Starting phenix.real_space_refine on Tue Aug 4 14:02:53 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9xmi_67025/08_2026/9xmi_67025.cif Found real_map, /net/cci-nas-00/data/ceres_data/9xmi_67025/08_2026/9xmi_67025.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9xmi_67025/08_2026/9xmi_67025.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9xmi_67025/08_2026/9xmi_67025.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9xmi_67025/08_2026/9xmi_67025.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9xmi_67025/08_2026/9xmi_67025.map" } resolution = 3.2 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= 0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 5 5.16 5 C 2325 2.51 5 N 590 2.21 5 O 675 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 49 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 3595 Number of models: 1 Model: "" Number of chains: 5 Chain: "E" Number of atoms: 719 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 719 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} Chain breaks: 1 Chain: "A" Number of atoms: 719 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 719 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} Chain breaks: 1 Chain: "B" Number of atoms: 719 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 719 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} Chain breaks: 1 Chain: "C" Number of atoms: 719 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 719 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} Chain breaks: 1 Chain: "D" Number of atoms: 719 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 719 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} Chain breaks: 1 Time building chain proxies: 1.11, per 1000 atoms: 0.31 Number of scatterers: 3595 At special positions: 0 Unit cell: (86.32, 69.72, 41.5, 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 5 16.00 O 675 8.00 N 590 7.00 C 2325 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.30 Conformation dependent library (CDL) restraints added in 149.9 milliseconds 880 Ramachandran restraints generated. 440 Oldfield, 0 Emsley, 440 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 870 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 11 sheets defined 0.0% alpha, 39.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.08 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 13 through 16 removed outlier: 6.217A pdb=" N VAL E 14 " --> pdb=" O LYS A 15 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 19 through 21 removed outlier: 6.296A pdb=" N VAL E 20 " --> pdb=" O ARG A 21 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 25 through 26 removed outlier: 6.307A pdb=" N ALA E 25 " --> pdb=" O ILE B 26 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N ALA B 25 " --> pdb=" O ILE C 26 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N ALA C 25 " --> pdb=" O ILE D 26 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 30 through 33 removed outlier: 6.315A pdb=" N HIS E 31 " --> pdb=" O VAL B 32 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N HIS B 31 " --> pdb=" O VAL C 32 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N HIS C 31 " --> pdb=" O VAL D 32 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 59 through 66 removed outlier: 6.214A pdb=" N THR E 59 " --> pdb=" O THR A 60 " (cutoff:3.500A) removed outlier: 8.150A pdb=" N GLU A 62 " --> pdb=" O THR E 59 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N GLU E 61 " --> pdb=" O GLU A 62 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N PHE A 64 " --> pdb=" O GLU E 61 " (cutoff:3.500A) removed outlier: 7.489A pdb=" N GLU E 63 " --> pdb=" O PHE A 64 " (cutoff:3.500A) removed outlier: 10.289A pdb=" N GLU A 66 " --> pdb=" O GLU E 63 " (cutoff:3.500A) removed outlier: 8.979A pdb=" N VAL E 65 " --> pdb=" O GLU A 66 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N PHE E 64 " --> pdb=" O GLU B 63 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N VAL B 65 " --> pdb=" O PHE E 64 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N GLU E 66 " --> pdb=" O VAL B 65 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N PHE B 64 " --> pdb=" O GLU C 63 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N VAL C 65 " --> pdb=" O PHE B 64 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N GLU B 66 " --> pdb=" O VAL C 65 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N PHE C 64 " --> pdb=" O GLU D 63 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N VAL D 65 " --> pdb=" O PHE C 64 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N GLU C 66 " --> pdb=" O VAL D 65 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 71 through 73 removed outlier: 6.526A pdb=" N GLU E 72 " --> pdb=" O ILE A 73 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 79 through 80 removed outlier: 6.548A pdb=" N TRP E 79 " --> pdb=" O LYS B 80 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N TRP B 79 " --> pdb=" O LYS C 80 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N TRP C 79 " --> pdb=" O LYS D 80 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 92 through 99 removed outlier: 6.450A pdb=" N GLU E 92 " --> pdb=" O VAL A 93 " (cutoff:3.500A) removed outlier: 7.803A pdb=" N PHE A 95 " --> pdb=" O GLU E 92 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N VAL E 94 " --> pdb=" O PHE A 95 " (cutoff:3.500A) removed outlier: 8.057A pdb=" N SER A 97 " --> pdb=" O VAL E 94 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N THR E 96 " --> pdb=" O SER A 97 " (cutoff:3.500A) removed outlier: 8.569A pdb=" N ASP A 99 " --> pdb=" O THR E 96 " (cutoff:3.500A) removed outlier: 7.098A pdb=" N ASN E 98 " --> pdb=" O ASP A 99 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 104 through 110 removed outlier: 6.930A pdb=" N TYR E 105 " --> pdb=" O ARG A 104 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N THR A 106 " --> pdb=" O TYR E 105 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N ILE E 107 " --> pdb=" O THR A 106 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N ALA A 108 " --> pdb=" O ILE E 107 " (cutoff:3.500A) removed outlier: 8.968A pdb=" N ARG E 104 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 10.107A pdb=" N ILE B 107 " --> pdb=" O ARG E 104 " (cutoff:3.500A) removed outlier: 8.954A pdb=" N THR E 106 " --> pdb=" O ILE B 107 " (cutoff:3.500A) removed outlier: 9.726A pdb=" N ALA B 109 " --> pdb=" O THR E 106 " (cutoff:3.500A) removed outlier: 6.024A pdb=" N ALA E 108 " --> pdb=" O ALA B 109 " (cutoff:3.500A) removed outlier: 9.000A pdb=" N ARG B 104 " --> pdb=" O TYR C 105 " (cutoff:3.500A) removed outlier: 10.137A pdb=" N ILE C 107 " --> pdb=" O ARG B 104 " (cutoff:3.500A) removed outlier: 8.984A pdb=" N THR B 106 " --> pdb=" O ILE C 107 " (cutoff:3.500A) removed outlier: 9.751A pdb=" N ALA C 109 " --> pdb=" O THR B 106 " (cutoff:3.500A) removed outlier: 6.044A pdb=" N ALA B 108 " --> pdb=" O ALA C 109 " (cutoff:3.500A) removed outlier: 8.963A pdb=" N ARG C 104 " --> pdb=" O TYR D 105 " (cutoff:3.500A) removed outlier: 10.104A pdb=" N ILE D 107 " --> pdb=" O ARG C 104 " (cutoff:3.500A) removed outlier: 8.950A pdb=" N THR C 106 " --> pdb=" O ILE D 107 " (cutoff:3.500A) removed outlier: 9.721A pdb=" N ALA D 109 " --> pdb=" O THR C 106 " (cutoff:3.500A) removed outlier: 6.021A pdb=" N ALA C 108 " --> pdb=" O ALA D 109 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 114 through 115 removed outlier: 7.023A pdb=" N TYR E 114 " --> pdb=" O SER A 115 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 118 through 121 removed outlier: 5.886A pdb=" N THR E 118 " --> pdb=" O THR B 119 " (cutoff:3.500A) removed outlier: 7.583A pdb=" N VAL B 121 " --> pdb=" O THR E 118 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N ALA E 120 " --> pdb=" O VAL B 121 " (cutoff:3.500A) removed outlier: 5.877A pdb=" N THR B 118 " --> pdb=" O THR C 119 " (cutoff:3.500A) removed outlier: 7.572A pdb=" N VAL C 121 " --> pdb=" O THR B 118 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N ALA B 120 " --> pdb=" O VAL C 121 " (cutoff:3.500A) removed outlier: 5.887A pdb=" N THR C 118 " --> pdb=" O THR D 119 " (cutoff:3.500A) removed outlier: 7.583A pdb=" N VAL D 121 " --> pdb=" O THR C 118 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N ALA C 120 " --> pdb=" O VAL D 121 " (cutoff:3.500A) 67 hydrogen bonds defined for protein. 201 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: 0.32 Time building geometry restraints manager: 0.42 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 1112 1.33 - 1.45: 504 1.45 - 1.57: 2054 1.57 - 1.68: 0 1.68 - 1.80: 10 Bond restraints: 3680 Sorted by residual: bond pdb=" CB ILE B 26 " pdb=" CG2 ILE B 26 " ideal model delta sigma weight residual 1.521 1.486 0.035 3.30e-02 9.18e+02 1.15e+00 bond pdb=" CB ILE A 26 " pdb=" CG2 ILE A 26 " ideal model delta sigma weight residual 1.521 1.486 0.035 3.30e-02 9.18e+02 1.14e+00 bond pdb=" CB ILE D 26 " pdb=" CG2 ILE D 26 " ideal model delta sigma weight residual 1.521 1.486 0.035 3.30e-02 9.18e+02 1.13e+00 bond pdb=" CB ILE C 26 " pdb=" CG2 ILE C 26 " ideal model delta sigma weight residual 1.521 1.486 0.035 3.30e-02 9.18e+02 1.11e+00 bond pdb=" CB ILE E 26 " pdb=" CG2 ILE E 26 " ideal model delta sigma weight residual 1.521 1.487 0.034 3.30e-02 9.18e+02 1.09e+00 ... (remaining 3675 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.98: 4382 0.98 - 1.95: 522 1.95 - 2.93: 71 2.93 - 3.91: 16 3.91 - 4.89: 14 Bond angle restraints: 5005 Sorted by residual: angle pdb=" NE ARG A 103 " pdb=" CZ ARG A 103 " pdb=" NH1 ARG A 103 " ideal model delta sigma weight residual 121.50 119.68 1.82 1.00e+00 1.00e+00 3.30e+00 angle pdb=" NE ARG B 103 " pdb=" CZ ARG B 103 " pdb=" NH1 ARG B 103 " ideal model delta sigma weight residual 121.50 119.70 1.80 1.00e+00 1.00e+00 3.23e+00 angle pdb=" N SER C 85 " pdb=" CA SER C 85 " pdb=" C SER C 85 " ideal model delta sigma weight residual 109.81 113.76 -3.95 2.21e+00 2.05e-01 3.19e+00 angle pdb=" NE ARG E 103 " pdb=" CZ ARG E 103 " pdb=" NH1 ARG E 103 " ideal model delta sigma weight residual 121.50 119.72 1.78 1.00e+00 1.00e+00 3.18e+00 angle pdb=" N SER A 85 " pdb=" CA SER A 85 " pdb=" C SER A 85 " ideal model delta sigma weight residual 109.81 113.74 -3.93 2.21e+00 2.05e-01 3.17e+00 ... (remaining 5000 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.62: 1925 15.62 - 31.23: 190 31.23 - 46.85: 40 46.85 - 62.46: 5 62.46 - 78.08: 10 Dihedral angle restraints: 2170 sinusoidal: 825 harmonic: 1345 Sorted by residual: dihedral pdb=" CA ALA C 25 " pdb=" C ALA C 25 " pdb=" N ILE C 26 " pdb=" CA ILE C 26 " ideal model delta harmonic sigma weight residual -180.00 -162.48 -17.52 0 5.00e+00 4.00e-02 1.23e+01 dihedral pdb=" CA ALA B 25 " pdb=" C ALA B 25 " pdb=" N ILE B 26 " pdb=" CA ILE B 26 " ideal model delta harmonic sigma weight residual -180.00 -162.49 -17.51 0 5.00e+00 4.00e-02 1.23e+01 dihedral pdb=" CA ALA A 25 " pdb=" C ALA A 25 " pdb=" N ILE A 26 " pdb=" CA ILE A 26 " ideal model delta harmonic sigma weight residual -180.00 -162.51 -17.49 0 5.00e+00 4.00e-02 1.22e+01 ... (remaining 2167 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.024: 182 0.024 - 0.048: 204 0.048 - 0.071: 98 0.071 - 0.095: 60 0.095 - 0.119: 46 Chirality restraints: 590 Sorted by residual: chirality pdb=" CA VAL A 71 " pdb=" N VAL A 71 " pdb=" C VAL A 71 " pdb=" CB VAL A 71 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.54e-01 chirality pdb=" CA VAL C 71 " pdb=" N VAL C 71 " pdb=" C VAL C 71 " pdb=" CB VAL C 71 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.49e-01 chirality pdb=" CA VAL E 121 " pdb=" N VAL E 121 " pdb=" C VAL E 121 " pdb=" CB VAL E 121 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.41e-01 ... (remaining 587 not shown) Planarity restraints: 615 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER A 100 " -0.008 2.00e-02 2.50e+03 1.72e-02 2.94e+00 pdb=" C SER A 100 " 0.030 2.00e-02 2.50e+03 pdb=" O SER A 100 " -0.011 2.00e-02 2.50e+03 pdb=" N GLY A 101 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER D 100 " -0.008 2.00e-02 2.50e+03 1.69e-02 2.85e+00 pdb=" C SER D 100 " 0.029 2.00e-02 2.50e+03 pdb=" O SER D 100 " -0.011 2.00e-02 2.50e+03 pdb=" N GLY D 101 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER B 100 " -0.008 2.00e-02 2.50e+03 1.68e-02 2.84e+00 pdb=" C SER B 100 " 0.029 2.00e-02 2.50e+03 pdb=" O SER B 100 " -0.011 2.00e-02 2.50e+03 pdb=" N GLY B 101 " -0.010 2.00e-02 2.50e+03 ... (remaining 612 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 754 2.78 - 3.31: 3211 3.31 - 3.84: 5811 3.84 - 4.37: 6897 4.37 - 4.90: 13643 Nonbonded interactions: 30316 Sorted by model distance: nonbonded pdb=" OG1 THR C 119 " pdb=" OH TYR D 114 " model vdw 2.255 3.040 nonbonded pdb=" OG1 THR E 119 " pdb=" OH TYR B 114 " model vdw 2.258 3.040 nonbonded pdb=" OH TYR E 114 " pdb=" OG1 THR A 119 " model vdw 2.267 3.040 nonbonded pdb=" OG1 THR B 119 " pdb=" OH TYR C 114 " model vdw 2.272 3.040 nonbonded pdb=" OD2 ASP A 74 " pdb=" NH1 ARG A 103 " model vdw 2.297 3.120 ... (remaining 30311 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: 0.01 Found NCS groups: ncs_group { reference = chain 'E' selection = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.130 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: 0.060 Check model and map are aligned: 0.010 Set scattering table: 0.000 Process input model: 4.300 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 7.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8843 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 : 0.009 0.042 3680 Z= 0.376 Angle : 0.714 4.887 5005 Z= 0.404 Chirality : 0.052 0.119 590 Planarity : 0.004 0.037 615 Dihedral : 13.862 78.081 1300 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 10.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.09 % Favored : 90.91 % Rotamer: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % 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: -4.50 (0.28), residues: 440 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.42 (0.21), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 21 TYR 0.020 0.002 TYR B 114 PHE 0.010 0.002 PHE E 33 TRP 0.002 0.001 TRP D 79 HIS 0.003 0.001 HIS C 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00887 / 0.38 ( 3680) covalent geometry : angle 0.71449 / 0.40 ( 5005) hydrogen bonds : bond 0.19452 / 13.75 ( 67) hydrogen bonds : angle 9.01873 / 6.22 ( 201) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 880 Ramachandran restraints generated. 440 Oldfield, 0 Emsley, 440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 880 Ramachandran restraints generated. 440 Oldfield, 0 Emsley, 440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 55 time to evaluate : 0.081 Fit side-chains REVERT: E 21 ARG cc_start: 0.7689 (ttm170) cc_final: 0.7298 (ttt180) REVERT: E 89 GLU cc_start: 0.8156 (mt-10) cc_final: 0.7717 (mt-10) REVERT: A 21 ARG cc_start: 0.7603 (ttm170) cc_final: 0.7143 (ttt180) REVERT: A 89 GLU cc_start: 0.8449 (mt-10) cc_final: 0.8082 (mt-10) REVERT: B 21 ARG cc_start: 0.7719 (ttm170) cc_final: 0.7416 (ttt180) REVERT: B 70 LYS cc_start: 0.8839 (tttp) cc_final: 0.8623 (tttt) REVERT: B 89 GLU cc_start: 0.8072 (mt-10) cc_final: 0.7628 (mt-10) REVERT: C 70 LYS cc_start: 0.8896 (tttp) cc_final: 0.8678 (tttt) REVERT: C 89 GLU cc_start: 0.8182 (mt-10) cc_final: 0.7844 (mt-10) REVERT: D 66 GLU cc_start: 0.8241 (tm-30) cc_final: 0.7974 (tt0) REVERT: D 70 LYS cc_start: 0.8811 (tttp) cc_final: 0.8499 (tttt) REVERT: D 89 GLU cc_start: 0.8028 (mt-10) cc_final: 0.7654 (mt-10) outliers start: 0 outliers final: 0 residues processed: 55 average time/residue: 0.0934 time to fit residues: 6.1060 Evaluate side-chains 46 residues out of total 395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 46 time to evaluate : 0.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 24 optimal weight: 8.9990 chunk 26 optimal weight: 3.9990 chunk 2 optimal weight: 9.9990 chunk 16 optimal weight: 0.6980 chunk 32 optimal weight: 8.9990 chunk 31 optimal weight: 0.9990 chunk 25 optimal weight: 0.4980 chunk 19 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 22 optimal weight: 0.9980 chunk 37 optimal weight: 0.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.125066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.105186 restraints weight = 4618.657| |-----------------------------------------------------------------------------| r_work (start): 0.3611 rms_B_bonded: 2.28 r_work: 0.3480 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3364 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3364 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8820 moved from start: 0.1308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.016 3680 Z= 0.103 Angle : 0.534 4.109 5005 Z= 0.282 Chirality : 0.048 0.117 590 Planarity : 0.004 0.033 615 Dihedral : 4.648 14.642 495 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 2.53 % Allowed : 5.57 % Favored : 91.90 % 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: -3.70 (0.29), residues: 440 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.81 (0.22), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 103 TYR 0.017 0.001 TYR B 114 PHE 0.013 0.002 PHE B 95 TRP 0.002 0.001 TRP A 79 HIS 0.001 0.000 HIS D 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00231 / 0.10 ( 3680) covalent geometry : angle 0.53359 / 0.28 ( 5005) hydrogen bonds : bond 0.03800 / 2.74 ( 67) hydrogen bonds : angle 6.24548 / 4.31 ( 201) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 880 Ramachandran restraints generated. 440 Oldfield, 0 Emsley, 440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 880 Ramachandran restraints generated. 440 Oldfield, 0 Emsley, 440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 65 time to evaluate : 0.134 Fit side-chains revert: symmetry clash REVERT: E 21 ARG cc_start: 0.7995 (ttm170) cc_final: 0.7285 (ttt180) REVERT: E 89 GLU cc_start: 0.8157 (mt-10) cc_final: 0.7730 (mt-10) REVERT: A 21 ARG cc_start: 0.7880 (ttm170) cc_final: 0.7148 (tpp80) REVERT: A 70 LYS cc_start: 0.9022 (tttt) cc_final: 0.8683 (mtpp) REVERT: A 89 GLU cc_start: 0.8555 (mt-10) cc_final: 0.8238 (mt-10) REVERT: A 104 ARG cc_start: 0.8420 (ptp-170) cc_final: 0.8201 (ptp-170) REVERT: B 21 ARG cc_start: 0.7923 (ttm170) cc_final: 0.7357 (ttt180) REVERT: B 89 GLU cc_start: 0.8125 (mt-10) cc_final: 0.7678 (mt-10) REVERT: C 21 ARG cc_start: 0.8107 (ttm170) cc_final: 0.7424 (ttt180) REVERT: C 70 LYS cc_start: 0.8845 (tttp) cc_final: 0.8536 (ttmt) REVERT: C 89 GLU cc_start: 0.8122 (mt-10) cc_final: 0.7728 (mt-10) REVERT: D 15 LYS cc_start: 0.8608 (mttt) cc_final: 0.7984 (mtpt) REVERT: D 70 LYS cc_start: 0.8828 (tttp) cc_final: 0.8221 (ttmt) REVERT: D 89 GLU cc_start: 0.8097 (mt-10) cc_final: 0.7751 (mt-10) REVERT: D 112 SER cc_start: 0.6632 (t) cc_final: 0.5736 (p) outliers start: 10 outliers final: 8 residues processed: 70 average time/residue: 0.1115 time to fit residues: 8.9956 Evaluate side-chains 65 residues out of total 395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 57 time to evaluate : 0.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 65 VAL Chi-restraints excluded: chain E residue 117 SER Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 117 SER Chi-restraints excluded: chain C residue 65 VAL Chi-restraints excluded: chain C residue 117 SER Chi-restraints excluded: chain D residue 62 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 29 optimal weight: 10.0000 chunk 30 optimal weight: 10.0000 chunk 5 optimal weight: 10.0000 chunk 38 optimal weight: 3.9990 chunk 17 optimal weight: 3.9990 chunk 41 optimal weight: 9.9990 chunk 18 optimal weight: 9.9990 chunk 25 optimal weight: 7.9990 chunk 21 optimal weight: 0.9990 chunk 42 optimal weight: 2.9990 chunk 19 optimal weight: 4.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.120010 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.099171 restraints weight = 4585.963| |-----------------------------------------------------------------------------| r_work (start): 0.3544 rms_B_bonded: 2.26 r_work: 0.3410 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3295 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3295 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8862 moved from start: 0.1241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.041 3680 Z= 0.240 Angle : 0.618 7.705 5005 Z= 0.322 Chirality : 0.049 0.132 590 Planarity : 0.004 0.030 615 Dihedral : 4.860 16.105 495 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 3.04 % Allowed : 9.87 % Favored : 87.09 % 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: -3.55 (0.30), residues: 440 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.70 (0.23), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 103 TYR 0.018 0.002 TYR B 114 PHE 0.020 0.003 PHE A 33 TRP 0.002 0.001 TRP C 79 HIS 0.002 0.001 HIS D 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00592 / 0.24 ( 3680) covalent geometry : angle 0.61838 / 0.32 ( 5005) hydrogen bonds : bond 0.04177 / 3.08 ( 67) hydrogen bonds : angle 6.06789 / 4.19 ( 201) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 880 Ramachandran restraints generated. 440 Oldfield, 0 Emsley, 440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 880 Ramachandran restraints generated. 440 Oldfield, 0 Emsley, 440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 54 time to evaluate : 0.138 Fit side-chains REVERT: E 21 ARG cc_start: 0.7974 (ttm170) cc_final: 0.7167 (tpp80) REVERT: E 89 GLU cc_start: 0.8219 (mt-10) cc_final: 0.7778 (mt-10) REVERT: A 21 ARG cc_start: 0.7869 (ttm170) cc_final: 0.7077 (tpp80) REVERT: A 89 GLU cc_start: 0.8612 (mt-10) cc_final: 0.8303 (mt-10) REVERT: B 21 ARG cc_start: 0.7890 (ttm170) cc_final: 0.7344 (ttt180) REVERT: B 70 LYS cc_start: 0.8803 (tttp) cc_final: 0.8486 (ttpt) REVERT: B 89 GLU cc_start: 0.8197 (mt-10) cc_final: 0.7757 (mt-10) REVERT: C 89 GLU cc_start: 0.8157 (mt-10) cc_final: 0.7754 (mt-10) REVERT: D 15 LYS cc_start: 0.8628 (mttt) cc_final: 0.7960 (mtpt) REVERT: D 70 LYS cc_start: 0.8677 (tttp) cc_final: 0.8252 (ttpt) REVERT: D 89 GLU cc_start: 0.8106 (mt-10) cc_final: 0.7763 (mt-10) outliers start: 12 outliers final: 10 residues processed: 58 average time/residue: 0.1016 time to fit residues: 6.9349 Evaluate side-chains 59 residues out of total 395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 49 time to evaluate : 0.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 65 VAL Chi-restraints excluded: chain E residue 117 SER Chi-restraints excluded: chain A residue 23 SER Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 117 SER Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 117 SER Chi-restraints excluded: chain C residue 65 VAL Chi-restraints excluded: chain D residue 62 GLU Chi-restraints excluded: chain D residue 117 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 32 optimal weight: 5.9990 chunk 30 optimal weight: 4.9990 chunk 31 optimal weight: 2.9990 chunk 24 optimal weight: 10.0000 chunk 17 optimal weight: 3.9990 chunk 41 optimal weight: 4.9990 chunk 29 optimal weight: 10.0000 chunk 21 optimal weight: 0.8980 chunk 39 optimal weight: 2.9990 chunk 34 optimal weight: 0.9980 chunk 40 optimal weight: 3.9990 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.126430 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.106947 restraints weight = 4632.912| |-----------------------------------------------------------------------------| r_work (start): 0.3603 rms_B_bonded: 2.20 r_work: 0.3477 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3362 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3362 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8858 moved from start: 0.1464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 3680 Z= 0.176 Angle : 0.581 7.212 5005 Z= 0.301 Chirality : 0.049 0.128 590 Planarity : 0.003 0.029 615 Dihedral : 4.722 15.221 495 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 3.29 % Allowed : 10.38 % Favored : 86.33 % 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: -3.32 (0.31), residues: 440 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.52 (0.24), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 103 TYR 0.017 0.001 TYR B 114 PHE 0.015 0.002 PHE A 33 TRP 0.001 0.000 TRP B 79 HIS 0.002 0.000 HIS D 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00433 / 0.18 ( 3680) covalent geometry : angle 0.58111 / 0.30 ( 5005) hydrogen bonds : bond 0.03579 / 2.64 ( 67) hydrogen bonds : angle 5.77125 / 3.96 ( 201) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 880 Ramachandran restraints generated. 440 Oldfield, 0 Emsley, 440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 880 Ramachandran restraints generated. 440 Oldfield, 0 Emsley, 440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 56 time to evaluate : 0.131 Fit side-chains REVERT: E 89 GLU cc_start: 0.8182 (mt-10) cc_final: 0.7759 (mt-10) REVERT: A 21 ARG cc_start: 0.7836 (ttm170) cc_final: 0.7145 (tpp80) REVERT: A 89 GLU cc_start: 0.8601 (mt-10) cc_final: 0.8292 (mt-10) REVERT: A 104 ARG cc_start: 0.8477 (ptp-170) cc_final: 0.8271 (ptp-170) REVERT: B 21 ARG cc_start: 0.7925 (ttm170) cc_final: 0.7436 (ttt180) REVERT: B 89 GLU cc_start: 0.8149 (mt-10) cc_final: 0.7708 (mt-10) REVERT: C 89 GLU cc_start: 0.8104 (mt-10) cc_final: 0.7708 (mt-10) REVERT: D 15 LYS cc_start: 0.8578 (mttt) cc_final: 0.7945 (mtpt) REVERT: D 70 LYS cc_start: 0.8610 (tttp) cc_final: 0.8242 (ttpt) REVERT: D 89 GLU cc_start: 0.8098 (mt-10) cc_final: 0.7754 (mt-10) outliers start: 13 outliers final: 10 residues processed: 60 average time/residue: 0.0932 time to fit residues: 6.6349 Evaluate side-chains 60 residues out of total 395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 50 time to evaluate : 0.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 65 VAL Chi-restraints excluded: chain A residue 23 SER Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 117 SER Chi-restraints excluded: chain B residue 61 GLU Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 117 SER Chi-restraints excluded: chain C residue 65 VAL Chi-restraints excluded: chain D residue 112 SER Chi-restraints excluded: chain D residue 117 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 20 optimal weight: 10.0000 chunk 4 optimal weight: 3.9990 chunk 31 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 23 optimal weight: 8.9990 chunk 28 optimal weight: 7.9990 chunk 42 optimal weight: 9.9990 chunk 3 optimal weight: 3.9990 chunk 17 optimal weight: 1.9990 chunk 36 optimal weight: 8.9990 chunk 43 optimal weight: 0.9980 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.124034 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.104115 restraints weight = 4662.489| |-----------------------------------------------------------------------------| r_work (start): 0.3585 rms_B_bonded: 2.20 r_work: 0.3453 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3334 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3334 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8884 moved from start: 0.1470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.042 3680 Z= 0.251 Angle : 0.630 8.398 5005 Z= 0.327 Chirality : 0.050 0.129 590 Planarity : 0.004 0.029 615 Dihedral : 4.926 15.865 495 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 3.29 % Allowed : 13.16 % Favored : 83.54 % 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: -3.29 (0.32), residues: 440 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.50 (0.24), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 103 TYR 0.019 0.002 TYR B 114 PHE 0.020 0.003 PHE D 33 TRP 0.002 0.001 TRP C 79 HIS 0.003 0.001 HIS D 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00621 / 0.25 ( 3680) covalent geometry : angle 0.63012 / 0.33 ( 5005) hydrogen bonds : bond 0.03889 / 2.89 ( 67) hydrogen bonds : angle 5.86843 / 4.04 ( 201) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 880 Ramachandran restraints generated. 440 Oldfield, 0 Emsley, 440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 880 Ramachandran restraints generated. 440 Oldfield, 0 Emsley, 440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 50 time to evaluate : 0.141 Fit side-chains REVERT: E 89 GLU cc_start: 0.8196 (mt-10) cc_final: 0.7779 (mt-10) REVERT: A 21 ARG cc_start: 0.7857 (ttm170) cc_final: 0.7367 (mtp180) REVERT: A 70 LYS cc_start: 0.8943 (mtpt) cc_final: 0.8583 (mtpp) REVERT: A 89 GLU cc_start: 0.8621 (mt-10) cc_final: 0.8309 (mt-10) REVERT: B 21 ARG cc_start: 0.7963 (ttm170) cc_final: 0.7468 (ttt180) REVERT: B 70 LYS cc_start: 0.8789 (tttt) cc_final: 0.8502 (ttpt) REVERT: B 89 GLU cc_start: 0.8190 (mt-10) cc_final: 0.7778 (mt-10) REVERT: C 89 GLU cc_start: 0.8137 (mt-10) cc_final: 0.7731 (mt-10) REVERT: D 15 LYS cc_start: 0.8601 (mttt) cc_final: 0.7952 (mtpt) REVERT: D 70 LYS cc_start: 0.8681 (tttp) cc_final: 0.8297 (ttpt) REVERT: D 89 GLU cc_start: 0.8091 (mt-10) cc_final: 0.7735 (mt-10) outliers start: 13 outliers final: 12 residues processed: 54 average time/residue: 0.0857 time to fit residues: 5.5924 Evaluate side-chains 60 residues out of total 395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 48 time to evaluate : 0.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 65 VAL Chi-restraints excluded: chain E residue 117 SER Chi-restraints excluded: chain A residue 23 SER Chi-restraints excluded: chain A residue 61 GLU Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 117 SER Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 117 SER Chi-restraints excluded: chain C residue 65 VAL Chi-restraints excluded: chain D residue 62 GLU Chi-restraints excluded: chain D residue 112 SER Chi-restraints excluded: chain D residue 117 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 44 optimal weight: 4.9990 chunk 10 optimal weight: 0.7980 chunk 21 optimal weight: 3.9990 chunk 29 optimal weight: 9.9990 chunk 23 optimal weight: 10.0000 chunk 8 optimal weight: 4.9990 chunk 25 optimal weight: 4.9990 chunk 26 optimal weight: 0.9990 chunk 9 optimal weight: 6.9990 chunk 3 optimal weight: 0.4980 chunk 20 optimal weight: 10.0000 overall best weight: 2.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.126438 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.106870 restraints weight = 4665.755| |-----------------------------------------------------------------------------| r_work (start): 0.3613 rms_B_bonded: 2.22 r_work: 0.3486 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3370 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3370 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8850 moved from start: 0.1653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 3680 Z= 0.169 Angle : 0.571 7.418 5005 Z= 0.296 Chirality : 0.048 0.124 590 Planarity : 0.003 0.029 615 Dihedral : 4.727 14.757 495 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 3.54 % Allowed : 14.43 % Favored : 82.03 % 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: -3.14 (0.32), residues: 440 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.38 (0.25), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 103 TYR 0.018 0.001 TYR B 114 PHE 0.013 0.002 PHE A 33 TRP 0.001 0.001 TRP C 79 HIS 0.002 0.000 HIS D 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00416 / 0.17 ( 3680) covalent geometry : angle 0.57054 / 0.30 ( 5005) hydrogen bonds : bond 0.03363 / 2.50 ( 67) hydrogen bonds : angle 5.65062 / 3.87 ( 201) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 880 Ramachandran restraints generated. 440 Oldfield, 0 Emsley, 440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 880 Ramachandran restraints generated. 440 Oldfield, 0 Emsley, 440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 49 time to evaluate : 0.136 Fit side-chains REVERT: E 61 GLU cc_start: 0.7569 (OUTLIER) cc_final: 0.7020 (pt0) REVERT: E 89 GLU cc_start: 0.8186 (mt-10) cc_final: 0.7769 (mt-10) REVERT: A 21 ARG cc_start: 0.7894 (ttm170) cc_final: 0.7418 (mtp180) REVERT: A 70 LYS cc_start: 0.8925 (mtpt) cc_final: 0.8458 (mtpp) REVERT: A 89 GLU cc_start: 0.8564 (mt-10) cc_final: 0.8267 (mt-10) REVERT: B 21 ARG cc_start: 0.7934 (ttm170) cc_final: 0.7427 (ttt180) REVERT: B 89 GLU cc_start: 0.8157 (mt-10) cc_final: 0.7731 (mt-10) REVERT: C 89 GLU cc_start: 0.8116 (mt-10) cc_final: 0.7707 (mt-10) REVERT: D 15 LYS cc_start: 0.8578 (mttt) cc_final: 0.7955 (mtpt) REVERT: D 70 LYS cc_start: 0.8659 (tttp) cc_final: 0.8291 (ttpt) REVERT: D 89 GLU cc_start: 0.8073 (mt-10) cc_final: 0.7706 (mt-10) outliers start: 14 outliers final: 12 residues processed: 53 average time/residue: 0.0944 time to fit residues: 5.9587 Evaluate side-chains 61 residues out of total 395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 48 time to evaluate : 0.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 61 GLU Chi-restraints excluded: chain E residue 65 VAL Chi-restraints excluded: chain E residue 117 SER Chi-restraints excluded: chain A residue 23 SER Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 117 SER Chi-restraints excluded: chain B residue 61 GLU Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 117 SER Chi-restraints excluded: chain C residue 65 VAL Chi-restraints excluded: chain D residue 62 GLU Chi-restraints excluded: chain D residue 112 SER Chi-restraints excluded: chain D residue 117 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 9 optimal weight: 0.2980 chunk 6 optimal weight: 10.0000 chunk 42 optimal weight: 9.9990 chunk 2 optimal weight: 10.0000 chunk 15 optimal weight: 1.9990 chunk 7 optimal weight: 0.7980 chunk 5 optimal weight: 3.9990 chunk 8 optimal weight: 5.9990 chunk 12 optimal weight: 6.9990 chunk 34 optimal weight: 5.9990 chunk 19 optimal weight: 3.9990 overall best weight: 2.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 31 HIS ** 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 = 0.3892 r_free = 0.3892 target = 0.126095 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.106402 restraints weight = 4770.604| |-----------------------------------------------------------------------------| r_work (start): 0.3618 rms_B_bonded: 2.25 r_work: 0.3485 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3368 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3368 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8854 moved from start: 0.1717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 3680 Z= 0.166 Angle : 0.570 8.348 5005 Z= 0.294 Chirality : 0.048 0.123 590 Planarity : 0.003 0.027 615 Dihedral : 4.686 14.514 495 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 4.05 % Allowed : 14.43 % Favored : 81.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -3.07 (0.33), residues: 440 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.33 (0.25), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 103 TYR 0.017 0.001 TYR B 114 PHE 0.013 0.002 PHE A 33 TRP 0.001 0.001 TRP C 79 HIS 0.002 0.000 HIS D 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00408 / 0.17 ( 3680) covalent geometry : angle 0.56951 / 0.29 ( 5005) hydrogen bonds : bond 0.03334 / 2.48 ( 67) hydrogen bonds : angle 5.63508 / 3.87 ( 201) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 880 Ramachandran restraints generated. 440 Oldfield, 0 Emsley, 440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 880 Ramachandran restraints generated. 440 Oldfield, 0 Emsley, 440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 49 time to evaluate : 0.138 Fit side-chains REVERT: E 61 GLU cc_start: 0.7587 (OUTLIER) cc_final: 0.7069 (pt0) REVERT: E 89 GLU cc_start: 0.8189 (mt-10) cc_final: 0.7772 (mt-10) REVERT: A 21 ARG cc_start: 0.7918 (ttm170) cc_final: 0.7431 (mtp180) REVERT: A 70 LYS cc_start: 0.8923 (mtpt) cc_final: 0.8462 (mtpp) REVERT: A 89 GLU cc_start: 0.8597 (mt-10) cc_final: 0.8292 (mt-10) REVERT: B 21 ARG cc_start: 0.7955 (ttm170) cc_final: 0.7447 (ttt180) REVERT: B 89 GLU cc_start: 0.8147 (mt-10) cc_final: 0.7735 (mt-10) REVERT: C 89 GLU cc_start: 0.8125 (mt-10) cc_final: 0.7717 (mt-10) REVERT: D 15 LYS cc_start: 0.8577 (mttt) cc_final: 0.7962 (mtpt) REVERT: D 70 LYS cc_start: 0.8663 (tttp) cc_final: 0.8288 (ttpt) REVERT: D 89 GLU cc_start: 0.8081 (mt-10) cc_final: 0.7728 (mt-10) outliers start: 16 outliers final: 13 residues processed: 55 average time/residue: 0.0848 time to fit residues: 5.6268 Evaluate side-chains 62 residues out of total 395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 48 time to evaluate : 0.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 61 GLU Chi-restraints excluded: chain E residue 65 VAL Chi-restraints excluded: chain E residue 117 SER Chi-restraints excluded: chain A residue 23 SER Chi-restraints excluded: chain A residue 61 GLU Chi-restraints excluded: chain A residue 62 GLU Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 117 SER Chi-restraints excluded: chain B residue 61 GLU Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain C residue 65 VAL Chi-restraints excluded: chain D residue 62 GLU Chi-restraints excluded: chain D residue 112 SER Chi-restraints excluded: chain D residue 117 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 3 optimal weight: 7.9990 chunk 27 optimal weight: 9.9990 chunk 42 optimal weight: 9.9990 chunk 38 optimal weight: 9.9990 chunk 35 optimal weight: 6.9990 chunk 12 optimal weight: 4.9990 chunk 32 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 1 optimal weight: 0.9980 chunk 44 optimal weight: 0.8980 chunk 39 optimal weight: 6.9990 overall best weight: 3.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 88 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.119158 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.098110 restraints weight = 4878.207| |-----------------------------------------------------------------------------| r_work (start): 0.3563 rms_B_bonded: 2.34 r_work: 0.3424 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3304 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3304 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8881 moved from start: 0.1634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 3680 Z= 0.260 Angle : 0.632 8.552 5005 Z= 0.329 Chirality : 0.050 0.124 590 Planarity : 0.004 0.027 615 Dihedral : 4.919 15.763 495 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 3.80 % Allowed : 15.19 % Favored : 81.01 % 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: -3.17 (0.32), residues: 440 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.41 (0.25), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 103 TYR 0.018 0.002 TYR B 114 PHE 0.020 0.003 PHE D 33 TRP 0.002 0.001 TRP A 79 HIS 0.003 0.001 HIS D 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00646 / 0.26 ( 3680) covalent geometry : angle 0.63247 / 0.33 ( 5005) hydrogen bonds : bond 0.03850 / 2.87 ( 67) hydrogen bonds : angle 5.83273 / 4.01 ( 201) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 880 Ramachandran restraints generated. 440 Oldfield, 0 Emsley, 440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 880 Ramachandran restraints generated. 440 Oldfield, 0 Emsley, 440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 49 time to evaluate : 0.140 Fit side-chains REVERT: E 61 GLU cc_start: 0.7662 (OUTLIER) cc_final: 0.7015 (pt0) REVERT: E 89 GLU cc_start: 0.8225 (mt-10) cc_final: 0.7813 (mt-10) REVERT: A 21 ARG cc_start: 0.7905 (ttm170) cc_final: 0.7421 (mtp180) REVERT: A 70 LYS cc_start: 0.8932 (mtpt) cc_final: 0.8551 (mtpp) REVERT: A 89 GLU cc_start: 0.8615 (mt-10) cc_final: 0.8307 (mt-10) REVERT: B 21 ARG cc_start: 0.7989 (ttm170) cc_final: 0.7478 (ttt180) REVERT: B 89 GLU cc_start: 0.8171 (mt-10) cc_final: 0.7750 (mt-10) REVERT: C 89 GLU cc_start: 0.8112 (mt-10) cc_final: 0.7738 (mt-10) REVERT: D 15 LYS cc_start: 0.8607 (mttt) cc_final: 0.7957 (mtpt) REVERT: D 70 LYS cc_start: 0.8662 (tttp) cc_final: 0.8269 (ttpt) REVERT: D 89 GLU cc_start: 0.8060 (mt-10) cc_final: 0.7724 (mt-10) outliers start: 15 outliers final: 14 residues processed: 53 average time/residue: 0.0955 time to fit residues: 6.0892 Evaluate side-chains 62 residues out of total 395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 47 time to evaluate : 0.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 61 GLU Chi-restraints excluded: chain E residue 65 VAL Chi-restraints excluded: chain E residue 117 SER Chi-restraints excluded: chain A residue 23 SER Chi-restraints excluded: chain A residue 61 GLU Chi-restraints excluded: chain A residue 62 GLU Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 117 SER Chi-restraints excluded: chain B residue 61 GLU Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 117 SER Chi-restraints excluded: chain C residue 65 VAL Chi-restraints excluded: chain D residue 62 GLU Chi-restraints excluded: chain D residue 112 SER Chi-restraints excluded: chain D residue 117 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 11 optimal weight: 10.0000 chunk 33 optimal weight: 10.0000 chunk 38 optimal weight: 5.9990 chunk 29 optimal weight: 5.9990 chunk 34 optimal weight: 6.9990 chunk 23 optimal weight: 6.9990 chunk 13 optimal weight: 5.9990 chunk 27 optimal weight: 5.9990 chunk 21 optimal weight: 3.9990 chunk 25 optimal weight: 5.9990 chunk 12 optimal weight: 0.9980 overall best weight: 4.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.122030 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.102099 restraints weight = 4691.027| |-----------------------------------------------------------------------------| r_work (start): 0.3530 rms_B_bonded: 2.25 r_work: 0.3399 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3281 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3281 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8914 moved from start: 0.1619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.047 3680 Z= 0.312 Angle : 0.672 8.855 5005 Z= 0.350 Chirality : 0.051 0.125 590 Planarity : 0.004 0.029 615 Dihedral : 5.073 16.751 495 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 3.80 % Allowed : 15.19 % Favored : 81.01 % 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: -3.29 (0.32), residues: 440 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.50 (0.24), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 103 TYR 0.018 0.002 TYR C 114 PHE 0.023 0.003 PHE A 33 TRP 0.002 0.001 TRP A 79 HIS 0.004 0.001 HIS D 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00773 / 0.31 ( 3680) covalent geometry : angle 0.67229 / 0.35 ( 5005) hydrogen bonds : bond 0.04093 / 3.05 ( 67) hydrogen bonds : angle 5.97878 / 4.12 ( 201) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 880 Ramachandran restraints generated. 440 Oldfield, 0 Emsley, 440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 880 Ramachandran restraints generated. 440 Oldfield, 0 Emsley, 440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 48 time to evaluate : 0.136 Fit side-chains REVERT: E 61 GLU cc_start: 0.7733 (OUTLIER) cc_final: 0.6909 (pt0) REVERT: E 89 GLU cc_start: 0.8309 (mt-10) cc_final: 0.7917 (mt-10) REVERT: A 21 ARG cc_start: 0.7889 (ttm170) cc_final: 0.7473 (mtp180) REVERT: A 70 LYS cc_start: 0.8943 (mtpt) cc_final: 0.8573 (mtpp) REVERT: A 89 GLU cc_start: 0.8653 (mt-10) cc_final: 0.8352 (mt-10) REVERT: B 89 GLU cc_start: 0.8198 (mt-10) cc_final: 0.7776 (mt-10) REVERT: B 99 ASP cc_start: 0.7746 (m-30) cc_final: 0.7503 (m-30) REVERT: C 89 GLU cc_start: 0.8200 (mt-10) cc_final: 0.7774 (mt-10) REVERT: D 15 LYS cc_start: 0.8629 (mttt) cc_final: 0.7971 (mtpt) REVERT: D 89 GLU cc_start: 0.8131 (mt-10) cc_final: 0.7763 (mt-10) outliers start: 15 outliers final: 13 residues processed: 52 average time/residue: 0.0871 time to fit residues: 5.4819 Evaluate side-chains 62 residues out of total 395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 48 time to evaluate : 0.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 61 GLU Chi-restraints excluded: chain E residue 65 VAL Chi-restraints excluded: chain E residue 117 SER Chi-restraints excluded: chain A residue 23 SER Chi-restraints excluded: chain A residue 61 GLU Chi-restraints excluded: chain A residue 62 GLU Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 117 SER Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 117 SER Chi-restraints excluded: chain C residue 65 VAL Chi-restraints excluded: chain D residue 62 GLU Chi-restraints excluded: chain D residue 112 SER Chi-restraints excluded: chain D residue 117 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 4 optimal weight: 3.9990 chunk 21 optimal weight: 4.9990 chunk 27 optimal weight: 6.9990 chunk 18 optimal weight: 2.9990 chunk 20 optimal weight: 9.9990 chunk 16 optimal weight: 0.9980 chunk 44 optimal weight: 3.9990 chunk 34 optimal weight: 4.9990 chunk 29 optimal weight: 2.9990 chunk 0 optimal weight: 7.9990 chunk 22 optimal weight: 0.9980 overall best weight: 2.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.125929 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.106282 restraints weight = 4763.248| |-----------------------------------------------------------------------------| r_work (start): 0.3586 rms_B_bonded: 2.26 r_work: 0.3459 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3340 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3340 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8856 moved from start: 0.1769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 3680 Z= 0.178 Angle : 0.581 7.624 5005 Z= 0.302 Chirality : 0.049 0.122 590 Planarity : 0.004 0.030 615 Dihedral : 4.805 15.003 495 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 3.54 % Allowed : 15.44 % Favored : 81.01 % 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: -3.16 (0.32), residues: 440 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.40 (0.25), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 103 TYR 0.017 0.001 TYR B 114 PHE 0.012 0.002 PHE A 33 TRP 0.001 0.001 TRP C 79 HIS 0.002 0.000 HIS D 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00440 / 0.18 ( 3680) covalent geometry : angle 0.58093 / 0.30 ( 5005) hydrogen bonds : bond 0.03416 / 2.53 ( 67) hydrogen bonds : angle 5.72902 / 3.93 ( 201) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 880 Ramachandran restraints generated. 440 Oldfield, 0 Emsley, 440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 880 Ramachandran restraints generated. 440 Oldfield, 0 Emsley, 440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 49 time to evaluate : 0.142 Fit side-chains REVERT: E 61 GLU cc_start: 0.7567 (OUTLIER) cc_final: 0.7026 (pt0) REVERT: E 89 GLU cc_start: 0.8244 (mt-10) cc_final: 0.7853 (mt-10) REVERT: A 21 ARG cc_start: 0.7927 (ttm170) cc_final: 0.7442 (mtp180) REVERT: A 70 LYS cc_start: 0.8906 (mtpt) cc_final: 0.8443 (mtpp) REVERT: A 89 GLU cc_start: 0.8623 (mt-10) cc_final: 0.8329 (mt-10) REVERT: B 21 ARG cc_start: 0.7871 (ttp-170) cc_final: 0.7321 (ttt180) REVERT: B 89 GLU cc_start: 0.8147 (mt-10) cc_final: 0.7735 (mt-10) REVERT: B 99 ASP cc_start: 0.7716 (m-30) cc_final: 0.7483 (m-30) REVERT: C 89 GLU cc_start: 0.8166 (mt-10) cc_final: 0.7755 (mt-10) REVERT: D 15 LYS cc_start: 0.8594 (mttt) cc_final: 0.7953 (mtpt) REVERT: D 70 LYS cc_start: 0.8669 (tttt) cc_final: 0.8309 (ttmt) REVERT: D 89 GLU cc_start: 0.8097 (mt-10) cc_final: 0.7761 (mt-10) outliers start: 14 outliers final: 12 residues processed: 53 average time/residue: 0.0694 time to fit residues: 4.5025 Evaluate side-chains 61 residues out of total 395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 48 time to evaluate : 0.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 61 GLU Chi-restraints excluded: chain E residue 65 VAL Chi-restraints excluded: chain E residue 117 SER Chi-restraints excluded: chain A residue 23 SER Chi-restraints excluded: chain A residue 61 GLU Chi-restraints excluded: chain A residue 62 GLU Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 117 SER Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain C residue 65 VAL Chi-restraints excluded: chain D residue 62 GLU Chi-restraints excluded: chain D residue 112 SER Chi-restraints excluded: chain D residue 117 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 9 optimal weight: 8.9990 chunk 39 optimal weight: 7.9990 chunk 26 optimal weight: 4.9990 chunk 10 optimal weight: 3.9990 chunk 3 optimal weight: 5.9990 chunk 35 optimal weight: 0.9980 chunk 7 optimal weight: 4.9990 chunk 34 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 22 optimal weight: 0.8980 chunk 44 optimal weight: 2.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.125840 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.106330 restraints weight = 4608.579| |-----------------------------------------------------------------------------| r_work (start): 0.3598 rms_B_bonded: 2.24 r_work: 0.3471 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3355 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3355 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8854 moved from start: 0.1835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 3680 Z= 0.164 Angle : 0.566 7.448 5005 Z= 0.294 Chirality : 0.048 0.122 590 Planarity : 0.004 0.029 615 Dihedral : 4.699 14.832 495 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 3.29 % Allowed : 16.20 % Favored : 80.51 % 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: -3.11 (0.33), residues: 440 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.36 (0.25), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 103 TYR 0.017 0.001 TYR B 114 PHE 0.012 0.002 PHE A 33 TRP 0.001 0.001 TRP C 79 HIS 0.001 0.000 HIS D 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00406 / 0.16 ( 3680) covalent geometry : angle 0.56641 / 0.29 ( 5005) hydrogen bonds : bond 0.03309 / 2.44 ( 67) hydrogen bonds : angle 5.59328 / 3.84 ( 201) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1078.17 seconds wall clock time: 19 minutes 8.90 seconds (1148.90 seconds total)