL C 27 " ideal model delta sigma weight residual 1.521 1.506 0.015 3.30e-02 9.18e+02 1.96e-01 bond pdb=" CB VAL F 27 " pdb=" CG2 VAL F 27 " ideal model delta sigma weight residual 1.521 1.506 0.015 3.30e-02 9.18e+02 1.96e-01 bond pdb=" CB VAL A 27 " pdb=" CG2 VAL A 27 " ideal model delta sigma weight residual 1.521 1.506 0.015 3.30e-02 9.18e+02 1.95e-01 ... (remaining 9877 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.94: 13034 0.94 - 1.88: 280 1.88 - 2.82: 21 2.82 - 3.75: 57 3.75 - 4.69: 6 Bond angle restraints: 13398 Sorted by residual: angle pdb=" C TRP F 117 " pdb=" N MET F 118 " pdb=" CA MET F 118 " ideal model delta sigma weight residual 122.38 120.24 2.14 1.81e+00 3.05e-01 1.40e+00 angle pdb=" C TRP C 117 " pdb=" N MET C 118 " pdb=" CA MET C 118 " ideal model delta sigma weight residual 122.38 120.24 2.14 1.81e+00 3.05e-01 1.40e+00 angle pdb=" C TRP E 117 " pdb=" N MET E 118 " pdb=" CA MET E 118 " ideal model delta sigma weight residual 122.38 120.27 2.11 1.81e+00 3.05e-01 1.36e+00 angle pdb=" C TRP B 117 " pdb=" N MET B 118 " pdb=" CA MET B 118 " ideal model delta sigma weight residual 122.38 120.27 2.11 1.81e+00 3.05e-01 1.36e+00 angle pdb=" C TRP D 117 " pdb=" N MET D 118 " pdb=" CA MET D 118 " ideal model delta sigma weight residual 122.38 120.28 2.10 1.81e+00 3.05e-01 1.35e+00 ... (remaining 13393 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.41: 5740 17.41 - 34.82: 254 34.82 - 52.22: 60 52.22 - 69.63: 6 69.63 - 87.04: 12 Dihedral angle restraints: 6072 sinusoidal: 2502 harmonic: 3570 Sorted by residual: dihedral pdb=" CB GLU F 45 " pdb=" CG GLU F 45 " pdb=" CD GLU F 45 " pdb=" OE1 GLU F 45 " ideal model delta sinusoidal sigma weight residual 0.00 -87.04 87.04 1 3.00e+01 1.11e-03 1.01e+01 dihedral pdb=" CB GLU C 45 " pdb=" CG GLU C 45 " pdb=" CD GLU C 45 " pdb=" OE1 GLU C 45 " ideal model delta sinusoidal sigma weight residual 0.00 -87.04 87.04 1 3.00e+01 1.11e-03 1.01e+01 dihedral pdb=" CB GLU A 45 " pdb=" CG GLU A 45 " pdb=" CD GLU A 45 " pdb=" OE1 GLU A 45 " ideal model delta sinusoidal sigma weight residual 0.00 -87.01 87.01 1 3.00e+01 1.11e-03 1.01e+01 ... (remaining 6069 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.024: 863 0.024 - 0.048: 352 0.048 - 0.072: 201 0.072 - 0.096: 54 0.096 - 0.120: 48 Chirality restraints: 1518 Sorted by residual: chirality pdb=" CA ILE C 124 " pdb=" N ILE C 124 " pdb=" C ILE C 124 " pdb=" CB ILE C 124 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.62e-01 chirality pdb=" CA ILE F 124 " pdb=" N ILE F 124 " pdb=" C ILE F 124 " pdb=" CB ILE F 124 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.62e-01 chirality pdb=" CA ILE A 124 " pdb=" N ILE A 124 " pdb=" C ILE A 124 " pdb=" CB ILE A 124 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.59e-01 ... (remaining 1515 not shown) Planarity restraints: 1722 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER B 33 " -0.022 5.00e-02 4.00e+02 3.39e-02 1.84e+00 pdb=" N PRO B 34 " 0.059 5.00e-02 4.00e+02 pdb=" CA PRO B 34 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO B 34 " -0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER E 33 " 0.022 5.00e-02 4.00e+02 3.39e-02 1.84e+00 pdb=" N PRO E 34 " -0.059 5.00e-02 4.00e+02 pdb=" CA PRO E 34 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO E 34 " 0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER D 33 " 0.022 5.00e-02 4.00e+02 3.38e-02 1.82e+00 pdb=" N PRO D 34 " -0.058 5.00e-02 4.00e+02 pdb=" CA PRO D 34 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO D 34 " 0.019 5.00e-02 4.00e+02 ... (remaining 1719 not shown) Histogram of nonbonded interaction distances: 0.55 - 1.42: 234 1.42 - 2.29: 1086 2.29 - 3.16: 10462 3.16 - 4.03: 28735 4.03 - 4.90: 51288 Warning: very small nonbonded interaction distances. Nonbonded interactions: 91805 Sorted by model distance: nonbonded pdb=" O THR A 54 " pdb=" O PRO F 38 " model vdw 0.551 3.040 nonbonded pdb=" O PRO C 38 " pdb=" O THR D 54 " model vdw 0.551 3.040 nonbonded pdb=" O PRO B 38 " pdb=" O THR C 54 " model vdw 0.552 3.040 nonbonded pdb=" O PRO E 38 " pdb=" O THR F 54 " model vdw 0.552 3.040 nonbonded pdb=" O PRO A 38 " pdb=" O THR B 54 " model vdw 0.552 3.040 ... (remaining 91800 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' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } 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: 2.380 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: 0.140 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 9.300 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1537 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 : 0.030 0.677 9930 Z= 2.983 Angle : 0.404 4.692 13398 Z= 0.205 Chirality : 0.038 0.120 1518 Planarity : 0.004 0.034 1722 Dihedral : 11.148 87.039 3744 Min Nonbonded Distance : 0.551 Molprobity Statistics. All-atom Clashscore : 93.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.50 % Favored : 99.50 % Rotamer: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.05 (0.23), residues: 1200 helix: 0.77 (0.18), residues: 864 sheet: None (None), residues: 0 loop : 0.89 (0.29), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG E 154 TYR 0.003 0.001 TYR E 169 PHE 0.005 0.001 PHE F 40 TRP 0.003 0.001 TRP E 23 HIS 0.001 0.000 HIS C 62 Details of bonding type rmsd covalent geometry : bond 0.00173 ( 9882) covalent geometry : angle 0.40422 (13398) hydrogen bonds : bond 0.21645 ( 594) hydrogen bonds : angle 5.64234 ( 1764) Misc. bond : bond 0.42895 ( 48) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 106 time to evaluate : 0.276 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 MET cc_start: 0.5708 (ptp) cc_final: 0.4638 (mmt) REVERT: A 124 ILE cc_start: 0.7050 (mt) cc_final: 0.6824 (tp) REVERT: B 185 MET cc_start: 0.0616 (mtt) cc_final: 0.0244 (ppp) REVERT: B 214 MET cc_start: 0.2105 (mtp) cc_final: 0.1502 (mtp) REVERT: E 10 MET cc_start: -0.0359 (ptp) cc_final: -0.0586 (mpt) REVERT: E 214 MET cc_start: -0.0911 (mtp) cc_final: -0.1210 (mtp) outliers start: 0 outliers final: 0 residues processed: 106 average time/residue: 0.5658 time to fit residues: 64.2459 Evaluate side-chains 93 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 93 time to evaluate : 0.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 108 optimal weight: 0.6980 chunk 49 optimal weight: 8.9990 chunk 97 optimal weight: 0.8980 chunk 113 optimal weight: 1.9990 chunk 53 optimal weight: 10.0000 chunk 5 optimal weight: 4.9990 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 8.9990 chunk 62 optimal weight: 0.9980 chunk 51 optimal weight: 0.5980 chunk 117 optimal weight: 1.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 50 GLN A 192 GLN ** B 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 50 GLN B 84 HIS B 192 GLN ** C 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 192 GLN ** D 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 192 GLN ** E 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 50 GLN E 62 HIS E 192 GLN ** F 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 50 GLN F 179 GLN F 192 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5423 r_free = 0.5423 target = 0.358583 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.5327 r_free = 0.5327 target = 0.344243 restraints weight = 12632.588| |-----------------------------------------------------------------------------| r_work (start): 0.5294 rms_B_bonded: 1.91 r_work: 0.5227 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work (final): 0.5227 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2081 moved from start: 0.4080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.014 0.284 9930 Z= 0.586 Angle : 1.637 24.820 13398 Z= 0.915 Chirality : 0.103 0.697 1518 Planarity : 0.015 0.176 1722 Dihedral : 7.974 39.406 1302 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 63.33 Ramachandran Plot: Outliers : 2.00 % Allowed : 3.75 % Favored : 94.25 % Rotamer: Outliers : 6.74 % Allowed : 8.05 % Favored : 85.21 % Cbeta Deviations : 0.86 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 1.75 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.04 (0.22), residues: 1200 helix: -0.59 (0.17), residues: 876 sheet: None (None), residues: 0 loop : -0.46 (0.30), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.042 0.003 ARG E 18 TYR 0.022 0.003 TYR E 169 PHE 0.019 0.003 PHE F 161 TRP 0.014 0.002 TRP D 23 HIS 0.006 0.002 HIS D 62 Details of bonding type rmsd covalent geometry : bond 0.01386 ( 9882) covalent geometry : angle 1.63696 (13398) hydrogen bonds : bond 0.21221 ( 594) hydrogen bonds : angle 7.06192 ( 1764) Misc. bond : bond 0.01673 ( 48) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 96 time to evaluate : 0.311 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 MET cc_start: 0.5001 (ptp) cc_final: 0.4646 (tpt) REVERT: A 59 VAL cc_start: 0.6383 (t) cc_final: 0.6083 (t) REVERT: B 144 MET cc_start: 0.0636 (ptm) cc_final: 0.0198 (ptm) REVERT: B 185 MET cc_start: 0.0773 (mtt) cc_final: -0.1109 (ppp) REVERT: B 214 MET cc_start: 0.2569 (mtp) cc_final: 0.1404 (mtp) REVERT: C 57 ASN cc_start: -0.2711 (OUTLIER) cc_final: -0.3069 (m-40) REVERT: C 185 MET cc_start: 0.2566 (OUTLIER) cc_final: 0.2038 (tmm) REVERT: F 19 THR cc_start: 0.2074 (OUTLIER) cc_final: 0.1727 (m) outliers start: 72 outliers final: 29 residues processed: 144 average time/residue: 0.5104 time to fit residues: 79.1674 Evaluate side-chains 123 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 91 time to evaluate : 0.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 ARG Chi-restraints excluded: chain A residue 19 THR Chi-restraints excluded: chain A residue 35 GLU Chi-restraints excluded: chain A residue 66 MET Chi-restraints excluded: chain A residue 148 SER Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 216 THR Chi-restraints excluded: chain B residue 18 ARG Chi-restraints excluded: chain B residue 19 THR Chi-restraints excluded: chain B residue 35 GLU Chi-restraints excluded: chain B residue 66 MET Chi-restraints excluded: chain B residue 149 SER Chi-restraints excluded: chain C residue 18 ARG Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 38 PRO Chi-restraints excluded: chain C residue 57 ASN Chi-restraints excluded: chain C residue 66 MET Chi-restraints excluded: chain C residue 68 MET Chi-restraints excluded: chain C residue 185 MET Chi-restraints excluded: chain D residue 66 MET Chi-restraints excluded: chain E residue 16 SER Chi-restraints excluded: chain E residue 18 ARG Chi-restraints excluded: chain E residue 37 ILE Chi-restraints excluded: chain E residue 39 MET Chi-restraints excluded: chain E residue 66 MET Chi-restraints excluded: chain E residue 190 LEU Chi-restraints excluded: chain F residue 18 ARG Chi-restraints excluded: chain F residue 19 THR Chi-restraints excluded: chain F residue 35 GLU Chi-restraints excluded: chain F residue 37 ILE Chi-restraints excluded: chain F residue 66 MET Chi-restraints excluded: chain F residue 144 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 30 optimal weight: 0.7980 chunk 58 optimal weight: 1.9990 chunk 87 optimal weight: 0.9990 chunk 85 optimal weight: 0.9990 chunk 118 optimal weight: 2.9990 chunk 106 optimal weight: 0.6980 chunk 61 optimal weight: 0.9990 chunk 37 optimal weight: 1.9990 chunk 112 optimal weight: 0.6980 chunk 16 optimal weight: 3.9990 chunk 49 optimal weight: 0.8980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 12 HIS ** B 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 62 HIS B 112 GLN ** C 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 50 GLN ** D 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 57 ASN ** F 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5433 r_free = 0.5433 target = 0.359324 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.5334 r_free = 0.5334 target = 0.344615 restraints weight = 12734.408| |-----------------------------------------------------------------------------| r_work (start): 0.5308 rms_B_bonded: 1.96 r_work: 0.5237 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work (final): 0.5237 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2224 moved from start: 0.5655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.249 9930 Z= 0.498 Angle : 1.587 28.031 13398 Z= 0.866 Chirality : 0.082 0.744 1518 Planarity : 0.014 0.152 1722 Dihedral : 9.317 64.718 1302 Min Nonbonded Distance : 1.730 Molprobity Statistics. All-atom Clashscore : 52.06 Ramachandran Plot: Outliers : 1.25 % Allowed : 5.83 % Favored : 92.92 % Rotamer: Outliers : 5.34 % Allowed : 10.86 % Favored : 83.80 % Cbeta Deviations : 0.86 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.28 % Twisted General : 1.67 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.31 (0.23), residues: 1200 helix: -0.70 (0.17), residues: 846 sheet: None (None), residues: 0 loop : -0.90 (0.30), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.026 0.002 ARG B 18 TYR 0.020 0.003 TYR E 169 PHE 0.028 0.004 PHE B 168 TRP 0.040 0.003 TRP E 23 HIS 0.007 0.002 HIS F 62 Details of bonding type rmsd covalent geometry : bond 0.01169 ( 9882) covalent geometry : angle 1.58717 (13398) hydrogen bonds : bond 0.13682 ( 594) hydrogen bonds : angle 6.50796 ( 1764) Misc. bond : bond 0.01897 ( 48) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 99 time to evaluate : 0.239 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 MET cc_start: 0.4935 (ptp) cc_final: 0.4641 (tpt) REVERT: A 183 ASN cc_start: 0.7322 (m-40) cc_final: 0.7118 (m110) REVERT: B 214 MET cc_start: 0.2595 (mtp) cc_final: 0.2335 (mtp) REVERT: B 215 MET cc_start: 0.2705 (ppp) cc_final: 0.2032 (ppp) REVERT: C 10 MET cc_start: 0.1246 (mpt) cc_final: 0.0255 (ttp) REVERT: C 214 MET cc_start: -0.0440 (tpp) cc_final: -0.0837 (tpt) REVERT: F 18 ARG cc_start: 0.0064 (OUTLIER) cc_final: -0.0415 (mtt180) REVERT: F 19 THR cc_start: 0.2154 (OUTLIER) cc_final: 0.1811 (m) outliers start: 57 outliers final: 37 residues processed: 138 average time/residue: 0.5110 time to fit residues: 75.9898 Evaluate side-chains 132 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 93 time to evaluate : 0.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 ARG Chi-restraints excluded: chain A residue 19 THR Chi-restraints excluded: chain A residue 21 ASN Chi-restraints excluded: chain A residue 35 GLU Chi-restraints excluded: chain A residue 39 MET Chi-restraints excluded: chain A residue 66 MET Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 148 SER Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain B residue 18 ARG Chi-restraints excluded: chain B residue 21 ASN Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 35 GLU Chi-restraints excluded: chain B residue 39 MET Chi-restraints excluded: chain B residue 66 MET Chi-restraints excluded: chain C residue 21 ASN Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 37 ILE Chi-restraints excluded: chain C residue 66 MET Chi-restraints excluded: chain C residue 68 MET Chi-restraints excluded: chain C residue 185 MET Chi-restraints excluded: chain D residue 10 MET Chi-restraints excluded: chain D residue 18 ARG Chi-restraints excluded: chain D residue 37 ILE Chi-restraints excluded: chain D residue 66 MET Chi-restraints excluded: chain D residue 132 ARG Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain E residue 21 ASN Chi-restraints excluded: chain E residue 24 VAL Chi-restraints excluded: chain E residue 35 GLU Chi-restraints excluded: chain E residue 66 MET Chi-restraints excluded: chain F residue 16 SER Chi-restraints excluded: chain F residue 18 ARG Chi-restraints excluded: chain F residue 19 THR Chi-restraints excluded: chain F residue 21 ASN Chi-restraints excluded: chain F residue 35 GLU Chi-restraints excluded: chain F residue 37 ILE Chi-restraints excluded: chain F residue 66 MET Chi-restraints excluded: chain F residue 144 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 56 optimal weight: 0.9990 chunk 97 optimal weight: 0.0770 chunk 32 optimal weight: 0.2980 chunk 95 optimal weight: 0.9990 chunk 13 optimal weight: 2.9990 chunk 35 optimal weight: 0.0980 chunk 20 optimal weight: 2.9990 chunk 17 optimal weight: 0.9990 chunk 47 optimal weight: 0.5980 chunk 88 optimal weight: 0.8980 chunk 49 optimal weight: 6.9990 overall best weight: 0.3938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 62 HIS ** B 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 12 HIS ** D 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5435 r_free = 0.5435 target = 0.359865 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.5346 r_free = 0.5346 target = 0.345986 restraints weight = 12633.824| |-----------------------------------------------------------------------------| r_work (start): 0.5354 rms_B_bonded: 1.96 r_work: 0.5274 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.5274 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2216 moved from start: 0.6124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.259 9930 Z= 0.443 Angle : 1.510 25.216 13398 Z= 0.813 Chirality : 0.077 0.867 1518 Planarity : 0.012 0.129 1722 Dihedral : 9.175 66.143 1302 Min Nonbonded Distance : 1.703 Molprobity Statistics. All-atom Clashscore : 45.45 Ramachandran Plot: Outliers : 1.00 % Allowed : 6.17 % Favored : 92.83 % Rotamer: Outliers : 5.52 % Allowed : 12.27 % Favored : 82.21 % Cbeta Deviations : 0.95 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 1.67 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.05 (0.23), residues: 1200 helix: -0.48 (0.18), residues: 846 sheet: None (None), residues: 0 loop : -0.85 (0.30), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.050 0.001 ARG D 18 TYR 0.016 0.002 TYR E 169 PHE 0.021 0.003 PHE B 168 TRP 0.034 0.002 TRP E 23 HIS 0.003 0.001 HIS D 62 Details of bonding type rmsd covalent geometry : bond 0.01036 ( 9882) covalent geometry : angle 1.50980 (13398) hydrogen bonds : bond 0.13033 ( 594) hydrogen bonds : angle 6.44724 ( 1764) Misc. bond : bond 0.01759 ( 48) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 91 time to evaluate : 0.230 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 214 MET cc_start: 0.2391 (mtp) cc_final: 0.1116 (mtp) REVERT: B 215 MET cc_start: 0.2773 (ppp) cc_final: 0.1977 (ppp) REVERT: C 10 MET cc_start: 0.1445 (mpt) cc_final: 0.0476 (ttp) REVERT: C 19 THR cc_start: 0.1341 (OUTLIER) cc_final: 0.1095 (t) REVERT: D 19 THR cc_start: 0.1618 (OUTLIER) cc_final: 0.1381 (m) REVERT: D 118 MET cc_start: 0.4475 (mmt) cc_final: 0.2991 (mpt) REVERT: E 21 ASN cc_start: 0.1254 (OUTLIER) cc_final: -0.0478 (t0) REVERT: F 19 THR cc_start: 0.1903 (OUTLIER) cc_final: 0.1288 (m) REVERT: F 21 ASN cc_start: 0.0486 (OUTLIER) cc_final: 0.0152 (m-40) REVERT: F 185 MET cc_start: 0.0851 (mtt) cc_final: 0.0245 (ptp) outliers start: 59 outliers final: 38 residues processed: 135 average time/residue: 0.4880 time to fit residues: 71.1065 Evaluate side-chains 132 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 89 time to evaluate : 0.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 ARG Chi-restraints excluded: chain A residue 19 THR Chi-restraints excluded: chain A residue 30 LYS Chi-restraints excluded: chain A residue 35 GLU Chi-restraints excluded: chain A residue 66 MET Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 148 SER Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain B residue 21 ASN Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 35 GLU Chi-restraints excluded: chain B residue 39 MET Chi-restraints excluded: chain B residue 66 MET Chi-restraints excluded: chain B residue 135 ILE Chi-restraints excluded: chain C residue 18 ARG Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 21 ASN Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 37 ILE Chi-restraints excluded: chain C residue 66 MET Chi-restraints excluded: chain C residue 68 MET Chi-restraints excluded: chain C residue 185 MET Chi-restraints excluded: chain D residue 10 MET Chi-restraints excluded: chain D residue 19 THR Chi-restraints excluded: chain D residue 37 ILE Chi-restraints excluded: chain D residue 56 LEU Chi-restraints excluded: chain D residue 66 MET Chi-restraints excluded: chain D residue 132 ARG Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain E residue 21 ASN Chi-restraints excluded: chain E residue 24 VAL Chi-restraints excluded: chain E residue 35 GLU Chi-restraints excluded: chain E residue 66 MET Chi-restraints excluded: chain F residue 16 SER Chi-restraints excluded: chain F residue 19 THR Chi-restraints excluded: chain F residue 21 ASN Chi-restraints excluded: chain F residue 27 VAL Chi-restraints excluded: chain F residue 35 GLU Chi-restraints excluded: chain F residue 62 HIS Chi-restraints excluded: chain F residue 66 MET Chi-restraints excluded: chain F residue 118 MET Chi-restraints excluded: chain F residue 144 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 68 optimal weight: 0.9990 chunk 66 optimal weight: 0.0870 chunk 94 optimal weight: 5.9990 chunk 79 optimal weight: 0.7980 chunk 62 optimal weight: 8.9990 chunk 115 optimal weight: 0.6980 chunk 97 optimal weight: 0.1980 chunk 13 optimal weight: 2.9990 chunk 67 optimal weight: 0.9990 chunk 33 optimal weight: 0.5980 chunk 118 optimal weight: 2.9990 overall best weight: 0.4758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 12 HIS ** D 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 57 ASN ** F 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5451 r_free = 0.5451 target = 0.361361 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.5368 r_free = 0.5368 target = 0.347749 restraints weight = 12677.983| |-----------------------------------------------------------------------------| r_work (start): 0.5341 rms_B_bonded: 1.89 r_work: 0.5237 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.5237 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2350 moved from start: 0.6703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.261 9930 Z= 0.423 Angle : 1.466 24.424 13398 Z= 0.789 Chirality : 0.075 0.722 1518 Planarity : 0.011 0.123 1722 Dihedral : 9.160 67.709 1302 Min Nonbonded Distance : 1.694 Molprobity Statistics. All-atom Clashscore : 44.06 Ramachandran Plot: Outliers : 0.92 % Allowed : 6.33 % Favored : 92.75 % Rotamer: Outliers : 6.65 % Allowed : 12.08 % Favored : 81.27 % Cbeta Deviations : 0.86 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 1.58 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.00 (0.24), residues: 1200 helix: -0.46 (0.18), residues: 846 sheet: None (None), residues: 0 loop : -0.76 (0.30), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.032 0.001 ARG D 18 TYR 0.018 0.002 TYR E 169 PHE 0.026 0.003 PHE C 32 TRP 0.027 0.002 TRP E 23 HIS 0.005 0.001 HIS F 62 Details of bonding type rmsd covalent geometry : bond 0.00971 ( 9882) covalent geometry : angle 1.46586 (13398) hydrogen bonds : bond 0.12666 ( 594) hydrogen bonds : angle 6.50576 ( 1764) Misc. bond : bond 0.01674 ( 48) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 97 time to evaluate : 0.359 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 161 PHE cc_start: 0.3888 (p90) cc_final: 0.0480 (t80) REVERT: B 214 MET cc_start: 0.2265 (mtp) cc_final: 0.1779 (mtp) REVERT: C 10 MET cc_start: 0.1684 (mpt) cc_final: 0.0790 (ttt) REVERT: C 96 MET cc_start: 0.2891 (pp-130) cc_final: 0.2640 (tmm) REVERT: D 118 MET cc_start: 0.4384 (mmt) cc_final: 0.3013 (mpt) REVERT: E 55 MET cc_start: 0.2131 (mtt) cc_final: 0.0386 (tmt) REVERT: E 80 TRP cc_start: 0.2715 (m-90) cc_final: 0.2473 (m-90) REVERT: F 19 THR cc_start: 0.1691 (OUTLIER) cc_final: 0.1393 (m) REVERT: F 62 HIS cc_start: 0.0936 (OUTLIER) cc_final: 0.0144 (m-70) REVERT: F 185 MET cc_start: 0.0891 (mtt) cc_final: 0.0276 (ptp) outliers start: 71 outliers final: 45 residues processed: 149 average time/residue: 0.4526 time to fit residues: 73.1894 Evaluate side-chains 141 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 94 time to evaluate : 0.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 ARG Chi-restraints excluded: chain A residue 19 THR Chi-restraints excluded: chain A residue 30 LYS Chi-restraints excluded: chain A residue 35 GLU Chi-restraints excluded: chain A residue 66 MET Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 148 SER Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain B residue 19 THR Chi-restraints excluded: chain B residue 21 ASN Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 35 GLU Chi-restraints excluded: chain B residue 39 MET Chi-restraints excluded: chain B residue 66 MET Chi-restraints excluded: chain B residue 135 ILE Chi-restraints excluded: chain C residue 18 ARG Chi-restraints excluded: chain C residue 21 ASN Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 35 GLU Chi-restraints excluded: chain C residue 66 MET Chi-restraints excluded: chain C residue 68 MET Chi-restraints excluded: chain C residue 144 MET Chi-restraints excluded: chain C residue 165 VAL Chi-restraints excluded: chain C residue 185 MET Chi-restraints excluded: chain D residue 10 MET Chi-restraints excluded: chain D residue 27 VAL Chi-restraints excluded: chain D residue 56 LEU Chi-restraints excluded: chain D residue 66 MET Chi-restraints excluded: chain D residue 132 ARG Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain E residue 18 ARG Chi-restraints excluded: chain E residue 24 VAL Chi-restraints excluded: chain E residue 35 GLU Chi-restraints excluded: chain E residue 66 MET Chi-restraints excluded: chain E residue 75 GLU Chi-restraints excluded: chain E residue 172 LEU Chi-restraints excluded: chain F residue 19 THR Chi-restraints excluded: chain F residue 21 ASN Chi-restraints excluded: chain F residue 27 VAL Chi-restraints excluded: chain F residue 35 GLU Chi-restraints excluded: chain F residue 43 LEU Chi-restraints excluded: chain F residue 62 HIS Chi-restraints excluded: chain F residue 66 MET Chi-restraints excluded: chain F residue 118 MET Chi-restraints excluded: chain F residue 144 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 77 optimal weight: 0.4980 chunk 116 optimal weight: 2.9990 chunk 55 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 14 optimal weight: 2.9990 chunk 15 optimal weight: 0.5980 chunk 38 optimal weight: 0.9980 chunk 47 optimal weight: 0.6980 chunk 103 optimal weight: 0.5980 chunk 45 optimal weight: 0.8980 chunk 1 optimal weight: 4.9990 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 183 ASN ** B 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 57 ASN D 193 ASN ** E 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 179 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5442 r_free = 0.5442 target = 0.359622 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.5358 r_free = 0.5358 target = 0.345930 restraints weight = 12470.361| |-----------------------------------------------------------------------------| r_work (start): 0.5330 rms_B_bonded: 1.86 r_work: 0.5229 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.5229 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2440 moved from start: 0.7229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.284 9930 Z= 0.432 Angle : 1.467 24.230 13398 Z= 0.793 Chirality : 0.076 0.797 1518 Planarity : 0.012 0.133 1722 Dihedral : 9.073 72.219 1302 Min Nonbonded Distance : 1.686 Molprobity Statistics. All-atom Clashscore : 43.54 Ramachandran Plot: Outliers : 0.92 % Allowed : 5.50 % Favored : 93.58 % Rotamer: Outliers : 5.52 % Allowed : 13.01 % Favored : 81.46 % Cbeta Deviations : 0.69 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.28 % Twisted General : 1.49 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.21 (0.23), residues: 1200 helix: -0.61 (0.18), residues: 846 sheet: None (None), residues: 0 loop : -0.88 (0.30), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG A 18 TYR 0.023 0.003 TYR E 169 PHE 0.017 0.003 PHE F 40 TRP 0.029 0.002 TRP D 23 HIS 0.005 0.001 HIS D 62 Details of bonding type rmsd covalent geometry : bond 0.00992 ( 9882) covalent geometry : angle 1.46689 (13398) hydrogen bonds : bond 0.12632 ( 594) hydrogen bonds : angle 6.69843 ( 1764) Misc. bond : bond 0.01657 ( 48) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 94 time to evaluate : 0.276 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 161 PHE cc_start: 0.4001 (p90) cc_final: 0.0483 (t80) REVERT: B 214 MET cc_start: 0.3057 (mtp) cc_final: 0.2643 (mtp) REVERT: C 10 MET cc_start: 0.1857 (mpt) cc_final: 0.1009 (ttt) REVERT: C 96 MET cc_start: 0.3079 (pp-130) cc_final: 0.2743 (tmm) REVERT: D 96 MET cc_start: -0.0922 (mmt) cc_final: -0.1133 (mtp) REVERT: D 118 MET cc_start: 0.4107 (mmt) cc_final: 0.2989 (mpt) REVERT: D 151 LEU cc_start: 0.2012 (mt) cc_final: 0.1535 (mp) REVERT: E 55 MET cc_start: 0.2318 (mtt) cc_final: 0.0811 (tmt) REVERT: E 80 TRP cc_start: 0.3088 (m-90) cc_final: 0.2793 (m-90) REVERT: F 19 THR cc_start: 0.2136 (OUTLIER) cc_final: 0.1607 (m) REVERT: F 21 ASN cc_start: 0.0648 (OUTLIER) cc_final: 0.0165 (m-40) REVERT: F 185 MET cc_start: 0.0677 (mtt) cc_final: 0.0131 (ptp) outliers start: 59 outliers final: 38 residues processed: 137 average time/residue: 0.5006 time to fit residues: 73.7688 Evaluate side-chains 133 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 93 time to evaluate : 0.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 ARG Chi-restraints excluded: chain A residue 19 THR Chi-restraints excluded: chain A residue 30 LYS Chi-restraints excluded: chain A residue 35 GLU Chi-restraints excluded: chain A residue 66 MET Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 148 SER Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain B residue 19 THR Chi-restraints excluded: chain B residue 21 ASN Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 35 GLU Chi-restraints excluded: chain B residue 39 MET Chi-restraints excluded: chain B residue 62 HIS Chi-restraints excluded: chain B residue 66 MET Chi-restraints excluded: chain C residue 18 ARG Chi-restraints excluded: chain C residue 21 ASN Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 66 MET Chi-restraints excluded: chain C residue 68 MET Chi-restraints excluded: chain C residue 144 MET Chi-restraints excluded: chain C residue 185 MET Chi-restraints excluded: chain D residue 27 VAL Chi-restraints excluded: chain D residue 66 MET Chi-restraints excluded: chain D residue 132 ARG Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain E residue 18 ARG Chi-restraints excluded: chain E residue 24 VAL Chi-restraints excluded: chain E residue 66 MET Chi-restraints excluded: chain E residue 75 GLU Chi-restraints excluded: chain E residue 172 LEU Chi-restraints excluded: chain F residue 19 THR Chi-restraints excluded: chain F residue 21 ASN Chi-restraints excluded: chain F residue 27 VAL Chi-restraints excluded: chain F residue 35 GLU Chi-restraints excluded: chain F residue 43 LEU Chi-restraints excluded: chain F residue 66 MET Chi-restraints excluded: chain F residue 144 MET Chi-restraints excluded: chain F residue 214 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 79 optimal weight: 1.9990 chunk 1 optimal weight: 4.9990 chunk 32 optimal weight: 0.5980 chunk 106 optimal weight: 0.3980 chunk 40 optimal weight: 7.9990 chunk 107 optimal weight: 0.9980 chunk 18 optimal weight: 0.9980 chunk 52 optimal weight: 0.2980 chunk 116 optimal weight: 0.2980 chunk 91 optimal weight: 0.0670 chunk 30 optimal weight: 1.9990 overall best weight: 0.3318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 12 HIS C 57 ASN ** E 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5452 r_free = 0.5452 target = 0.361176 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.5375 r_free = 0.5375 target = 0.348299 restraints weight = 12410.064| |-----------------------------------------------------------------------------| r_work (start): 0.5346 rms_B_bonded: 1.85 r_work: 0.5247 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.5247 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2338 moved from start: 0.7494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.245 9930 Z= 0.416 Angle : 1.504 50.413 13398 Z= 0.789 Chirality : 0.080 0.938 1518 Planarity : 0.011 0.121 1722 Dihedral : 8.997 67.727 1302 Min Nonbonded Distance : 1.717 Molprobity Statistics. All-atom Clashscore : 42.67 Ramachandran Plot: Outliers : 0.83 % Allowed : 5.58 % Favored : 93.58 % Rotamer: Outliers : 5.34 % Allowed : 14.23 % Favored : 80.43 % Cbeta Deviations : 0.77 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.28 % Twisted General : 1.40 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.13 (0.23), residues: 1200 helix: -0.53 (0.18), residues: 834 sheet: None (None), residues: 0 loop : -0.90 (0.30), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.027 0.001 ARG A 18 TYR 0.019 0.002 TYR E 169 PHE 0.021 0.003 PHE B 40 TRP 0.025 0.002 TRP D 23 HIS 0.007 0.001 HIS D 62 Details of bonding type rmsd covalent geometry : bond 0.00966 ( 9882) covalent geometry : angle 1.50361 (13398) hydrogen bonds : bond 0.12485 ( 594) hydrogen bonds : angle 6.75507 ( 1764) Misc. bond : bond 0.01705 ( 48) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 92 time to evaluate : 0.300 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 LEU cc_start: 0.5845 (OUTLIER) cc_final: 0.5645 (mm) REVERT: B 39 MET cc_start: -0.1050 (OUTLIER) cc_final: -0.2887 (mpt) REVERT: B 144 MET cc_start: 0.0530 (ptm) cc_final: -0.0792 (ptp) REVERT: B 161 PHE cc_start: 0.3871 (p90) cc_final: 0.0382 (t80) REVERT: B 214 MET cc_start: 0.2819 (mtp) cc_final: 0.1882 (mtp) REVERT: C 10 MET cc_start: 0.1956 (mpt) cc_final: 0.1046 (ttt) REVERT: C 19 THR cc_start: 0.1232 (OUTLIER) cc_final: 0.0993 (t) REVERT: C 24 VAL cc_start: -0.3083 (OUTLIER) cc_final: -0.3295 (t) REVERT: C 96 MET cc_start: 0.3173 (pp-130) cc_final: 0.2781 (tmm) REVERT: D 96 MET cc_start: -0.1021 (mmt) cc_final: -0.1293 (mtp) REVERT: D 118 MET cc_start: 0.4255 (mmt) cc_final: 0.2996 (mpt) REVERT: D 190 LEU cc_start: -0.2254 (OUTLIER) cc_final: -0.2487 (tt) REVERT: E 55 MET cc_start: 0.2092 (mtt) cc_final: 0.0779 (tmt) REVERT: E 80 TRP cc_start: 0.3095 (m-90) cc_final: 0.2814 (m-90) REVERT: F 21 ASN cc_start: 0.0606 (OUTLIER) cc_final: 0.0277 (m110) REVERT: F 185 MET cc_start: 0.1098 (mtt) cc_final: 0.0571 (ptp) REVERT: F 214 MET cc_start: -0.1540 (ptt) cc_final: -0.1979 (ptt) outliers start: 57 outliers final: 39 residues processed: 134 average time/residue: 0.4751 time to fit residues: 68.8688 Evaluate side-chains 135 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 90 time to evaluate : 0.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 THR Chi-restraints excluded: chain A residue 35 GLU Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 66 MET Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 148 SER Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain B residue 21 ASN Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 35 GLU Chi-restraints excluded: chain B residue 39 MET Chi-restraints excluded: chain B residue 55 MET Chi-restraints excluded: chain B residue 62 HIS Chi-restraints excluded: chain B residue 66 MET Chi-restraints excluded: chain B residue 142 VAL Chi-restraints excluded: chain C residue 18 ARG Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 21 ASN Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 35 GLU Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain C residue 66 MET Chi-restraints excluded: chain C residue 68 MET Chi-restraints excluded: chain C residue 144 MET Chi-restraints excluded: chain C residue 165 VAL Chi-restraints excluded: chain C residue 185 MET Chi-restraints excluded: chain D residue 39 MET Chi-restraints excluded: chain D residue 66 MET Chi-restraints excluded: chain D residue 132 ARG Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain D residue 190 LEU Chi-restraints excluded: chain E residue 18 ARG Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 27 VAL Chi-restraints excluded: chain E residue 66 MET Chi-restraints excluded: chain E residue 75 GLU Chi-restraints excluded: chain E residue 172 LEU Chi-restraints excluded: chain F residue 19 THR Chi-restraints excluded: chain F residue 21 ASN Chi-restraints excluded: chain F residue 27 VAL Chi-restraints excluded: chain F residue 35 GLU Chi-restraints excluded: chain F residue 43 LEU Chi-restraints excluded: chain F residue 66 MET Chi-restraints excluded: chain F residue 144 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 92 optimal weight: 0.7980 chunk 44 optimal weight: 0.9980 chunk 5 optimal weight: 0.8980 chunk 61 optimal weight: 0.6980 chunk 28 optimal weight: 0.0470 chunk 25 optimal weight: 0.6980 chunk 40 optimal weight: 1.9990 chunk 37 optimal weight: 0.4980 chunk 96 optimal weight: 0.9990 chunk 20 optimal weight: 0.0570 chunk 52 optimal weight: 0.1980 overall best weight: 0.2996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 62 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5462 r_free = 0.5462 target = 0.362402 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.5389 r_free = 0.5389 target = 0.349998 restraints weight = 12396.333| |-----------------------------------------------------------------------------| r_work (start): 0.5355 rms_B_bonded: 1.80 r_work: 0.5260 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.5260 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2324 moved from start: 0.7811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.253 9930 Z= 0.413 Angle : 1.506 49.397 13398 Z= 0.787 Chirality : 0.076 0.728 1518 Planarity : 0.011 0.137 1722 Dihedral : 8.975 66.276 1302 Min Nonbonded Distance : 1.691 Molprobity Statistics. All-atom Clashscore : 40.70 Ramachandran Plot: Outliers : 0.83 % Allowed : 6.00 % Favored : 93.17 % Rotamer: Outliers : 5.06 % Allowed : 14.51 % Favored : 80.43 % Cbeta Deviations : 0.77 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.28 % Twisted General : 1.58 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.14 (0.23), residues: 1200 helix: -0.57 (0.18), residues: 846 sheet: None (None), residues: 0 loop : -0.82 (0.30), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.030 0.001 ARG A 18 TYR 0.018 0.002 TYR E 169 PHE 0.018 0.003 PHE B 40 TRP 0.025 0.002 TRP F 23 HIS 0.009 0.001 HIS B 62 Details of bonding type rmsd covalent geometry : bond 0.00956 ( 9882) covalent geometry : angle 1.50629 (13398) hydrogen bonds : bond 0.12257 ( 594) hydrogen bonds : angle 6.77994 ( 1764) Misc. bond : bond 0.01708 ( 48) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 92 time to evaluate : 0.354 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 21 ASN cc_start: 0.4188 (OUTLIER) cc_final: 0.3665 (t0) REVERT: B 39 MET cc_start: -0.0824 (OUTLIER) cc_final: -0.2785 (mpt) REVERT: B 144 MET cc_start: 0.0502 (ptm) cc_final: -0.1135 (ptp) REVERT: B 161 PHE cc_start: 0.4104 (p90) cc_final: 0.0589 (t80) REVERT: B 185 MET cc_start: 0.1398 (mtt) cc_final: -0.1286 (ppp) REVERT: B 214 MET cc_start: 0.2718 (mtp) cc_final: 0.1759 (mtp) REVERT: C 10 MET cc_start: 0.2061 (mpt) cc_final: 0.1117 (ttt) REVERT: C 19 THR cc_start: 0.1236 (OUTLIER) cc_final: 0.0915 (t) REVERT: C 24 VAL cc_start: -0.3305 (OUTLIER) cc_final: -0.3530 (t) REVERT: C 96 MET cc_start: 0.3210 (pp-130) cc_final: 0.2733 (tmm) REVERT: D 96 MET cc_start: -0.0845 (mmt) cc_final: -0.1144 (mtp) REVERT: D 118 MET cc_start: 0.4109 (mmt) cc_final: 0.2939 (mpt) REVERT: D 190 LEU cc_start: -0.2374 (OUTLIER) cc_final: -0.2595 (tt) REVERT: E 55 MET cc_start: 0.1494 (mtt) cc_final: 0.0719 (tmt) REVERT: E 80 TRP cc_start: 0.2969 (m-90) cc_final: 0.2704 (m-90) REVERT: F 185 MET cc_start: 0.1389 (mtt) cc_final: 0.0859 (ptp) REVERT: F 214 MET cc_start: -0.1651 (OUTLIER) cc_final: -0.2151 (ptt) outliers start: 54 outliers final: 39 residues processed: 129 average time/residue: 0.5400 time to fit residues: 75.2727 Evaluate side-chains 134 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 89 time to evaluate : 0.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 GLU Chi-restraints excluded: chain A residue 66 MET Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 148 SER Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain B residue 19 THR Chi-restraints excluded: chain B residue 21 ASN Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 35 GLU Chi-restraints excluded: chain B residue 39 MET Chi-restraints excluded: chain B residue 55 MET Chi-restraints excluded: chain B residue 62 HIS Chi-restraints excluded: chain B residue 66 MET Chi-restraints excluded: chain B residue 142 VAL Chi-restraints excluded: chain C residue 18 ARG Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 21 ASN Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 35 GLU Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain C residue 66 MET Chi-restraints excluded: chain C residue 68 MET Chi-restraints excluded: chain C residue 185 MET Chi-restraints excluded: chain D residue 10 MET Chi-restraints excluded: chain D residue 39 MET Chi-restraints excluded: chain D residue 59 VAL Chi-restraints excluded: chain D residue 66 MET Chi-restraints excluded: chain D residue 132 ARG Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain D residue 190 LEU Chi-restraints excluded: chain E residue 18 ARG Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 66 MET Chi-restraints excluded: chain E residue 75 GLU Chi-restraints excluded: chain E residue 172 LEU Chi-restraints excluded: chain E residue 190 LEU Chi-restraints excluded: chain F residue 19 THR Chi-restraints excluded: chain F residue 21 ASN Chi-restraints excluded: chain F residue 27 VAL Chi-restraints excluded: chain F residue 35 GLU Chi-restraints excluded: chain F residue 43 LEU Chi-restraints excluded: chain F residue 66 MET Chi-restraints excluded: chain F residue 144 MET Chi-restraints excluded: chain F residue 214 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 14 optimal weight: 0.5980 chunk 70 optimal weight: 2.9990 chunk 105 optimal weight: 0.8980 chunk 119 optimal weight: 0.0980 chunk 104 optimal weight: 0.7980 chunk 89 optimal weight: 0.2980 chunk 53 optimal weight: 6.9990 chunk 80 optimal weight: 6.9990 chunk 72 optimal weight: 0.8980 chunk 107 optimal weight: 2.9990 chunk 47 optimal weight: 1.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 62 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5452 r_free = 0.5452 target = 0.361187 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.5374 r_free = 0.5374 target = 0.348115 restraints weight = 12284.072| |-----------------------------------------------------------------------------| r_work (start): 0.5341 rms_B_bonded: 1.81 r_work: 0.5237 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.5237 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2424 moved from start: 0.8137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.242 9930 Z= 0.420 Angle : 1.524 50.420 13398 Z= 0.795 Chirality : 0.089 1.614 1518 Planarity : 0.011 0.114 1722 Dihedral : 8.926 64.868 1302 Min Nonbonded Distance : 1.696 Molprobity Statistics. All-atom Clashscore : 40.44 Ramachandran Plot: Outliers : 0.83 % Allowed : 6.08 % Favored : 93.08 % Rotamer: Outliers : 5.34 % Allowed : 14.70 % Favored : 79.96 % Cbeta Deviations : 0.77 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.28 % Twisted General : 1.49 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.24 (0.23), residues: 1200 helix: -0.63 (0.18), residues: 846 sheet: None (None), residues: 0 loop : -0.88 (0.31), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG A 18 TYR 0.021 0.002 TYR E 169 PHE 0.019 0.003 PHE F 40 TRP 0.029 0.002 TRP F 23 HIS 0.005 0.001 HIS E 62 Details of bonding type rmsd covalent geometry : bond 0.00982 ( 9882) covalent geometry : angle 1.52375 (13398) hydrogen bonds : bond 0.12354 ( 594) hydrogen bonds : angle 6.87407 ( 1764) Misc. bond : bond 0.01685 ( 48) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 90 time to evaluate : 0.365 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 MET cc_start: 0.5241 (mmm) cc_final: 0.3952 (mmm) REVERT: B 21 ASN cc_start: 0.4107 (OUTLIER) cc_final: 0.3624 (t0) REVERT: B 39 MET cc_start: -0.0909 (OUTLIER) cc_final: -0.2128 (tpp) REVERT: B 96 MET cc_start: 0.2601 (tpp) cc_final: 0.1676 (tpp) REVERT: B 214 MET cc_start: 0.3032 (mtp) cc_final: 0.1914 (mtp) REVERT: C 10 MET cc_start: 0.2142 (mpt) cc_final: 0.1186 (ttt) REVERT: C 96 MET cc_start: 0.3273 (pp-130) cc_final: 0.2730 (tmm) REVERT: D 96 MET cc_start: -0.0966 (mmt) cc_final: -0.1235 (mtp) REVERT: D 118 MET cc_start: 0.3932 (mmt) cc_final: 0.2897 (mpt) REVERT: D 190 LEU cc_start: -0.2556 (OUTLIER) cc_final: -0.2797 (tt) REVERT: E 55 MET cc_start: 0.1386 (mtt) cc_final: 0.0875 (tmt) REVERT: E 80 TRP cc_start: 0.3366 (m-90) cc_final: 0.3056 (m-90) REVERT: F 185 MET cc_start: 0.0982 (mtt) cc_final: 0.0566 (ptp) REVERT: F 214 MET cc_start: -0.1478 (OUTLIER) cc_final: -0.2031 (ptt) outliers start: 57 outliers final: 39 residues processed: 129 average time/residue: 0.4911 time to fit residues: 68.2619 Evaluate side-chains 132 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 89 time to evaluate : 0.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 THR Chi-restraints excluded: chain A residue 35 GLU Chi-restraints excluded: chain A residue 66 MET Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 148 SER Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain B residue 19 THR Chi-restraints excluded: chain B residue 21 ASN Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 35 GLU Chi-restraints excluded: chain B residue 39 MET Chi-restraints excluded: chain B residue 55 MET Chi-restraints excluded: chain B residue 66 MET Chi-restraints excluded: chain B residue 118 MET Chi-restraints excluded: chain B residue 142 VAL Chi-restraints excluded: chain C residue 18 ARG Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 21 ASN Chi-restraints excluded: chain C residue 35 GLU Chi-restraints excluded: chain C residue 66 MET Chi-restraints excluded: chain C residue 68 MET Chi-restraints excluded: chain C residue 144 MET Chi-restraints excluded: chain C residue 185 MET Chi-restraints excluded: chain D residue 10 MET Chi-restraints excluded: chain D residue 39 MET Chi-restraints excluded: chain D residue 59 VAL Chi-restraints excluded: chain D residue 66 MET Chi-restraints excluded: chain D residue 132 ARG Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain D residue 190 LEU Chi-restraints excluded: chain E residue 18 ARG Chi-restraints excluded: chain E residue 27 VAL Chi-restraints excluded: chain E residue 66 MET Chi-restraints excluded: chain E residue 75 GLU Chi-restraints excluded: chain E residue 190 LEU Chi-restraints excluded: chain F residue 19 THR Chi-restraints excluded: chain F residue 21 ASN Chi-restraints excluded: chain F residue 27 VAL Chi-restraints excluded: chain F residue 35 GLU Chi-restraints excluded: chain F residue 66 MET Chi-restraints excluded: chain F residue 144 MET Chi-restraints excluded: chain F residue 214 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 86 optimal weight: 0.7980 chunk 60 optimal weight: 9.9990 chunk 74 optimal weight: 0.8980 chunk 101 optimal weight: 0.7980 chunk 11 optimal weight: 0.3980 chunk 90 optimal weight: 0.6980 chunk 29 optimal weight: 0.7980 chunk 85 optimal weight: 1.9990 chunk 28 optimal weight: 0.8980 chunk 17 optimal weight: 0.7980 chunk 111 optimal weight: 0.3980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 50 GLN E 62 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5439 r_free = 0.5439 target = 0.359052 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.5354 r_free = 0.5354 target = 0.345282 restraints weight = 12275.231| |-----------------------------------------------------------------------------| r_work (start): 0.5337 rms_B_bonded: 1.82 r_work: 0.5233 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.5233 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2507 moved from start: 0.8541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.226 9930 Z= 0.423 Angle : 1.510 48.535 13398 Z= 0.792 Chirality : 0.075 0.670 1518 Planarity : 0.011 0.116 1722 Dihedral : 9.046 64.315 1302 Min Nonbonded Distance : 1.700 Molprobity Statistics. All-atom Clashscore : 40.70 Ramachandran Plot: Outliers : 0.83 % Allowed : 6.50 % Favored : 92.67 % Rotamer: Outliers : 4.31 % Allowed : 15.45 % Favored : 80.24 % Cbeta Deviations : 0.77 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.28 % Twisted General : 1.49 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.36 (0.23), residues: 1200 helix: -0.70 (0.18), residues: 834 sheet: None (None), residues: 0 loop : -1.00 (0.31), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG A 18 TYR 0.024 0.003 TYR E 169 PHE 0.021 0.003 PHE D 40 TRP 0.036 0.003 TRP E 23 HIS 0.005 0.001 HIS E 62 Details of bonding type rmsd covalent geometry : bond 0.00981 ( 9882) covalent geometry : angle 1.51023 (13398) hydrogen bonds : bond 0.12380 ( 594) hydrogen bonds : angle 6.99806 ( 1764) Misc. bond : bond 0.01678 ( 48) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 90 time to evaluate : 0.336 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 21 ASN cc_start: 0.3372 (OUTLIER) cc_final: 0.2977 (t0) REVERT: B 39 MET cc_start: -0.0708 (OUTLIER) cc_final: -0.2188 (tpt) REVERT: B 96 MET cc_start: 0.2581 (tpp) cc_final: 0.1650 (tpp) REVERT: B 144 MET cc_start: 0.0750 (ptm) cc_final: 0.0359 (pmm) REVERT: B 214 MET cc_start: 0.3356 (mtp) cc_final: 0.2504 (mtp) REVERT: C 19 THR cc_start: 0.1137 (OUTLIER) cc_final: 0.0795 (t) REVERT: C 96 MET cc_start: 0.3245 (pp-130) cc_final: 0.2523 (tmm) REVERT: D 118 MET cc_start: 0.3986 (mmt) cc_final: 0.2875 (mpt) REVERT: E 55 MET cc_start: 0.1601 (mtt) cc_final: 0.0834 (tmt) REVERT: E 80 TRP cc_start: 0.3746 (m-90) cc_final: 0.3391 (m-90) REVERT: E 185 MET cc_start: 0.3500 (mtt) cc_final: 0.3243 (mtp) REVERT: F 96 MET cc_start: 0.3770 (ptp) cc_final: 0.2980 (mtm) REVERT: F 185 MET cc_start: 0.1207 (mtt) cc_final: 0.0726 (ptp) REVERT: F 214 MET cc_start: -0.1490 (OUTLIER) cc_final: -0.2023 (ptt) outliers start: 46 outliers final: 38 residues processed: 118 average time/residue: 0.5197 time to fit residues: 65.9903 Evaluate side-chains 130 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 88 time to evaluate : 0.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 THR Chi-restraints excluded: chain A residue 35 GLU Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 66 MET Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 148 SER Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain B residue 19 THR Chi-restraints excluded: chain B residue 21 ASN Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 35 GLU Chi-restraints excluded: chain B residue 39 MET Chi-restraints excluded: chain B residue 55 MET Chi-restraints excluded: chain B residue 66 MET Chi-restraints excluded: chain B residue 118 MET Chi-restraints excluded: chain C residue 18 ARG Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 35 GLU Chi-restraints excluded: chain C residue 66 MET Chi-restraints excluded: chain C residue 68 MET Chi-restraints excluded: chain C residue 144 MET Chi-restraints excluded: chain C residue 185 MET Chi-restraints excluded: chain D residue 39 MET Chi-restraints excluded: chain D residue 59 VAL Chi-restraints excluded: chain D residue 66 MET Chi-restraints excluded: chain D residue 132 ARG Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain E residue 18 ARG Chi-restraints excluded: chain E residue 66 MET Chi-restraints excluded: chain E residue 75 GLU Chi-restraints excluded: chain E residue 190 LEU Chi-restraints excluded: chain F residue 16 SER Chi-restraints excluded: chain F residue 19 THR Chi-restraints excluded: chain F residue 21 ASN Chi-restraints excluded: chain F residue 27 VAL Chi-restraints excluded: chain F residue 35 GLU Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 66 MET Chi-restraints excluded: chain F residue 144 MET Chi-restraints excluded: chain F residue 214 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 44 optimal weight: 0.6980 chunk 46 optimal weight: 1.9990 chunk 110 optimal weight: 0.5980 chunk 10 optimal weight: 0.8980 chunk 1 optimal weight: 3.9990 chunk 118 optimal weight: 0.5980 chunk 34 optimal weight: 0.5980 chunk 0 optimal weight: 0.6980 chunk 22 optimal weight: 0.0670 chunk 31 optimal weight: 0.9990 chunk 8 optimal weight: 0.8980 overall best weight: 0.5118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 13 GLN E 62 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5413 r_free = 0.5413 target = 0.356749 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.5332 r_free = 0.5332 target = 0.343073 restraints weight = 12269.354| |-----------------------------------------------------------------------------| r_work (start): 0.5337 rms_B_bonded: 1.80 r_work: 0.5231 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.5231 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2509 moved from start: 0.8872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.239 9930 Z= 0.418 Angle : 1.485 46.053 13398 Z= 0.781 Chirality : 0.078 0.918 1518 Planarity : 0.011 0.123 1722 Dihedral : 8.989 63.508 1302 Min Nonbonded Distance : 1.703 Molprobity Statistics. All-atom Clashscore : 40.29 Ramachandran Plot: Outliers : 0.83 % Allowed : 6.00 % Favored : 93.17 % Rotamer: Outliers : 4.40 % Allowed : 15.73 % Favored : 79.87 % Cbeta Deviations : 0.77 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 1.49 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.35 (0.23), residues: 1200 helix: -0.70 (0.18), residues: 834 sheet: None (None), residues: 0 loop : -0.97 (0.31), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 18 TYR 0.021 0.002 TYR C 169 PHE 0.031 0.003 PHE F 40 TRP 0.035 0.002 TRP B 23 HIS 0.005 0.001 HIS E 62 Details of bonding type rmsd covalent geometry : bond 0.00970 ( 9882) covalent geometry : angle 1.48457 (13398) hydrogen bonds : bond 0.12174 ( 594) hydrogen bonds : angle 7.02276 ( 1764) Misc. bond : bond 0.01662 ( 48) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2780.36 seconds wall clock time: 48 minutes 36.64 seconds (2916.64 seconds total)