Starting phenix.real_space_refine on Wed Jul 1 22:40:18 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9els_48160/07_2026/9els_48160.cif Found real_map, /net/cci-nas-00/data/ceres_data/9els_48160/07_2026/9els_48160.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.02 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9els_48160/07_2026/9els_48160.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9els_48160/07_2026/9els_48160.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9els_48160/07_2026/9els_48160.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9els_48160/07_2026/9els_48160.map" } resolution = 3.02 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= 0.006 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 15 5.16 5 C 2170 2.51 5 N 580 2.21 5 O 745 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 3510 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 702 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 702 Classifications: {'peptide': 92} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 89} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Restraints were copied for chains: B, C, D, E Time building chain proxies: 0.82, per 1000 atoms: 0.23 Number of scatterers: 3510 At special positions: 0 Unit cell: (91.14, 83.3, 50.96, 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 15 16.00 O 745 8.00 N 580 7.00 C 2170 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 22 " - pdb=" SG CYS A 91 " distance=2.03 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 91 " distance=2.03 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 91 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 91 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 91 " distance=2.03 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: 0.16 Conformation dependent library (CDL) restraints added in 95.5 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: 850 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 11 sheets defined 0.0% alpha, 42.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.13 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'C' and resid 2 through 5 removed outlier: 6.214A pdb=" N MET A 3 " --> pdb=" O LEU D 4 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N MET D 3 " --> pdb=" O LEU E 4 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 9 through 12 removed outlier: 6.398A pdb=" N VAL A 10 " --> pdb=" O SER D 11 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N VAL D 10 " --> pdb=" O SER E 11 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 15 through 22 removed outlier: 6.983A pdb=" N GLY A 15 " --> pdb=" O LYS D 16 " (cutoff:3.500A) removed outlier: 8.595A pdb=" N VAL D 18 " --> pdb=" O GLY A 15 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N THR A 17 " --> pdb=" O VAL D 18 " (cutoff:3.500A) removed outlier: 8.197A pdb=" N ILE D 20 " --> pdb=" O THR A 17 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N THR A 19 " --> pdb=" O ILE D 20 " (cutoff:3.500A) removed outlier: 7.986A pdb=" N CYS D 22 " --> pdb=" O THR A 19 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N SER A 21 " --> pdb=" O CYS D 22 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N GLY D 15 " --> pdb=" O LYS E 16 " (cutoff:3.500A) removed outlier: 8.602A pdb=" N VAL E 18 " --> pdb=" O GLY D 15 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N THR D 17 " --> pdb=" O VAL E 18 " (cutoff:3.500A) removed outlier: 8.204A pdb=" N ILE E 20 " --> pdb=" O THR D 17 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N THR D 19 " --> pdb=" O ILE E 20 " (cutoff:3.500A) removed outlier: 7.992A pdb=" N CYS E 22 " --> pdb=" O THR D 19 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N SER D 21 " --> pdb=" O CYS E 22 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 27 through 29 removed outlier: 3.540A pdb=" N SER C 28 " --> pdb=" O GLY B 27 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N SER B 28 " --> pdb=" O GLY A 27 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N SER A 28 " --> pdb=" O ILE D 29 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N SER D 28 " --> pdb=" O ILE E 29 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 33 through 35 removed outlier: 6.670A pdb=" N TYR B 33 " --> pdb=" O VAL C 34 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N TYR A 33 " --> pdb=" O VAL B 34 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 66 through 68 removed outlier: 6.390A pdb=" N ILE B 67 " --> pdb=" O ASP C 68 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N ILE A 67 " --> pdb=" O ASP B 68 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 75 through 78 removed outlier: 6.508A pdb=" N SER A 75 " --> pdb=" O LEU D 76 " (cutoff:3.500A) removed outlier: 8.327A pdb=" N ILE D 78 " --> pdb=" O SER A 75 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N THR A 77 " --> pdb=" O ILE D 78 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N SER D 75 " --> pdb=" O LEU E 76 " (cutoff:3.500A) removed outlier: 8.329A pdb=" N ILE E 78 " --> pdb=" O SER D 75 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N THR D 77 " --> pdb=" O ILE E 78 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 81 through 84 removed outlier: 6.568A pdb=" N LEU B 81 " --> pdb=" O LYS C 82 " (cutoff:3.500A) removed outlier: 8.636A pdb=" N GLU C 84 " --> pdb=" O LEU B 81 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N LYS B 83 " --> pdb=" O GLU C 84 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N LEU A 81 " --> pdb=" O LYS B 82 " (cutoff:3.500A) removed outlier: 8.630A pdb=" N GLU B 84 " --> pdb=" O LEU A 81 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N LYS A 83 " --> pdb=" O GLU B 84 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 88 through 95 removed outlier: 6.262A pdb=" N GLU B 88 " --> pdb=" O TYR C 89 " (cutoff:3.500A) removed outlier: 8.064A pdb=" N CYS C 91 " --> pdb=" O GLU B 88 " (cutoff:3.500A) removed outlier: 9.217A pdb=" N TYR B 90 " --> pdb=" O CYS C 91 " (cutoff:3.500A) removed outlier: 8.606A pdb=" N SER C 93 " --> pdb=" O TYR B 90 " (cutoff:3.500A) removed outlier: 9.625A pdb=" N GLN B 92 " --> pdb=" O SER C 93 " (cutoff:3.500A) removed outlier: 10.776A pdb=" N GLU C 95 " --> pdb=" O GLN B 92 " (cutoff:3.500A) removed outlier: 9.561A pdb=" N TYR B 94 " --> pdb=" O GLU C 95 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N GLU A 88 " --> pdb=" O TYR B 89 " (cutoff:3.500A) removed outlier: 8.056A pdb=" N CYS B 91 " --> pdb=" O GLU A 88 " (cutoff:3.500A) removed outlier: 9.203A pdb=" N TYR A 90 " --> pdb=" O CYS B 91 " (cutoff:3.500A) removed outlier: 8.591A pdb=" N SER B 93 " --> pdb=" O TYR A 90 " (cutoff:3.500A) removed outlier: 9.608A pdb=" N GLN A 92 " --> pdb=" O SER B 93 " (cutoff:3.500A) removed outlier: 10.760A pdb=" N GLU B 95 " --> pdb=" O GLN A 92 " (cutoff:3.500A) removed outlier: 9.543A pdb=" N TYR A 94 " --> pdb=" O GLU B 95 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N CYS A 91 " --> pdb=" O TYR D 90 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N GLN D 92 " --> pdb=" O CYS A 91 " (cutoff:3.500A) removed outlier: 7.125A pdb=" N SER A 93 " --> pdb=" O GLN D 92 " (cutoff:3.500A) removed outlier: 7.197A pdb=" N TYR D 94 " --> pdb=" O SER A 93 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N GLU A 95 " --> pdb=" O TYR D 94 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N CYS D 91 " --> pdb=" O TYR E 90 " (cutoff:3.500A) removed outlier: 7.062A pdb=" N GLN E 92 " --> pdb=" O CYS D 91 " (cutoff:3.500A) removed outlier: 7.141A pdb=" N SER D 93 " --> pdb=" O GLN E 92 " (cutoff:3.500A) removed outlier: 7.213A pdb=" N TYR E 94 " --> pdb=" O SER D 93 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N GLU D 95 " --> pdb=" O TYR E 94 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 98 through 101 removed outlier: 6.318A pdb=" N LEU A 99 " --> pdb=" O TYR D 100 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N LEU D 99 " --> pdb=" O TYR E 100 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 107 through 111 removed outlier: 6.603A pdb=" N THR B 107 " --> pdb=" O LYS C 108 " (cutoff:3.500A) removed outlier: 8.337A pdb=" N THR C 110 " --> pdb=" O THR B 107 " (cutoff:3.500A) removed outlier: 7.073A pdb=" N LEU B 109 " --> pdb=" O THR C 110 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N THR A 107 " --> pdb=" O LYS B 108 " (cutoff:3.500A) removed outlier: 8.334A pdb=" N THR B 110 " --> pdb=" O THR A 107 " (cutoff:3.500A) removed outlier: 7.069A pdb=" N LEU A 109 " --> pdb=" O THR B 110 " (cutoff:3.500A) 66 hydrogen bonds defined for protein. 198 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: 0.48 Time building geometry restraints manager: 0.22 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 1135 1.35 - 1.47: 974 1.47 - 1.59: 1441 1.59 - 1.71: 0 1.71 - 1.83: 20 Bond restraints: 3570 Sorted by residual: bond pdb=" CA SER A 71 " pdb=" C SER A 71 " ideal model delta sigma weight residual 1.529 1.518 0.011 1.04e-02 9.25e+03 1.18e+00 bond pdb=" CA SER B 71 " pdb=" C SER B 71 " ideal model delta sigma weight residual 1.529 1.518 0.011 1.04e-02 9.25e+03 1.10e+00 bond pdb=" CA SER D 71 " pdb=" C SER D 71 " ideal model delta sigma weight residual 1.529 1.518 0.011 1.04e-02 9.25e+03 1.08e+00 bond pdb=" CA SER C 71 " pdb=" C SER C 71 " ideal model delta sigma weight residual 1.529 1.519 0.010 1.04e-02 9.25e+03 9.70e-01 bond pdb=" CA SER E 71 " pdb=" C SER E 71 " ideal model delta sigma weight residual 1.529 1.519 0.010 1.04e-02 9.25e+03 9.32e-01 ... (remaining 3565 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.72: 4291 0.72 - 1.44: 448 1.44 - 2.16: 61 2.16 - 2.89: 5 2.89 - 3.61: 20 Bond angle restraints: 4825 Sorted by residual: angle pdb=" N GLN C 6 " pdb=" CA GLN C 6 " pdb=" C GLN C 6 " ideal model delta sigma weight residual 109.81 113.42 -3.61 2.21e+00 2.05e-01 2.66e+00 angle pdb=" N GLN E 6 " pdb=" CA GLN E 6 " pdb=" C GLN E 6 " ideal model delta sigma weight residual 109.81 113.39 -3.58 2.21e+00 2.05e-01 2.63e+00 angle pdb=" N GLN D 6 " pdb=" CA GLN D 6 " pdb=" C GLN D 6 " ideal model delta sigma weight residual 109.81 113.37 -3.56 2.21e+00 2.05e-01 2.59e+00 angle pdb=" N GLN B 6 " pdb=" CA GLN B 6 " pdb=" C GLN B 6 " ideal model delta sigma weight residual 109.81 113.36 -3.55 2.21e+00 2.05e-01 2.58e+00 angle pdb=" N GLN A 6 " pdb=" CA GLN A 6 " pdb=" C GLN A 6 " ideal model delta sigma weight residual 109.81 113.31 -3.50 2.21e+00 2.05e-01 2.51e+00 ... (remaining 4820 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.98: 1799 13.98 - 27.95: 196 27.95 - 41.93: 70 41.93 - 55.90: 35 55.90 - 69.88: 25 Dihedral angle restraints: 2125 sinusoidal: 795 harmonic: 1330 Sorted by residual: dihedral pdb=" CB CYS A 22 " pdb=" SG CYS A 22 " pdb=" SG CYS A 91 " pdb=" CB CYS A 91 " ideal model delta sinusoidal sigma weight residual 93.00 122.64 -29.64 1 1.00e+01 1.00e-02 1.26e+01 dihedral pdb=" CB CYS B 22 " pdb=" SG CYS B 22 " pdb=" SG CYS B 91 " pdb=" CB CYS B 91 " ideal model delta sinusoidal sigma weight residual 93.00 122.64 -29.64 1 1.00e+01 1.00e-02 1.26e+01 dihedral pdb=" CB CYS C 22 " pdb=" SG CYS C 22 " pdb=" SG CYS C 91 " pdb=" CB CYS C 91 " ideal model delta sinusoidal sigma weight residual 93.00 122.63 -29.63 1 1.00e+01 1.00e-02 1.26e+01 ... (remaining 2122 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 313 0.026 - 0.053: 120 0.053 - 0.079: 44 0.079 - 0.105: 26 0.105 - 0.132: 37 Chirality restraints: 540 Sorted by residual: chirality pdb=" CA ILE E 78 " pdb=" N ILE E 78 " pdb=" C ILE E 78 " pdb=" CB ILE E 78 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.34e-01 chirality pdb=" CA ILE C 78 " pdb=" N ILE C 78 " pdb=" C ILE C 78 " pdb=" CB ILE C 78 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.23e-01 chirality pdb=" CA ILE D 78 " pdb=" N ILE D 78 " pdb=" C ILE D 78 " pdb=" CB ILE D 78 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.19e-01 ... (remaining 537 not shown) Planarity restraints: 615 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE E 2 " -0.002 2.00e-02 2.50e+03 1.12e-02 2.18e+00 pdb=" CG PHE E 2 " 0.021 2.00e-02 2.50e+03 pdb=" CD1 PHE E 2 " -0.016 2.00e-02 2.50e+03 pdb=" CD2 PHE E 2 " -0.011 2.00e-02 2.50e+03 pdb=" CE1 PHE E 2 " 0.007 2.00e-02 2.50e+03 pdb=" CE2 PHE E 2 " 0.001 2.00e-02 2.50e+03 pdb=" CZ PHE E 2 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE D 2 " -0.002 2.00e-02 2.50e+03 1.11e-02 2.14e+00 pdb=" CG PHE D 2 " 0.021 2.00e-02 2.50e+03 pdb=" CD1 PHE D 2 " -0.016 2.00e-02 2.50e+03 pdb=" CD2 PHE D 2 " -0.011 2.00e-02 2.50e+03 pdb=" CE1 PHE D 2 " 0.007 2.00e-02 2.50e+03 pdb=" CE2 PHE D 2 " 0.002 2.00e-02 2.50e+03 pdb=" CZ PHE D 2 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE C 2 " -0.002 2.00e-02 2.50e+03 1.10e-02 2.13e+00 pdb=" CG PHE C 2 " 0.021 2.00e-02 2.50e+03 pdb=" CD1 PHE C 2 " -0.016 2.00e-02 2.50e+03 pdb=" CD2 PHE C 2 " -0.011 2.00e-02 2.50e+03 pdb=" CE1 PHE C 2 " 0.007 2.00e-02 2.50e+03 pdb=" CE2 PHE C 2 " 0.002 2.00e-02 2.50e+03 pdb=" CZ PHE C 2 " -0.001 2.00e-02 2.50e+03 ... (remaining 612 not shown) Histogram of nonbonded interaction distances: 2.64 - 3.09: 2219 3.09 - 3.54: 3170 3.54 - 4.00: 4612 4.00 - 4.45: 5508 4.45 - 4.90: 9438 Nonbonded interactions: 24947 Sorted by model distance: nonbonded pdb=" CG LYS B 82 " pdb=" NZ LYS B 82 " model vdw 2.642 2.816 nonbonded pdb=" CG LYS E 82 " pdb=" NZ LYS E 82 " model vdw 2.642 2.816 nonbonded pdb=" CG LYS D 82 " pdb=" NZ LYS D 82 " model vdw 2.642 2.816 nonbonded pdb=" CG LYS C 82 " pdb=" NZ LYS C 82 " model vdw 2.642 2.816 nonbonded pdb=" CG LYS A 82 " pdb=" NZ LYS A 82 " model vdw 2.643 2.816 ... (remaining 24942 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 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.510 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.060 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 4.750 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 7.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8428 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 : 0.002 0.023 3575 Z= 0.123 Angle : 0.511 3.716 4835 Z= 0.289 Chirality : 0.047 0.132 540 Planarity : 0.003 0.023 615 Dihedral : 17.050 69.879 1260 Min Nonbonded Distance : 2.642 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 0.00 % Allowed : 17.78 % Favored : 82.22 % 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: -3.36 (0.32), residues: 440 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.56 (0.25), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 24 TYR 0.023 0.003 TYR B 89 PHE 0.021 0.003 PHE E 2 TRP 0.002 0.000 TRP E 36 HIS 0.001 0.000 HIS B 8 Details of bonding type rmsd/Z covalent geometry : bond 0.00240 / 0.12 ( 3570) covalent geometry : angle 0.49561 / 0.28 ( 4825) SS BOND : bond 0.00043 / 0.02 ( 5) SS BOND : angle 2.78832 / 1.91 ( 10) hydrogen bonds : bond 0.34802 / 22.94 ( 66) hydrogen bonds : angle 7.84496 / 5.61 ( 198) *********************** 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 52 residues out of total 410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 52 time to evaluate : 0.140 Fit side-chains REVERT: C 3 MET cc_start: 0.8323 (mtp) cc_final: 0.8098 (mtp) REVERT: C 62 ARG cc_start: 0.8244 (mtp85) cc_final: 0.7004 (tpm170) REVERT: C 108 LYS cc_start: 0.8496 (mtmm) cc_final: 0.8287 (ttmm) outliers start: 0 outliers final: 0 residues processed: 52 average time/residue: 0.1348 time to fit residues: 7.8777 Evaluate side-chains 44 residues out of total 410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 44 time to evaluate : 0.088 ------------------------------------------------------------------------------- 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: 5.9990 chunk 26 optimal weight: 4.9990 chunk 2 optimal weight: 3.9990 chunk 16 optimal weight: 0.2980 chunk 32 optimal weight: 8.9990 chunk 31 optimal weight: 0.7980 chunk 25 optimal weight: 0.6980 chunk 19 optimal weight: 0.7980 chunk 30 optimal weight: 0.8980 chunk 22 optimal weight: 2.9990 chunk 37 optimal weight: 0.3980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 6 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.130064 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.113208 restraints weight = 5016.325| |-----------------------------------------------------------------------------| r_work (start): 0.3871 rms_B_bonded: 2.63 r_work: 0.3763 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3645 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3645 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 moved from start: 0.1267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 3575 Z= 0.107 Angle : 0.508 3.818 4835 Z= 0.284 Chirality : 0.044 0.139 540 Planarity : 0.003 0.040 615 Dihedral : 3.975 12.607 495 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 1.23 % Allowed : 17.28 % Favored : 81.48 % 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: -3.27 (0.33), residues: 440 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.49 (0.25), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 62 TYR 0.011 0.002 TYR E 89 PHE 0.014 0.001 PHE A 2 TRP 0.004 0.001 TRP E 36 HIS 0.001 0.000 HIS D 8 Details of bonding type rmsd/Z covalent geometry : bond 0.00237 / 0.11 ( 3570) covalent geometry : angle 0.49879 / 0.28 ( 4825) SS BOND : bond 0.00540 / 0.29 ( 5) SS BOND : angle 2.17694 / 1.49 ( 10) hydrogen bonds : bond 0.04008 / 2.59 ( 66) hydrogen bonds : angle 5.53510 / 3.81 ( 198) *********************** 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 49 residues out of total 410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 44 time to evaluate : 0.094 Fit side-chains revert: symmetry clash REVERT: A 91 CYS cc_start: 0.8650 (OUTLIER) cc_final: 0.8127 (m) REVERT: C 62 ARG cc_start: 0.8248 (mtp85) cc_final: 0.6459 (tpm170) REVERT: C 91 CYS cc_start: 0.8917 (OUTLIER) cc_final: 0.8419 (m) REVERT: C 108 LYS cc_start: 0.8394 (mtmm) cc_final: 0.8145 (ttmm) outliers start: 5 outliers final: 2 residues processed: 49 average time/residue: 0.1016 time to fit residues: 5.7768 Evaluate side-chains 44 residues out of total 410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 40 time to evaluate : 0.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 CYS Chi-restraints excluded: chain B residue 91 CYS Chi-restraints excluded: chain C residue 91 CYS Chi-restraints excluded: chain E residue 91 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 24 optimal weight: 5.9990 chunk 35 optimal weight: 7.9990 chunk 8 optimal weight: 2.9990 chunk 34 optimal weight: 2.9990 chunk 36 optimal weight: 4.9990 chunk 9 optimal weight: 0.0980 chunk 41 optimal weight: 0.3980 chunk 2 optimal weight: 2.9990 chunk 19 optimal weight: 5.9990 chunk 39 optimal weight: 3.9990 chunk 28 optimal weight: 5.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 1 ASN B 1 ASN D 1 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.122146 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.105658 restraints weight = 5026.201| |-----------------------------------------------------------------------------| r_work (start): 0.3762 rms_B_bonded: 2.55 r_work: 0.3649 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3532 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3532 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8475 moved from start: 0.1976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 3575 Z= 0.209 Angle : 0.704 7.255 4835 Z= 0.388 Chirality : 0.048 0.158 540 Planarity : 0.004 0.044 615 Dihedral : 4.693 14.900 495 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 2.47 % Allowed : 15.80 % Favored : 81.73 % 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: -3.47 (0.31), residues: 440 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.64 (0.23), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 62 TYR 0.008 0.002 TYR B 89 PHE 0.008 0.001 PHE A 2 TRP 0.012 0.002 TRP A 36 HIS 0.003 0.001 HIS A 8 Details of bonding type rmsd/Z covalent geometry : bond 0.00485 / 0.21 ( 3570) covalent geometry : angle 0.68275 / 0.38 ( 4825) SS BOND : bond 0.01052 / 0.57 ( 5) SS BOND : angle 3.80780 / 2.60 ( 10) hydrogen bonds : bond 0.05950 / 3.92 ( 66) hydrogen bonds : angle 5.75868 / 3.87 ( 198) *********************** 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 54 residues out of total 410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 44 time to evaluate : 0.086 Fit side-chains revert: symmetry clash REVERT: A 91 CYS cc_start: 0.8798 (OUTLIER) cc_final: 0.8296 (m) REVERT: C 62 ARG cc_start: 0.8298 (mtp85) cc_final: 0.7975 (mtp180) REVERT: C 91 CYS cc_start: 0.9035 (OUTLIER) cc_final: 0.8549 (m) REVERT: C 108 LYS cc_start: 0.8430 (mtmm) cc_final: 0.8109 (ttmm) outliers start: 10 outliers final: 4 residues processed: 54 average time/residue: 0.0824 time to fit residues: 5.1764 Evaluate side-chains 49 residues out of total 410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 43 time to evaluate : 0.084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 CYS Chi-restraints excluded: chain B residue 91 CYS Chi-restraints excluded: chain C residue 4 LEU Chi-restraints excluded: chain C residue 9 SER Chi-restraints excluded: chain C residue 91 CYS Chi-restraints excluded: chain E residue 91 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 12 optimal weight: 0.9980 chunk 22 optimal weight: 0.2980 chunk 38 optimal weight: 0.5980 chunk 20 optimal weight: 0.0870 chunk 21 optimal weight: 0.7980 chunk 44 optimal weight: 4.9990 chunk 39 optimal weight: 1.9990 chunk 1 optimal weight: 0.9990 chunk 27 optimal weight: 0.5980 chunk 41 optimal weight: 6.9990 chunk 6 optimal weight: 0.9990 overall best weight: 0.4758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 39 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.129453 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.112599 restraints weight = 4910.458| |-----------------------------------------------------------------------------| r_work (start): 0.3863 rms_B_bonded: 2.58 r_work: 0.3755 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3637 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3637 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8356 moved from start: 0.1937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 3575 Z= 0.095 Angle : 0.502 6.333 4835 Z= 0.275 Chirality : 0.043 0.135 540 Planarity : 0.003 0.042 615 Dihedral : 4.132 14.232 495 Min Nonbonded Distance : 2.633 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 2.22 % Allowed : 16.30 % Favored : 81.48 % 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: -3.28 (0.32), residues: 440 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.49 (0.24), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 62 TYR 0.009 0.001 TYR D 90 PHE 0.006 0.001 PHE A 2 TRP 0.002 0.000 TRP E 36 HIS 0.001 0.001 HIS D 8 Details of bonding type rmsd/Z covalent geometry : bond 0.00206 / 0.09 ( 3570) covalent geometry : angle 0.49376 / 0.27 ( 4825) SS BOND : bond 0.00471 / 0.25 ( 5) SS BOND : angle 2.02560 / 1.40 ( 10) hydrogen bonds : bond 0.02963 / 1.93 ( 66) hydrogen bonds : angle 5.00888 / 3.34 ( 198) *********************** 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 49 residues out of total 410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 40 time to evaluate : 0.131 Fit side-chains revert: symmetry clash REVERT: A 91 CYS cc_start: 0.8640 (OUTLIER) cc_final: 0.8116 (m) REVERT: C 62 ARG cc_start: 0.8288 (mtp85) cc_final: 0.8014 (mtp180) REVERT: C 91 CYS cc_start: 0.8926 (OUTLIER) cc_final: 0.8410 (m) REVERT: C 108 LYS cc_start: 0.8452 (mtmm) cc_final: 0.8144 (ttmm) outliers start: 9 outliers final: 4 residues processed: 49 average time/residue: 0.0711 time to fit residues: 4.2087 Evaluate side-chains 45 residues out of total 410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 39 time to evaluate : 0.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 CYS Chi-restraints excluded: chain B residue 91 CYS Chi-restraints excluded: chain C residue 91 CYS Chi-restraints excluded: chain D residue 4 LEU Chi-restraints excluded: chain D residue 9 SER Chi-restraints excluded: chain E residue 91 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 35 optimal weight: 5.9990 chunk 42 optimal weight: 2.9990 chunk 31 optimal weight: 6.9990 chunk 3 optimal weight: 0.9980 chunk 39 optimal weight: 0.0270 chunk 30 optimal weight: 1.9990 chunk 2 optimal weight: 0.9990 chunk 1 optimal weight: 0.6980 chunk 44 optimal weight: 0.9990 chunk 6 optimal weight: 0.8980 chunk 43 optimal weight: 3.9990 overall best weight: 0.7240 ------------------------------------------------------------------------------- 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 = 0.4054 r_free = 0.4054 target = 0.127825 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.111073 restraints weight = 4983.238| |-----------------------------------------------------------------------------| r_work (start): 0.3842 rms_B_bonded: 2.60 r_work: 0.3729 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3609 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3609 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8390 moved from start: 0.2028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3575 Z= 0.114 Angle : 0.538 8.206 4835 Z= 0.292 Chirality : 0.044 0.142 540 Planarity : 0.003 0.042 615 Dihedral : 4.098 13.710 495 Min Nonbonded Distance : 2.629 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.68 % Favored : 94.32 % Rotamer: Outliers : 3.21 % Allowed : 17.04 % Favored : 79.75 % 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: -3.27 (0.32), residues: 440 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.48 (0.24), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 62 TYR 0.008 0.001 TYR D 90 PHE 0.004 0.001 PHE A 2 TRP 0.003 0.001 TRP A 36 HIS 0.001 0.001 HIS D 8 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.11 ( 3570) covalent geometry : angle 0.52722 / 0.29 ( 4825) SS BOND : bond 0.00640 / 0.35 ( 5) SS BOND : angle 2.46366 / 1.69 ( 10) hydrogen bonds : bond 0.03526 / 2.31 ( 66) hydrogen bonds : angle 5.05155 / 3.35 ( 198) *********************** 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 55 residues out of total 410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 42 time to evaluate : 0.136 Fit side-chains revert: symmetry clash REVERT: A 91 CYS cc_start: 0.8717 (OUTLIER) cc_final: 0.8173 (m) REVERT: C 62 ARG cc_start: 0.8282 (mtp85) cc_final: 0.8040 (mtp180) REVERT: C 91 CYS cc_start: 0.8967 (OUTLIER) cc_final: 0.8474 (m) REVERT: C 108 LYS cc_start: 0.8456 (mtmm) cc_final: 0.8128 (ttmm) outliers start: 13 outliers final: 9 residues processed: 53 average time/residue: 0.0871 time to fit residues: 5.4168 Evaluate side-chains 52 residues out of total 410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 41 time to evaluate : 0.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 CYS Chi-restraints excluded: chain B residue 91 CYS Chi-restraints excluded: chain C residue 3 MET Chi-restraints excluded: chain C residue 4 LEU Chi-restraints excluded: chain C residue 9 SER Chi-restraints excluded: chain C residue 91 CYS Chi-restraints excluded: chain D residue 9 SER Chi-restraints excluded: chain E residue 4 LEU Chi-restraints excluded: chain E residue 9 SER Chi-restraints excluded: chain E residue 61 ASP Chi-restraints excluded: chain E residue 91 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 32 optimal weight: 7.9990 chunk 38 optimal weight: 5.9990 chunk 39 optimal weight: 0.9980 chunk 0 optimal weight: 6.9990 chunk 3 optimal weight: 3.9990 chunk 14 optimal weight: 2.9990 chunk 18 optimal weight: 6.9990 chunk 40 optimal weight: 4.9990 chunk 13 optimal weight: 5.9990 chunk 1 optimal weight: 0.8980 chunk 19 optimal weight: 1.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 1 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.121071 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.104537 restraints weight = 5033.064| |-----------------------------------------------------------------------------| r_work (start): 0.3746 rms_B_bonded: 2.58 r_work: 0.3631 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3515 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3515 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8487 moved from start: 0.2358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 3575 Z= 0.234 Angle : 0.748 5.677 4835 Z= 0.413 Chirality : 0.049 0.162 540 Planarity : 0.005 0.045 615 Dihedral : 4.811 14.959 495 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.27 % Favored : 92.73 % Rotamer: Outliers : 3.46 % Allowed : 16.79 % Favored : 79.75 % 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: -3.46 (0.30), residues: 440 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.63 (0.23), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 62 TYR 0.010 0.002 TYR D 37 PHE 0.006 0.001 PHE D 63 TRP 0.011 0.002 TRP A 36 HIS 0.003 0.001 HIS D 8 Details of bonding type rmsd/Z covalent geometry : bond 0.00542 / 0.23 ( 3570) covalent geometry : angle 0.72398 / 0.40 ( 4825) SS BOND : bond 0.01269 / 0.68 ( 5) SS BOND : angle 4.17274 / 2.82 ( 10) hydrogen bonds : bond 0.06184 / 4.04 ( 66) hydrogen bonds : angle 5.73804 / 3.79 ( 198) *********************** 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 57 residues out of total 410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 43 time to evaluate : 0.105 Fit side-chains revert: symmetry clash REVERT: A 91 CYS cc_start: 0.8866 (OUTLIER) cc_final: 0.8331 (m) REVERT: C 62 ARG cc_start: 0.8259 (mtp85) cc_final: 0.7975 (mtp180) REVERT: C 91 CYS cc_start: 0.9074 (OUTLIER) cc_final: 0.8591 (m) REVERT: C 108 LYS cc_start: 0.8425 (mtmm) cc_final: 0.8075 (ttmm) outliers start: 14 outliers final: 7 residues processed: 56 average time/residue: 0.0873 time to fit residues: 5.7726 Evaluate side-chains 50 residues out of total 410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 41 time to evaluate : 0.089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 CYS Chi-restraints excluded: chain B residue 91 CYS Chi-restraints excluded: chain C residue 4 LEU Chi-restraints excluded: chain C residue 9 SER Chi-restraints excluded: chain C residue 91 CYS Chi-restraints excluded: chain D residue 4 LEU Chi-restraints excluded: chain D residue 9 SER Chi-restraints excluded: chain E residue 4 LEU Chi-restraints excluded: chain E residue 91 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 33 optimal weight: 5.9990 chunk 29 optimal weight: 0.5980 chunk 25 optimal weight: 0.6980 chunk 0 optimal weight: 5.9990 chunk 8 optimal weight: 3.9990 chunk 14 optimal weight: 7.9990 chunk 36 optimal weight: 0.6980 chunk 13 optimal weight: 1.9990 chunk 30 optimal weight: 5.9990 chunk 27 optimal weight: 0.9980 chunk 39 optimal weight: 2.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- 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 = 0.4018 r_free = 0.4018 target = 0.125156 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.108332 restraints weight = 5043.535| |-----------------------------------------------------------------------------| r_work (start): 0.3803 rms_B_bonded: 2.61 r_work: 0.3689 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3572 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3572 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8430 moved from start: 0.2282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 3575 Z= 0.137 Angle : 0.595 9.000 4835 Z= 0.323 Chirality : 0.045 0.144 540 Planarity : 0.004 0.043 615 Dihedral : 4.435 14.044 495 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.14 % Favored : 93.86 % Rotamer: Outliers : 2.96 % Allowed : 17.53 % Favored : 79.51 % 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: -3.41 (0.31), residues: 440 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.59 (0.23), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 62 TYR 0.008 0.001 TYR D 90 PHE 0.004 0.001 PHE A 63 TRP 0.004 0.001 TRP A 36 HIS 0.002 0.001 HIS D 8 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.14 ( 3570) covalent geometry : angle 0.58080 / 0.32 ( 4825) SS BOND : bond 0.00779 / 0.43 ( 5) SS BOND : angle 2.93997 / 2.00 ( 10) hydrogen bonds : bond 0.04004 / 2.62 ( 66) hydrogen bonds : angle 5.28235 / 3.47 ( 198) *********************** 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 54 residues out of total 410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 42 time to evaluate : 0.107 Fit side-chains revert: symmetry clash REVERT: A 91 CYS cc_start: 0.8723 (OUTLIER) cc_final: 0.8194 (m) REVERT: C 62 ARG cc_start: 0.8266 (mtp85) cc_final: 0.7994 (mtp180) REVERT: C 91 CYS cc_start: 0.8993 (OUTLIER) cc_final: 0.8487 (m) REVERT: C 108 LYS cc_start: 0.8460 (mtmm) cc_final: 0.8115 (ttmm) outliers start: 12 outliers final: 8 residues processed: 53 average time/residue: 0.0880 time to fit residues: 5.4720 Evaluate side-chains 52 residues out of total 410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 42 time to evaluate : 0.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 CYS Chi-restraints excluded: chain B residue 91 CYS Chi-restraints excluded: chain C residue 4 LEU Chi-restraints excluded: chain C residue 9 SER Chi-restraints excluded: chain C residue 84 GLU Chi-restraints excluded: chain C residue 91 CYS Chi-restraints excluded: chain D residue 4 LEU Chi-restraints excluded: chain D residue 9 SER Chi-restraints excluded: chain E residue 4 LEU Chi-restraints excluded: chain E residue 91 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 9 optimal weight: 5.9990 chunk 39 optimal weight: 1.9990 chunk 25 optimal weight: 0.5980 chunk 32 optimal weight: 10.0000 chunk 6 optimal weight: 5.9990 chunk 14 optimal weight: 8.9990 chunk 33 optimal weight: 0.7980 chunk 16 optimal weight: 0.7980 chunk 36 optimal weight: 0.6980 chunk 29 optimal weight: 0.1980 chunk 41 optimal weight: 0.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 = 0.4055 r_free = 0.4055 target = 0.128046 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.111301 restraints weight = 5010.436| |-----------------------------------------------------------------------------| r_work (start): 0.3847 rms_B_bonded: 2.61 r_work: 0.3735 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3620 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3620 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8367 moved from start: 0.2243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 3575 Z= 0.104 Angle : 0.528 8.769 4835 Z= 0.285 Chirality : 0.044 0.139 540 Planarity : 0.003 0.042 615 Dihedral : 4.113 14.063 495 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 2.96 % Allowed : 17.78 % Favored : 79.26 % 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: -3.30 (0.31), residues: 440 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.51 (0.24), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 62 TYR 0.008 0.001 TYR D 90 PHE 0.004 0.001 PHE C 63 TRP 0.002 0.000 TRP A 36 HIS 0.001 0.000 HIS A 8 Details of bonding type rmsd/Z covalent geometry : bond 0.00228 / 0.10 ( 3570) covalent geometry : angle 0.51905 / 0.28 ( 4825) SS BOND : bond 0.00580 / 0.31 ( 5) SS BOND : angle 2.21453 / 1.52 ( 10) hydrogen bonds : bond 0.03130 / 2.05 ( 66) hydrogen bonds : angle 4.94315 / 3.25 ( 198) *********************** 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 55 residues out of total 410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 43 time to evaluate : 0.085 Fit side-chains revert: symmetry clash REVERT: A 91 CYS cc_start: 0.8681 (OUTLIER) cc_final: 0.8150 (m) REVERT: C 62 ARG cc_start: 0.8172 (mtp85) cc_final: 0.7917 (mtp180) REVERT: C 91 CYS cc_start: 0.8945 (OUTLIER) cc_final: 0.8422 (m) REVERT: C 108 LYS cc_start: 0.8469 (mtmm) cc_final: 0.8118 (ttmm) outliers start: 12 outliers final: 7 residues processed: 54 average time/residue: 0.0898 time to fit residues: 5.6103 Evaluate side-chains 52 residues out of total 410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 43 time to evaluate : 0.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 CYS Chi-restraints excluded: chain B residue 91 CYS Chi-restraints excluded: chain C residue 9 SER Chi-restraints excluded: chain C residue 84 GLU Chi-restraints excluded: chain C residue 91 CYS Chi-restraints excluded: chain D residue 4 LEU Chi-restraints excluded: chain D residue 9 SER Chi-restraints excluded: chain E residue 4 LEU Chi-restraints excluded: chain E residue 91 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 5 optimal weight: 8.9990 chunk 31 optimal weight: 0.6980 chunk 32 optimal weight: 2.9990 chunk 35 optimal weight: 6.9990 chunk 11 optimal weight: 5.9990 chunk 0 optimal weight: 6.9990 chunk 33 optimal weight: 4.9990 chunk 1 optimal weight: 0.0770 chunk 26 optimal weight: 4.9990 chunk 10 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 overall best weight: 1.7544 ------------------------------------------------------------------------------- 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 = 0.3977 r_free = 0.3977 target = 0.122339 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.105697 restraints weight = 4990.652| |-----------------------------------------------------------------------------| r_work (start): 0.3765 rms_B_bonded: 2.57 r_work: 0.3649 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3532 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3532 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8475 moved from start: 0.2455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 3575 Z= 0.196 Angle : 0.698 8.465 4835 Z= 0.381 Chirality : 0.048 0.157 540 Planarity : 0.004 0.044 615 Dihedral : 4.628 14.104 495 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.73 % Favored : 92.27 % Rotamer: Outliers : 2.72 % Allowed : 17.28 % Favored : 80.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -3.40 (0.31), residues: 440 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.59 (0.23), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 62 TYR 0.008 0.002 TYR D 37 PHE 0.006 0.001 PHE D 63 TRP 0.008 0.002 TRP A 36 HIS 0.002 0.001 HIS D 8 Details of bonding type rmsd/Z covalent geometry : bond 0.00451 / 0.20 ( 3570) covalent geometry : angle 0.67643 / 0.37 ( 4825) SS BOND : bond 0.01084 / 0.58 ( 5) SS BOND : angle 3.85150 / 2.60 ( 10) hydrogen bonds : bond 0.05405 / 3.53 ( 66) hydrogen bonds : angle 5.51799 / 3.62 ( 198) *********************** 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 52 residues out of total 410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 41 time to evaluate : 0.084 Fit side-chains revert: symmetry clash REVERT: A 91 CYS cc_start: 0.8833 (OUTLIER) cc_final: 0.8316 (m) REVERT: C 62 ARG cc_start: 0.8242 (mtp85) cc_final: 0.7967 (mtp180) REVERT: C 91 CYS cc_start: 0.9051 (OUTLIER) cc_final: 0.8558 (m) outliers start: 11 outliers final: 8 residues processed: 51 average time/residue: 0.0913 time to fit residues: 5.4152 Evaluate side-chains 50 residues out of total 410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 40 time to evaluate : 0.090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 CYS Chi-restraints excluded: chain B residue 91 CYS Chi-restraints excluded: chain C residue 4 LEU Chi-restraints excluded: chain C residue 9 SER Chi-restraints excluded: chain C residue 84 GLU Chi-restraints excluded: chain C residue 91 CYS Chi-restraints excluded: chain D residue 4 LEU Chi-restraints excluded: chain D residue 9 SER Chi-restraints excluded: chain E residue 4 LEU Chi-restraints excluded: chain E residue 91 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 39 optimal weight: 4.9990 chunk 1 optimal weight: 3.9990 chunk 32 optimal weight: 10.0000 chunk 28 optimal weight: 1.9990 chunk 44 optimal weight: 0.0980 chunk 18 optimal weight: 3.9990 chunk 38 optimal weight: 5.9990 chunk 26 optimal weight: 0.8980 chunk 29 optimal weight: 5.9990 chunk 31 optimal weight: 1.9990 chunk 0 optimal weight: 6.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- 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 = 0.3978 r_free = 0.3978 target = 0.122059 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.105327 restraints weight = 5108.454| |-----------------------------------------------------------------------------| r_work (start): 0.3763 rms_B_bonded: 2.59 r_work: 0.3645 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3529 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3529 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8490 moved from start: 0.2524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 3575 Z= 0.200 Angle : 0.713 8.657 4835 Z= 0.387 Chirality : 0.048 0.156 540 Planarity : 0.004 0.043 615 Dihedral : 4.727 14.494 495 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.27 % Favored : 92.73 % Rotamer: Outliers : 2.47 % Allowed : 17.78 % Favored : 79.75 % 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: -3.42 (0.30), residues: 440 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.60 (0.23), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 62 TYR 0.008 0.002 TYR D 37 PHE 0.006 0.001 PHE A 63 TRP 0.008 0.002 TRP A 36 HIS 0.002 0.001 HIS D 8 Details of bonding type rmsd/Z covalent geometry : bond 0.00462 / 0.20 ( 3570) covalent geometry : angle 0.69135 / 0.38 ( 4825) SS BOND : bond 0.01102 / 0.60 ( 5) SS BOND : angle 3.87985 / 2.61 ( 10) hydrogen bonds : bond 0.05395 / 3.52 ( 66) hydrogen bonds : angle 5.55584 / 3.64 ( 198) ********************** 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 49 residues out of total 410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 39 time to evaluate : 0.143 Fit side-chains revert: symmetry clash REVERT: A 91 CYS cc_start: 0.8826 (OUTLIER) cc_final: 0.8309 (m) REVERT: C 91 CYS cc_start: 0.9079 (OUTLIER) cc_final: 0.8611 (m) outliers start: 10 outliers final: 8 residues processed: 48 average time/residue: 0.0912 time to fit residues: 5.1316 Evaluate side-chains 49 residues out of total 410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 39 time to evaluate : 0.100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 CYS Chi-restraints excluded: chain B residue 91 CYS Chi-restraints excluded: chain C residue 4 LEU Chi-restraints excluded: chain C residue 9 SER Chi-restraints excluded: chain C residue 84 GLU Chi-restraints excluded: chain C residue 91 CYS Chi-restraints excluded: chain D residue 4 LEU Chi-restraints excluded: chain D residue 9 SER Chi-restraints excluded: chain E residue 4 LEU Chi-restraints excluded: chain E residue 91 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 36 optimal weight: 0.7980 chunk 22 optimal weight: 0.5980 chunk 15 optimal weight: 6.9990 chunk 40 optimal weight: 5.9990 chunk 32 optimal weight: 9.9990 chunk 0 optimal weight: 6.9990 chunk 4 optimal weight: 4.9990 chunk 24 optimal weight: 0.4980 chunk 23 optimal weight: 2.9990 chunk 25 optimal weight: 4.9990 chunk 43 optimal weight: 2.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- 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 = 0.3990 r_free = 0.3990 target = 0.122874 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.106057 restraints weight = 4983.509| |-----------------------------------------------------------------------------| r_work (start): 0.3773 rms_B_bonded: 2.57 r_work: 0.3656 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3540 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3540 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8480 moved from start: 0.2545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 3575 Z= 0.182 Angle : 0.682 8.695 4835 Z= 0.370 Chirality : 0.047 0.153 540 Planarity : 0.004 0.043 615 Dihedral : 4.632 14.180 495 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.50 % Favored : 92.50 % Rotamer: Outliers : 2.22 % Allowed : 18.02 % Favored : 79.75 % 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: -3.39 (0.31), residues: 440 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.58 (0.23), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 62 TYR 0.007 0.002 TYR D 90 PHE 0.006 0.001 PHE D 63 TRP 0.007 0.001 TRP A 36 HIS 0.002 0.001 HIS D 8 Details of bonding type rmsd/Z covalent geometry : bond 0.00419 / 0.18 ( 3570) covalent geometry : angle 0.66209 / 0.36 ( 4825) SS BOND : bond 0.01028 / 0.56 ( 5) SS BOND : angle 3.61978 / 2.44 ( 10) hydrogen bonds : bond 0.05060 / 3.31 ( 66) hydrogen bonds : angle 5.49723 / 3.59 ( 198) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 956.47 seconds wall clock time: 16 minutes 58.19 seconds (1018.19 seconds total)