Starting phenix.real_space_refine on Fri Oct 23 11:24:05 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9prz_71817/10_2026/9prz_71817.cif Found real_map, /net/cci-nas-00/data/ceres_data/9prz_71817/10_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_71817/10_2026/9prz_71817.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9prz_71817/10_2026/9prz_71817.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9prz_71817/10_2026/9prz_71817.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9prz_71817/10_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-2.3rc1-6221/lib/python3.11/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: 1.36, per 1000 atoms: 0.14 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=54, symmetry=0 Number of additional bonds: simple=54, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.26 Conformation dependent library (CDL) restraints added in 231.4 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: 0.20 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: 1.41 Time building geometry restraints manager: 1.50 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: 1074 2.29 - 3.16: 10450 3.16 - 4.03: 28735 4.03 - 4.90: 51288 Warning: very small nonbonded interaction distances. Nonbonded interactions: 91781 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 91776 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: 0.02 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: 3.020 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 8.990 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1624 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 : 0.031 0.677 9936 Z= 3.083 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 : 93.66 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/Z covalent geometry : bond 0.00173 / 0.08 ( 9882) covalent geometry : angle 0.40422 / 0.21 (13398) hydrogen bonds : bond 0.21645 / 14.82 ( 594) hydrogen bonds : angle 5.64234 / 4.02 ( 1764) Misc. bond : bond 0.41805 / 28.47 ( 54) *********************** 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 : 0.416 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: 0.5666 time to fit residues: 64.6376 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 : 0.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: [108, 49, 97, 113, 53, 5, 33, 65, 62, 51, 117] 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... ** 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 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 ** both conformations clash, **PLEASE CHECK MANUALLY** F 179 GLN F 192 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5428 r_free = 0.5428 target = 0.359299 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.5329 r_free = 0.5329 target = 0.344519 restraints weight = 12638.884| |-----------------------------------------------------------------------------| r_work (start): 0.5298 rms_B_bonded: 1.95 r_work: 0.5229 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work (final): 0.5229 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2181 moved from start: 0.4114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.017 0.309 9936 Z= 0.700 Angle : 1.597 24.610 13398 Z= 0.906 Chirality : 0.099 0.733 1518 Planarity : 0.026 0.421 1722 Dihedral : 11.531 130.457 1302 Min Nonbonded Distance : 1.855 Molprobity Statistics. All-atom Clashscore : 65.00 Ramachandran Plot: Outliers : 2.08 % Allowed : 3.92 % Favored : 94.00 % Rotamer: Outliers : 6.18 % Allowed : 8.52 % Favored : 85.30 % Cbeta Deviations : 0.77 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 1.84 % 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: -1.03 (0.22), residues: 1200 helix: -0.57 (0.16), residues: 882 sheet: None (None), residues: 0 loop : -0.52 (0.31), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.024 0.001 ARG F 18 TYR 0.022 0.003 TYR E 169 PHE 0.019 0.003 PHE F 161 TRP 0.018 0.002 TRP D 23 HIS 0.006 0.002 HIS D 62 Details of bonding type rmsd/Z covalent geometry : bond 0.01648 / 0.69 ( 9882) covalent geometry : angle 1.59735 / 0.91 (13398) hydrogen bonds : bond 0.20841 / 14.21 ( 594) hydrogen bonds : angle 7.07489 / 5.11 ( 1764) Misc. bond : bond 0.02014 / 1.37 ( 54) *********************** 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 162 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 96 time to evaluate : 0.366 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: A 10 MET cc_start: 0.4968 (ptp) cc_final: 0.4655 (tpt) REVERT: A 37 ILE cc_start: 0.6376 (OUTLIER) cc_final: 0.6169 (mp) REVERT: A 59 VAL cc_start: 0.6360 (t) cc_final: 0.6009 (t) REVERT: B 144 MET cc_start: 0.0505 (ptm) cc_final: 0.0067 (ptm) REVERT: B 185 MET cc_start: 0.0768 (mtt) cc_final: -0.1143 (ppp) REVERT: B 214 MET cc_start: 0.2609 (mtp) cc_final: 0.2326 (mtp) REVERT: C 185 MET cc_start: 0.2475 (OUTLIER) cc_final: 0.1960 (tmm) REVERT: E 39 MET cc_start: 0.0587 (OUTLIER) cc_final: -0.0875 (tmt) REVERT: F 19 THR cc_start: 0.1882 (OUTLIER) cc_final: 0.1387 (m) outliers start: 66 outliers final: 24 residues processed: 141 average time/residue: 0.4857 time to fit residues: 74.4233 Evaluate side-chains 119 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 91 time to evaluate : 0.362 ------------------------------------------------------------------------------- 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 37 ILE 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 35 GLU Chi-restraints excluded: chain B residue 66 MET Chi-restraints excluded: chain B residue 149 SER Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 38 PRO 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 39 MET Chi-restraints excluded: chain D residue 66 MET Chi-restraints excluded: chain E residue 16 SER Chi-restraints excluded: chain E residue 17 PRO 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 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: [30, 58, 87, 85, 118, 106, 61, 37, 112, 16, 49] chunk 30 optimal weight: 0.0050 chunk 58 optimal weight: 1.9990 chunk 87 optimal weight: 0.9980 chunk 85 optimal weight: 3.9990 chunk 118 optimal weight: 0.6980 chunk 106 optimal weight: 0.5980 chunk 61 optimal weight: 20.0000 chunk 37 optimal weight: 0.9980 chunk 112 optimal weight: 0.7980 chunk 16 optimal weight: 3.9990 chunk 49 optimal weight: 0.3980 overall best weight: 0.4994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 12 HIS ** B 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 50 GLN B 62 HIS B 112 GLN C 50 GLN ** D 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 50 GLN ** E 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 57 ASN ** F 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 50 GLN F 62 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5443 r_free = 0.5443 target = 0.361288 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.5349 r_free = 0.5349 target = 0.347335 restraints weight = 12787.609| |-----------------------------------------------------------------------------| r_work (start): 0.5312 rms_B_bonded: 1.94 r_work: 0.5239 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work (final): 0.5239 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2224 moved from start: 0.5439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.015 0.481 9936 Z= 0.612 Angle : 1.497 25.781 13398 Z= 0.827 Chirality : 0.083 0.791 1518 Planarity : 0.025 0.427 1722 Dihedral : 11.502 140.727 1302 Min Nonbonded Distance : 1.754 Molprobity Statistics. All-atom Clashscore : 51.32 Ramachandran Plot: Outliers : 1.17 % Allowed : 5.58 % Favored : 93.25 % Rotamer: Outliers : 5.06 % Allowed : 11.70 % Favored : 83.24 % Cbeta Deviations : 0.95 % 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: -1.08 (0.23), residues: 1200 helix: -0.48 (0.17), residues: 876 sheet: None (None), residues: 0 loop : -0.93 (0.31), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.033 0.002 ARG D 18 TYR 0.016 0.003 TYR E 169 PHE 0.026 0.003 PHE B 168 TRP 0.033 0.002 TRP E 80 HIS 0.006 0.002 HIS E 62 Details of bonding type rmsd/Z covalent geometry : bond 0.01545 / 0.59 ( 9882) covalent geometry : angle 1.49690 / 0.83 (13398) hydrogen bonds : bond 0.13695 / 9.32 ( 594) hydrogen bonds : angle 6.51348 / 4.74 ( 1764) Misc. bond : bond 0.02021 / 1.40 ( 54) *********************** 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 151 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 97 time to evaluate : 0.329 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: B 214 MET cc_start: 0.2739 (mtp) cc_final: 0.1530 (mtp) REVERT: C 10 MET cc_start: 0.1186 (mpt) cc_final: 0.0242 (ttp) REVERT: C 21 ASN cc_start: 0.1502 (OUTLIER) cc_final: -0.2476 (t0) REVERT: C 214 MET cc_start: -0.0491 (tpp) cc_final: -0.1264 (tpt) REVERT: D 19 THR cc_start: 0.0091 (OUTLIER) cc_final: -0.0152 (m) REVERT: E 21 ASN cc_start: 0.1198 (OUTLIER) cc_final: -0.0835 (t0) REVERT: F 19 THR cc_start: 0.1685 (OUTLIER) cc_final: 0.1206 (m) REVERT: F 21 ASN cc_start: 0.0485 (OUTLIER) cc_final: 0.0197 (m-40) outliers start: 54 outliers final: 33 residues processed: 130 average time/residue: 0.4857 time to fit residues: 68.4538 Evaluate side-chains 131 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 93 time to evaluate : 0.335 ------------------------------------------------------------------------------- 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 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 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 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 39 MET Chi-restraints excluded: chain D residue 55 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 39 MET Chi-restraints excluded: chain E residue 62 HIS Chi-restraints excluded: chain E residue 66 MET 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: [56, 97, 32, 95, 13, 35, 20, 17, 47, 88, 49] chunk 56 optimal weight: 0.9980 chunk 97 optimal weight: 0.8980 chunk 32 optimal weight: 0.6980 chunk 95 optimal weight: 0.7980 chunk 13 optimal weight: 0.0980 chunk 35 optimal weight: 0.6980 chunk 20 optimal weight: 0.0770 chunk 17 optimal weight: 0.6980 chunk 47 optimal weight: 0.9980 chunk 88 optimal weight: 1.9990 chunk 49 optimal weight: 10.0000 overall best weight: 0.4538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 62 HIS ** B 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 12 HIS D 12 HIS ** E 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5442 r_free = 0.5442 target = 0.360832 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.5357 r_free = 0.5357 target = 0.347875 restraints weight = 12621.867| |-----------------------------------------------------------------------------| r_work (start): 0.5331 rms_B_bonded: 1.80 r_work: 0.5265 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work (final): 0.5265 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2190 moved from start: 0.6114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.015 0.522 9936 Z= 0.584 Angle : 1.472 31.670 13398 Z= 0.790 Chirality : 0.077 0.735 1518 Planarity : 0.022 0.428 1722 Dihedral : 11.458 139.748 1302 Min Nonbonded Distance : 1.829 Molprobity Statistics. All-atom Clashscore : 45.63 Ramachandran Plot: Outliers : 0.75 % Allowed : 6.33 % Favored : 92.92 % Rotamer: Outliers : 5.81 % Allowed : 11.70 % Favored : 82.49 % Cbeta Deviations : 0.95 % 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: -0.93 (0.23), residues: 1200 helix: -0.41 (0.18), residues: 846 sheet: None (None), residues: 0 loop : -0.75 (0.30), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.050 0.002 ARG D 18 TYR 0.017 0.002 TYR E 169 PHE 0.022 0.003 PHE B 168 TRP 0.027 0.002 TRP E 23 HIS 0.004 0.001 HIS F 62 Details of bonding type rmsd/Z covalent geometry : bond 0.01474 / 0.57 ( 9882) covalent geometry : angle 1.47221 / 0.79 (13398) hydrogen bonds : bond 0.13146 / 9.06 ( 594) hydrogen bonds : angle 6.54561 / 4.76 ( 1764) Misc. bond : bond 0.01912 / 1.30 ( 54) *********************** 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 155 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 93 time to evaluate : 0.363 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: 0.2710 (mtp) cc_final: 0.1415 (mtp) REVERT: B 215 MET cc_start: 0.2707 (ppp) cc_final: 0.1885 (ppp) REVERT: C 10 MET cc_start: 0.1407 (mpt) cc_final: 0.0482 (ttp) REVERT: E 144 MET cc_start: 0.1122 (pmm) cc_final: -0.2341 (ttm) REVERT: F 19 THR cc_start: 0.1787 (OUTLIER) cc_final: 0.1242 (m) outliers start: 62 outliers final: 38 residues processed: 137 average time/residue: 0.4774 time to fit residues: 71.0729 Evaluate side-chains 130 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 91 time to evaluate : 0.308 ------------------------------------------------------------------------------- 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 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 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 27 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 20 LEU 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 185 MET Chi-restraints excluded: chain D residue 10 MET Chi-restraints excluded: chain D residue 24 VAL Chi-restraints excluded: chain D residue 35 GLU Chi-restraints excluded: chain D residue 37 ILE Chi-restraints excluded: chain D residue 55 MET 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 24 VAL Chi-restraints excluded: chain E residue 35 GLU Chi-restraints excluded: chain E residue 59 VAL Chi-restraints excluded: chain E residue 66 MET 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: [68, 66, 94, 79, 62, 115, 97, 13, 67, 33, 118] chunk 68 optimal weight: 0.9980 chunk 66 optimal weight: 0.2980 chunk 94 optimal weight: 5.9990 chunk 79 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 115 optimal weight: 0.5980 chunk 97 optimal weight: 0.0980 chunk 13 optimal weight: 2.9990 chunk 67 optimal weight: 0.5980 chunk 33 optimal weight: 0.6980 chunk 118 optimal weight: 0.7980 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 57 ASN E 62 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5457 r_free = 0.5457 target = 0.362444 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.5377 r_free = 0.5377 target = 0.349652 restraints weight = 12547.645| |-----------------------------------------------------------------------------| r_work (start): 0.5355 rms_B_bonded: 1.80 r_work: 0.5255 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.5255 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2385 moved from start: 0.6681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.014 0.563 9936 Z= 0.566 Angle : 1.458 28.756 13398 Z= 0.779 Chirality : 0.077 0.839 1518 Planarity : 0.022 0.429 1722 Dihedral : 11.526 142.110 1302 Min Nonbonded Distance : 1.882 Molprobity Statistics. All-atom Clashscore : 42.58 Ramachandran Plot: Outliers : 0.67 % Allowed : 5.67 % Favored : 93.67 % Rotamer: Outliers : 5.15 % Allowed : 13.01 % Favored : 81.84 % Cbeta Deviations : 0.60 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -0.94 (0.23), residues: 1200 helix: -0.43 (0.18), residues: 846 sheet: None (None), residues: 0 loop : -0.73 (0.30), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.054 0.002 ARG D 18 TYR 0.017 0.002 TYR C 169 PHE 0.016 0.003 PHE B 168 TRP 0.023 0.002 TRP B 23 HIS 0.007 0.001 HIS E 62 Details of bonding type rmsd/Z covalent geometry : bond 0.01425 / 0.55 ( 9882) covalent geometry : angle 1.45788 / 0.78 (13398) hydrogen bonds : bond 0.12677 / 8.87 ( 594) hydrogen bonds : angle 6.55708 / 4.82 ( 1764) Misc. bond : bond 0.01895 / 1.28 ( 54) *********************** 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 152 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 97 time to evaluate : 0.344 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 28 GLU cc_start: 0.7824 (mm-30) cc_final: 0.7413 (mp0) REVERT: B 39 MET cc_start: -0.0100 (OUTLIER) cc_final: -0.3512 (mpm) REVERT: B 161 PHE cc_start: 0.3667 (p90) cc_final: 0.0503 (t80) REVERT: B 214 MET cc_start: 0.2116 (mtp) cc_final: 0.1682 (mtp) REVERT: C 10 MET cc_start: 0.1735 (mpt) cc_final: 0.1021 (ttt) REVERT: C 20 LEU cc_start: 0.0179 (OUTLIER) cc_final: -0.0759 (pp) REVERT: D 56 LEU cc_start: 0.0832 (OUTLIER) cc_final: 0.0631 (mt) REVERT: D 68 MET cc_start: 0.3147 (OUTLIER) cc_final: 0.2542 (ppp) REVERT: D 118 MET cc_start: 0.4345 (mmt) cc_final: 0.2987 (mpt) REVERT: E 144 MET cc_start: 0.0665 (pmm) cc_final: -0.3761 (mtp) REVERT: F 19 THR cc_start: 0.1827 (OUTLIER) cc_final: 0.1179 (m) outliers start: 55 outliers final: 36 residues processed: 135 average time/residue: 0.5280 time to fit residues: 76.8710 Evaluate side-chains 134 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 93 time to evaluate : 0.349 ------------------------------------------------------------------------------- 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 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 A residue 190 LEU Chi-restraints excluded: chain B residue 18 ARG 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 C residue 20 LEU 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 165 VAL 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 27 VAL 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 68 MET Chi-restraints excluded: chain D residue 132 ARG Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain E residue 24 VAL Chi-restraints excluded: chain E residue 66 MET 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 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: [77, 116, 55, 0, 14, 15, 38, 47, 103, 45, 1] chunk 77 optimal weight: 0.9990 chunk 116 optimal weight: 0.6980 chunk 55 optimal weight: 0.8980 chunk 0 optimal weight: 3.9990 chunk 14 optimal weight: 3.9990 chunk 15 optimal weight: 0.8980 chunk 38 optimal weight: 0.9990 chunk 47 optimal weight: 0.9990 chunk 103 optimal weight: 0.9980 chunk 45 optimal weight: 0.9990 chunk 1 optimal weight: 9.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 12 HIS ** C 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 57 ASN ** D 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 84 HIS D 193 ASN ** E 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.359615 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.5353 r_free = 0.5353 target = 0.345341 restraints weight = 12370.254| |-----------------------------------------------------------------------------| r_work (start): 0.5338 rms_B_bonded: 1.83 r_work: 0.5241 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.5241 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2607 moved from start: 0.7366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.361 9936 Z= 0.515 Angle : 1.488 31.279 13398 Z= 0.791 Chirality : 0.075 0.624 1518 Planarity : 0.021 0.412 1722 Dihedral : 11.682 154.236 1302 Min Nonbonded Distance : 1.885 Molprobity Statistics. All-atom Clashscore : 45.48 Ramachandran Plot: Outliers : 0.75 % Allowed : 5.83 % Favored : 93.42 % Rotamer: Outliers : 5.52 % Allowed : 14.23 % Favored : 80.24 % Cbeta Deviations : 0.69 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 1.32 % 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: -1.34 (0.23), residues: 1200 helix: -0.72 (0.17), residues: 846 sheet: None (None), residues: 0 loop : -0.89 (0.30), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.053 0.002 ARG D 18 TYR 0.026 0.003 TYR E 169 PHE 0.018 0.003 PHE B 168 TRP 0.028 0.003 TRP B 23 HIS 0.005 0.001 HIS D 62 Details of bonding type rmsd/Z covalent geometry : bond 0.01238 / 0.50 ( 9882) covalent geometry : angle 1.48810 / 0.79 (13398) hydrogen bonds : bond 0.12332 / 8.83 ( 594) hydrogen bonds : angle 6.82892 / 5.03 ( 1764) Misc. bond : bond 0.01742 / 1.13 ( 54) *********************** 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 152 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 93 time to evaluate : 0.292 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: B 161 PHE cc_start: 0.4136 (p90) cc_final: 0.0572 (t80) REVERT: C 10 MET cc_start: 0.1899 (mpt) cc_final: 0.0976 (ttt) REVERT: C 68 MET cc_start: 0.2590 (OUTLIER) cc_final: -0.2103 (tpp) REVERT: C 96 MET cc_start: 0.2911 (tmm) cc_final: 0.2412 (tmt) REVERT: C 118 MET cc_start: 0.2596 (ttt) cc_final: 0.2275 (ttm) REVERT: D 118 MET cc_start: 0.4227 (OUTLIER) cc_final: 0.2947 (mpt) REVERT: D 151 LEU cc_start: 0.2005 (mt) cc_final: 0.1328 (mp) REVERT: D 190 LEU cc_start: -0.2057 (OUTLIER) cc_final: -0.2295 (tt) REVERT: E 80 TRP cc_start: 0.3005 (m-90) cc_final: 0.2725 (m-90) REVERT: E 144 MET cc_start: 0.1480 (pmm) cc_final: -0.1887 (mmt) REVERT: F 214 MET cc_start: -0.1873 (OUTLIER) cc_final: -0.2330 (ptt) outliers start: 59 outliers final: 38 residues processed: 134 average time/residue: 0.4991 time to fit residues: 72.3709 Evaluate side-chains 134 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 92 time to evaluate : 0.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 ARG 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 A residue 190 LEU Chi-restraints excluded: chain B residue 18 ARG 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 C residue 24 VAL Chi-restraints excluded: chain C residue 27 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 10 MET Chi-restraints excluded: chain D residue 27 VAL Chi-restraints excluded: chain D residue 66 MET Chi-restraints excluded: chain D residue 118 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 24 VAL Chi-restraints excluded: chain E residue 39 MET 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: [79, 1, 32, 106, 40, 107, 18, 52, 116, 91, 30] chunk 79 optimal weight: 0.7980 chunk 1 optimal weight: 8.9990 chunk 32 optimal weight: 0.8980 chunk 106 optimal weight: 0.4980 chunk 40 optimal weight: 0.0670 chunk 107 optimal weight: 0.5980 chunk 18 optimal weight: 1.9990 chunk 52 optimal weight: 0.0970 chunk 116 optimal weight: 0.9980 chunk 91 optimal weight: 0.9990 chunk 30 optimal weight: 1.9990 overall best weight: 0.4116 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 183 ASN C 50 GLN ** D 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 12 HIS E 179 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5444 r_free = 0.5444 target = 0.359930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.5361 r_free = 0.5361 target = 0.346664 restraints weight = 12329.277| |-----------------------------------------------------------------------------| r_work (start): 0.5347 rms_B_bonded: 1.75 r_work: 0.5250 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.5250 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2477 moved from start: 0.7705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.424 9936 Z= 0.490 Angle : 1.437 31.384 13398 Z= 0.752 Chirality : 0.073 0.974 1518 Planarity : 0.022 0.474 1722 Dihedral : 11.998 162.378 1302 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 40.62 Ramachandran Plot: Outliers : 0.67 % Allowed : 5.58 % Favored : 93.75 % Rotamer: Outliers : 5.24 % Allowed : 14.98 % Favored : 79.78 % Cbeta Deviations : 0.60 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -1.12 (0.23), residues: 1200 helix: -0.53 (0.18), residues: 834 sheet: None (None), residues: 0 loop : -0.87 (0.30), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.053 0.002 ARG D 18 TYR 0.019 0.002 TYR E 169 PHE 0.021 0.003 PHE F 40 TRP 0.020 0.002 TRP B 23 HIS 0.010 0.001 HIS F 62 Details of bonding type rmsd/Z covalent geometry : bond 0.01197 / 0.47 ( 9882) covalent geometry : angle 1.43720 / 0.75 (13398) hydrogen bonds : bond 0.11890 / 8.52 ( 594) hydrogen bonds : angle 6.67464 / 4.92 ( 1764) Misc. bond : bond 0.01745 / 1.16 ( 54) *********************** 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 151 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 95 time to evaluate : 0.373 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: B 144 MET cc_start: 0.0717 (ptm) cc_final: -0.1418 (pmm) REVERT: B 161 PHE cc_start: 0.4201 (p90) cc_final: 0.0654 (t80) REVERT: C 10 MET cc_start: 0.2130 (mpt) cc_final: 0.1126 (ttt) REVERT: C 96 MET cc_start: 0.3254 (tmm) cc_final: 0.2682 (tmt) REVERT: C 118 MET cc_start: 0.2990 (ttt) cc_final: 0.2711 (ttm) REVERT: D 68 MET cc_start: 0.2783 (ptt) cc_final: 0.2497 (ppp) REVERT: D 118 MET cc_start: 0.3900 (OUTLIER) cc_final: 0.2595 (mpt) REVERT: D 190 LEU cc_start: -0.2175 (OUTLIER) cc_final: -0.2408 (tt) REVERT: E 80 TRP cc_start: 0.2945 (m-90) cc_final: 0.2665 (m-90) REVERT: E 144 MET cc_start: 0.1672 (OUTLIER) cc_final: -0.1820 (mmt) REVERT: F 214 MET cc_start: -0.1633 (OUTLIER) cc_final: -0.2095 (ptt) outliers start: 56 outliers final: 41 residues processed: 132 average time/residue: 0.5212 time to fit residues: 74.2826 Evaluate side-chains 138 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 93 time to evaluate : 0.336 ------------------------------------------------------------------------------- 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 39 MET Chi-restraints excluded: chain A residue 66 MET Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain B residue 18 ARG 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 C residue 27 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 27 VAL Chi-restraints excluded: chain D residue 35 GLU Chi-restraints excluded: chain D residue 66 MET Chi-restraints excluded: chain D residue 118 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 24 VAL Chi-restraints excluded: chain E residue 39 MET Chi-restraints excluded: chain E residue 66 MET Chi-restraints excluded: chain E residue 75 GLU Chi-restraints excluded: chain E residue 144 MET Chi-restraints excluded: chain E residue 172 LEU Chi-restraints excluded: chain E residue 190 LEU Chi-restraints excluded: chain F residue 15 ILE 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 55 MET 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: [92, 44, 5, 61, 28, 25, 40, 37, 96, 20, 52] chunk 92 optimal weight: 0.9980 chunk 44 optimal weight: 0.9980 chunk 5 optimal weight: 0.0980 chunk 61 optimal weight: 1.9990 chunk 28 optimal weight: 0.7980 chunk 25 optimal weight: 1.9990 chunk 40 optimal weight: 3.9990 chunk 37 optimal weight: 0.0870 chunk 96 optimal weight: 0.9980 chunk 20 optimal weight: 2.9990 chunk 52 optimal weight: 0.6980 overall best weight: 0.5358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 12 HIS ** C 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5432 r_free = 0.5432 target = 0.358320 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.5347 r_free = 0.5347 target = 0.344485 restraints weight = 12310.317| |-----------------------------------------------------------------------------| r_work (start): 0.5336 rms_B_bonded: 1.78 r_work: 0.5237 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.5237 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2571 moved from start: 0.8113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.389 9936 Z= 0.480 Angle : 1.463 31.459 13398 Z= 0.759 Chirality : 0.078 1.339 1518 Planarity : 0.020 0.391 1722 Dihedral : 12.351 164.456 1302 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 41.71 Ramachandran Plot: Outliers : 0.67 % Allowed : 6.00 % Favored : 93.33 % Rotamer: Outliers : 5.90 % Allowed : 14.61 % Favored : 79.49 % Cbeta Deviations : 0.52 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 1.23 % 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: -1.23 (0.23), residues: 1200 helix: -0.58 (0.18), residues: 834 sheet: None (None), residues: 0 loop : -1.03 (0.30), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.039 0.002 ARG D 18 TYR 0.022 0.002 TYR E 169 PHE 0.022 0.003 PHE F 40 TRP 0.036 0.002 TRP B 23 HIS 0.006 0.001 HIS C 12 Details of bonding type rmsd/Z covalent geometry : bond 0.01171 / 0.47 ( 9882) covalent geometry : angle 1.46340 / 0.76 (13398) hydrogen bonds : bond 0.11698 / 8.42 ( 594) hydrogen bonds : angle 6.74671 / 4.95 ( 1764) Misc. bond : bond 0.01643 / 1.08 ( 54) *********************** 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 157 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 94 time to evaluate : 0.280 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: symmetry clash REVERT: A 142 VAL cc_start: 0.8831 (OUTLIER) cc_final: 0.8527 (t) REVERT: C 10 MET cc_start: 0.2201 (mpt) cc_final: 0.1064 (ttt) REVERT: C 96 MET cc_start: 0.3470 (tmm) cc_final: 0.2958 (tmt) REVERT: C 118 MET cc_start: 0.3073 (ttt) cc_final: 0.2695 (ttm) REVERT: D 118 MET cc_start: 0.3793 (OUTLIER) cc_final: 0.2520 (mpt) REVERT: D 151 LEU cc_start: 0.2461 (mt) cc_final: 0.1884 (mp) REVERT: E 55 MET cc_start: 0.1776 (mtt) cc_final: 0.0550 (tmm) REVERT: E 80 TRP cc_start: 0.3080 (m-90) cc_final: 0.2791 (m-90) REVERT: E 144 MET cc_start: 0.2184 (OUTLIER) cc_final: -0.1470 (mmt) REVERT: F 17 PRO cc_start: -0.1253 (OUTLIER) cc_final: -0.1502 (Cg_endo) REVERT: F 62 HIS cc_start: 0.0730 (OUTLIER) cc_final: -0.0552 (m-70) REVERT: F 214 MET cc_start: -0.1750 (OUTLIER) cc_final: -0.2248 (ptt) outliers start: 63 outliers final: 45 residues processed: 137 average time/residue: 0.4856 time to fit residues: 72.2365 Evaluate side-chains 142 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 91 time to evaluate : 0.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 ARG Chi-restraints excluded: chain A residue 35 GLU Chi-restraints excluded: chain A residue 39 MET 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 151 LEU Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain B residue 18 ARG 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 142 VAL Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 27 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 10 MET Chi-restraints excluded: chain D residue 24 VAL Chi-restraints excluded: chain D residue 27 VAL Chi-restraints excluded: chain D residue 35 GLU Chi-restraints excluded: chain D residue 66 MET Chi-restraints excluded: chain D residue 118 MET Chi-restraints excluded: chain D residue 132 ARG Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain E residue 24 VAL Chi-restraints excluded: chain E residue 39 MET Chi-restraints excluded: chain E residue 66 MET Chi-restraints excluded: chain E residue 75 GLU Chi-restraints excluded: chain E residue 144 MET Chi-restraints excluded: chain E residue 172 LEU Chi-restraints excluded: chain E residue 190 LEU Chi-restraints excluded: chain F residue 17 PRO 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 55 MET Chi-restraints excluded: chain F residue 62 HIS 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: [14, 70, 105, 119, 104, 89, 53, 80, 72, 107, 47] chunk 14 optimal weight: 0.8980 chunk 70 optimal weight: 1.9990 chunk 105 optimal weight: 0.9990 chunk 119 optimal weight: 0.5980 chunk 104 optimal weight: 0.6980 chunk 89 optimal weight: 0.4980 chunk 53 optimal weight: 0.9990 chunk 80 optimal weight: 0.0000 chunk 72 optimal weight: 0.0470 chunk 107 optimal weight: 0.5980 chunk 47 optimal weight: 0.8980 overall best weight: 0.3482 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 195 ASN ** C 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5457 r_free = 0.5457 target = 0.361041 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.5377 r_free = 0.5377 target = 0.348120 restraints weight = 12260.010| |-----------------------------------------------------------------------------| r_work (start): 0.5357 rms_B_bonded: 1.70 r_work: 0.5258 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.5258 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2484 moved from start: 0.8395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.415 9936 Z= 0.477 Angle : 1.441 32.174 13398 Z= 0.747 Chirality : 0.073 1.059 1518 Planarity : 0.020 0.365 1722 Dihedral : 12.301 163.302 1302 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 41.19 Ramachandran Plot: Outliers : 0.83 % Allowed : 5.92 % Favored : 93.25 % Rotamer: Outliers : 5.43 % Allowed : 14.98 % Favored : 79.59 % Cbeta Deviations : 0.69 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 1.23 % 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: -1.17 (0.23), residues: 1200 helix: -0.44 (0.18), residues: 852 sheet: None (None), residues: 0 loop : -1.28 (0.30), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.044 0.002 ARG D 18 TYR 0.020 0.002 TYR D 169 PHE 0.020 0.003 PHE F 32 TRP 0.021 0.002 TRP B 23 HIS 0.006 0.001 HIS F 62 Details of bonding type rmsd/Z covalent geometry : bond 0.01169 / 0.46 ( 9882) covalent geometry : angle 1.44081 / 0.75 (13398) hydrogen bonds : bond 0.11567 / 8.32 ( 594) hydrogen bonds : angle 6.72508 / 4.94 ( 1764) Misc. bond : bond 0.01664 / 1.09 ( 54) *********************** 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 151 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 93 time to evaluate : 0.339 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: B 39 MET cc_start: -0.0185 (OUTLIER) cc_final: -0.2559 (mpt) REVERT: B 144 MET cc_start: 0.0704 (ptm) cc_final: -0.1350 (pmm) REVERT: C 10 MET cc_start: 0.2226 (mpt) cc_final: 0.1039 (ttt) REVERT: C 15 ILE cc_start: 0.1808 (OUTLIER) cc_final: 0.1145 (mp) REVERT: C 20 LEU cc_start: -0.0821 (OUTLIER) cc_final: -0.1578 (pp) REVERT: C 96 MET cc_start: 0.3304 (tmm) cc_final: 0.2721 (tmt) REVERT: C 118 MET cc_start: 0.3552 (ttt) cc_final: 0.3349 (ttm) REVERT: D 118 MET cc_start: 0.3828 (OUTLIER) cc_final: 0.2527 (mpt) REVERT: E 39 MET cc_start: 0.2843 (OUTLIER) cc_final: 0.2120 (ttm) REVERT: E 55 MET cc_start: 0.1703 (mtt) cc_final: 0.0949 (tmt) REVERT: E 80 TRP cc_start: 0.2986 (m-90) cc_final: 0.2684 (m-90) REVERT: E 144 MET cc_start: 0.2084 (OUTLIER) cc_final: -0.1861 (mpt) REVERT: F 185 MET cc_start: 0.0850 (mtt) cc_final: -0.0255 (ptp) REVERT: F 214 MET cc_start: -0.1495 (OUTLIER) cc_final: -0.1903 (ptt) outliers start: 58 outliers final: 44 residues processed: 131 average time/residue: 0.5135 time to fit residues: 72.7262 Evaluate side-chains 142 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 91 time to evaluate : 0.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 ARG 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 151 LEU Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain B residue 18 ARG 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 142 VAL Chi-restraints excluded: chain C residue 15 ILE Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 27 VAL Chi-restraints excluded: chain C residue 35 GLU Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain C residue 59 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 24 VAL Chi-restraints excluded: chain D residue 27 VAL Chi-restraints excluded: chain D residue 35 GLU Chi-restraints excluded: chain D residue 66 MET Chi-restraints excluded: chain D residue 118 MET Chi-restraints excluded: chain D residue 132 ARG Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain E residue 24 VAL Chi-restraints excluded: chain E residue 39 MET Chi-restraints excluded: chain E residue 66 MET Chi-restraints excluded: chain E residue 75 GLU Chi-restraints excluded: chain E residue 144 MET Chi-restraints excluded: chain E residue 172 LEU Chi-restraints excluded: chain E residue 190 LEU Chi-restraints excluded: chain F residue 15 ILE 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 54 THR Chi-restraints excluded: chain F residue 55 MET 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: [86, 60, 74, 101, 11, 90, 29, 85, 28, 17, 111] chunk 86 optimal weight: 0.0870 chunk 60 optimal weight: 9.9990 chunk 74 optimal weight: 5.9990 chunk 101 optimal weight: 1.9990 chunk 11 optimal weight: 0.0980 chunk 90 optimal weight: 0.9990 chunk 29 optimal weight: 10.0000 chunk 85 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 17 optimal weight: 0.0970 chunk 111 optimal weight: 0.9980 overall best weight: 0.4558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5450 r_free = 0.5450 target = 0.360626 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.5372 r_free = 0.5372 target = 0.347545 restraints weight = 12260.002| |-----------------------------------------------------------------------------| r_work (start): 0.5351 rms_B_bonded: 1.74 r_work: 0.5252 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.5252 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2530 moved from start: 0.8588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.411 9936 Z= 0.482 Angle : 1.489 35.220 13398 Z= 0.772 Chirality : 0.074 0.946 1518 Planarity : 0.020 0.373 1722 Dihedral : 12.317 163.084 1302 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 41.14 Ramachandran Plot: Outliers : 0.75 % Allowed : 6.25 % Favored : 93.00 % Rotamer: Outliers : 5.43 % Allowed : 15.36 % Favored : 79.21 % Cbeta Deviations : 0.60 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 1.32 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.18 (0.23), residues: 1200 helix: -0.53 (0.18), residues: 834 sheet: None (None), residues: 0 loop : -1.02 (0.30), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.038 0.002 ARG D 18 TYR 0.020 0.002 TYR E 169 PHE 0.018 0.003 PHE F 32 TRP 0.028 0.002 TRP B 23 HIS 0.005 0.001 HIS F 62 Details of bonding type rmsd/Z covalent geometry : bond 0.01186 / 0.47 ( 9882) covalent geometry : angle 1.48940 / 0.77 (13398) hydrogen bonds : bond 0.11428 / 8.28 ( 594) hydrogen bonds : angle 6.82528 / 5.00 ( 1764) Misc. bond : bond 0.01660 / 1.09 ( 54) ********************** 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 149 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 91 time to evaluate : 0.388 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: symmetry clash revert: symmetry clash REVERT: A 142 VAL cc_start: 0.8794 (OUTLIER) cc_final: 0.8479 (t) REVERT: B 144 MET cc_start: 0.0649 (ptm) cc_final: -0.1574 (pmm) REVERT: C 10 MET cc_start: 0.2268 (mpt) cc_final: 0.1034 (ttt) REVERT: C 15 ILE cc_start: 0.1943 (OUTLIER) cc_final: 0.1425 (mp) REVERT: C 55 MET cc_start: -0.1282 (OUTLIER) cc_final: -0.1656 (mtt) REVERT: C 96 MET cc_start: 0.3197 (tmm) cc_final: 0.2558 (tmt) REVERT: D 118 MET cc_start: 0.3927 (OUTLIER) cc_final: 0.2624 (mpt) REVERT: E 80 TRP cc_start: 0.3066 (m-90) cc_final: 0.2765 (m-90) REVERT: E 144 MET cc_start: 0.2112 (OUTLIER) cc_final: -0.1785 (mpt) REVERT: F 17 PRO cc_start: -0.1102 (OUTLIER) cc_final: -0.1454 (Cg_endo) REVERT: F 96 MET cc_start: 0.3761 (ptp) cc_final: 0.2993 (mtm) REVERT: F 185 MET cc_start: 0.0775 (mtt) cc_final: -0.0342 (ptp) REVERT: F 214 MET cc_start: -0.1344 (OUTLIER) cc_final: -0.1796 (ptt) outliers start: 58 outliers final: 43 residues processed: 129 average time/residue: 0.4851 time to fit residues: 67.9379 Evaluate side-chains 140 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 90 time to evaluate : 0.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 ARG 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 151 LEU Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain B residue 18 ARG 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 142 VAL Chi-restraints excluded: chain C residue 15 ILE Chi-restraints excluded: chain C residue 27 VAL Chi-restraints excluded: chain C residue 35 GLU Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain C residue 55 MET Chi-restraints excluded: chain C residue 59 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 172 LEU Chi-restraints excluded: chain C residue 185 MET Chi-restraints excluded: chain D residue 27 VAL Chi-restraints excluded: chain D residue 35 GLU Chi-restraints excluded: chain D residue 66 MET Chi-restraints excluded: chain D residue 118 MET Chi-restraints excluded: chain D residue 132 ARG Chi-restraints excluded: chain E residue 24 VAL Chi-restraints excluded: chain E residue 39 MET Chi-restraints excluded: chain E residue 66 MET Chi-restraints excluded: chain E residue 75 GLU Chi-restraints excluded: chain E residue 144 MET Chi-restraints excluded: chain E residue 190 LEU Chi-restraints excluded: chain F residue 15 ILE Chi-restraints excluded: chain F residue 17 PRO 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 54 THR Chi-restraints excluded: chain F residue 55 MET 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: [44, 46, 110, 10, 1, 118, 34, 0, 22, 31, 8] chunk 44 optimal weight: 0.7980 chunk 46 optimal weight: 2.9990 chunk 110 optimal weight: 2.9990 chunk 10 optimal weight: 0.0980 chunk 1 optimal weight: 5.9990 chunk 118 optimal weight: 6.9990 chunk 34 optimal weight: 0.0770 chunk 0 optimal weight: 0.5980 chunk 22 optimal weight: 0.8980 chunk 31 optimal weight: 0.8980 chunk 8 optimal weight: 0.8980 overall best weight: 0.4938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5449 r_free = 0.5449 target = 0.360559 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.5372 r_free = 0.5372 target = 0.347564 restraints weight = 12236.277| |-----------------------------------------------------------------------------| r_work (start): 0.5349 rms_B_bonded: 1.70 r_work: 0.5249 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.5249 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2545 moved from start: 0.8585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.014 0.411 9936 Z= 0.721 Angle : 1.677 79.100 13398 Z= 0.894 Chirality : 0.082 1.152 1518 Planarity : 0.020 0.373 1722 Dihedral : 12.353 163.357 1302 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 43.46 Ramachandran Plot: Outliers : 0.83 % Allowed : 6.17 % Favored : 93.00 % Rotamer: Outliers : 5.06 % Allowed : 15.64 % Favored : 79.31 % Cbeta Deviations : 0.86 % 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: -1.17 (0.23), residues: 1200 helix: -0.53 (0.18), residues: 834 sheet: None (None), residues: 0 loop : -1.03 (0.30), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.037 0.002 ARG D 18 TYR 0.019 0.002 TYR E 169 PHE 0.016 0.003 PHE F 32 TRP 0.043 0.002 TRP D 23 HIS 0.005 0.001 HIS F 62 Details of bonding type rmsd/Z covalent geometry : bond 0.01326 / 0.64 ( 9882) covalent geometry : angle 1.67690 / 0.89 (13398) hydrogen bonds : bond 0.11714 / 8.49 ( 594) hydrogen bonds : angle 6.82563 / 5.01 ( 1764) Misc. bond : bond 0.04454 / 4.10 ( 54) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2837.04 seconds wall clock time: 49 minutes 37.11 seconds (2977.11 seconds total)