Starting phenix.real_space_refine on Thu Mar 6 01:13:50 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8a7o_15222/03_2025/8a7o_15222.cif Found real_map, /net/cci-nas-00/data/ceres_data/8a7o_15222/03_2025/8a7o_15222.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8a7o_15222/03_2025/8a7o_15222.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8a7o_15222/03_2025/8a7o_15222.map" model { file = "/net/cci-nas-00/data/ceres_data/8a7o_15222/03_2025/8a7o_15222.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8a7o_15222/03_2025/8a7o_15222.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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 18 5.16 5 C 2790 2.51 5 N 714 2.21 5 O 840 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 60 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 4362 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 727 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 727 Classifications: {'peptide': 88} Link IDs: {'PTRANS': 4, 'TRANS': 83} Chain: "B" Number of atoms: 727 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 727 Classifications: {'peptide': 88} Link IDs: {'PTRANS': 4, 'TRANS': 83} Restraints were copied for chains: C, E, D, F Time building chain proxies: 3.91, per 1000 atoms: 0.90 Number of scatterers: 4362 At special positions: 0 Unit cell: (122.84, 109.56, 34.86, 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 18 16.00 O 840 8.00 N 714 7.00 C 2790 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 25 " - pdb=" SG CYS A 80 " distance=2.03 Simple disulfide: pdb=" SG CYS B 25 " - pdb=" SG CYS B 80 " distance=2.03 Simple disulfide: pdb=" SG CYS C 25 " - pdb=" SG CYS C 80 " distance=2.03 Simple disulfide: pdb=" SG CYS E 25 " - pdb=" SG CYS E 80 " distance=2.03 Simple disulfide: pdb=" SG CYS D 25 " - pdb=" SG CYS D 80 " distance=2.03 Simple disulfide: pdb=" SG CYS F 25 " - pdb=" SG CYS F 80 " 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: 1.02 Conformation dependent library (CDL) restraints added in 531.4 milliseconds 1032 Ramachandran restraints generated. 516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1020 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 24 sheets defined 0.0% alpha, 46.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.94 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 7 through 12 removed outlier: 6.494A pdb=" N GLN A 8 " --> pdb=" O VAL C 9 " (cutoff:3.500A) removed outlier: 7.736A pdb=" N SER C 11 " --> pdb=" O GLN A 8 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N TYR A 10 " --> pdb=" O SER C 11 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N GLN C 8 " --> pdb=" O VAL E 9 " (cutoff:3.500A) removed outlier: 7.740A pdb=" N SER E 11 " --> pdb=" O GLN C 8 " (cutoff:3.500A) removed outlier: 6.170A pdb=" N TYR C 10 " --> pdb=" O SER E 11 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 15 through 17 Processing sheet with id=AA3, first strand: chain 'A' and resid 20 through 23 Processing sheet with id=AA4, first strand: chain 'A' and resid 26 through 27 removed outlier: 6.222A pdb=" N TYR A 26 " --> pdb=" O VAL C 27 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N TYR C 26 " --> pdb=" O VAL E 27 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 33 through 39 removed outlier: 6.868A pdb=" N ASP C 34 " --> pdb=" O SER A 33 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N ASP E 34 " --> pdb=" O SER C 33 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 42 through 46 removed outlier: 7.032A pdb=" N ILE C 46 " --> pdb=" O ARG A 45 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N ILE E 46 " --> pdb=" O ARG C 45 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 49 through 50 removed outlier: 6.660A pdb=" N VAL A 49 " --> pdb=" O GLU C 50 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N VAL C 49 " --> pdb=" O GLU E 50 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'A' and resid 60 through 66 removed outlier: 6.346A pdb=" N SER A 61 " --> pdb=" O PHE C 62 " (cutoff:3.500A) removed outlier: 7.232A pdb=" N LEU C 64 " --> pdb=" O SER A 61 " (cutoff:3.500A) removed outlier: 6.026A pdb=" N TYR A 63 " --> pdb=" O LEU C 64 " (cutoff:3.500A) removed outlier: 7.578A pdb=" N TYR C 66 " --> pdb=" O TYR A 63 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N LEU A 65 " --> pdb=" O TYR C 66 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N SER C 61 " --> pdb=" O PHE E 62 " (cutoff:3.500A) removed outlier: 7.229A pdb=" N LEU E 64 " --> pdb=" O SER C 61 " (cutoff:3.500A) removed outlier: 6.023A pdb=" N TYR C 63 " --> pdb=" O LEU E 64 " (cutoff:3.500A) removed outlier: 7.575A pdb=" N TYR E 66 " --> pdb=" O TYR C 63 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N LEU C 65 " --> pdb=" O TYR E 66 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'A' and resid 69 through 70 Processing sheet with id=AB1, first strand: chain 'A' and resid 73 through 78 Processing sheet with id=AB2, first strand: chain 'A' and resid 81 through 88 removed outlier: 6.528A pdb=" N ARG A 81 " --> pdb=" O VAL C 82 " (cutoff:3.500A) removed outlier: 7.954A pdb=" N HIS C 84 " --> pdb=" O ARG A 81 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N ASN A 83 " --> pdb=" O HIS C 84 " (cutoff:3.500A) removed outlier: 7.869A pdb=" N THR C 86 " --> pdb=" O ASN A 83 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N VAL A 85 " --> pdb=" O THR C 86 " (cutoff:3.500A) removed outlier: 8.137A pdb=" N SER C 88 " --> pdb=" O VAL A 85 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N LEU A 87 " --> pdb=" O SER C 88 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N ARG C 81 " --> pdb=" O VAL E 82 " (cutoff:3.500A) removed outlier: 7.950A pdb=" N HIS E 84 " --> pdb=" O ARG C 81 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N ASN C 83 " --> pdb=" O HIS E 84 " (cutoff:3.500A) removed outlier: 7.865A pdb=" N THR E 86 " --> pdb=" O ASN C 83 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N VAL C 85 " --> pdb=" O THR E 86 " (cutoff:3.500A) removed outlier: 8.132A pdb=" N SER E 88 " --> pdb=" O VAL C 85 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N LEU C 87 " --> pdb=" O SER E 88 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'A' and resid 91 through 92 removed outlier: 6.559A pdb=" N LYS A 91 " --> pdb=" O ILE C 92 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N LYS C 91 " --> pdb=" O ILE E 92 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'B' and resid 7 through 12 Processing sheet with id=AB5, first strand: chain 'B' and resid 15 through 17 Processing sheet with id=AB6, first strand: chain 'B' and resid 20 through 22 removed outlier: 6.947A pdb=" N ASN D 21 " --> pdb=" O SER B 20 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N ASN F 21 " --> pdb=" O SER D 20 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 33 through 39 removed outlier: 6.919A pdb=" N ASP D 34 " --> pdb=" O SER B 33 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N ASP F 34 " --> pdb=" O SER D 33 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 42 through 44 Processing sheet with id=AB9, first strand: chain 'B' and resid 48 through 53 removed outlier: 9.168A pdb=" N LYS B 48 " --> pdb=" O VAL D 49 " (cutoff:3.500A) removed outlier: 10.212A pdb=" N HIS D 51 " --> pdb=" O LYS B 48 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N GLU B 50 " --> pdb=" O HIS D 51 " (cutoff:3.500A) removed outlier: 8.633A pdb=" N ASP D 53 " --> pdb=" O GLU B 50 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N SER B 52 " --> pdb=" O ASP D 53 " (cutoff:3.500A) removed outlier: 9.167A pdb=" N LYS D 48 " --> pdb=" O VAL F 49 " (cutoff:3.500A) removed outlier: 10.211A pdb=" N HIS F 51 " --> pdb=" O LYS D 48 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N GLU D 50 " --> pdb=" O HIS F 51 " (cutoff:3.500A) removed outlier: 8.634A pdb=" N ASP F 53 " --> pdb=" O GLU D 50 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N SER D 52 " --> pdb=" O ASP F 53 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'B' and resid 59 through 66 removed outlier: 7.096A pdb=" N TYR D 63 " --> pdb=" O PHE B 62 " (cutoff:3.500A) removed outlier: 7.198A pdb=" N LEU B 64 " --> pdb=" O TYR D 63 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N LEU D 65 " --> pdb=" O LEU B 64 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N TYR B 66 " --> pdb=" O LEU D 65 " (cutoff:3.500A) removed outlier: 7.094A pdb=" N TYR F 63 " --> pdb=" O PHE D 62 " (cutoff:3.500A) removed outlier: 7.197A pdb=" N LEU D 64 " --> pdb=" O TYR F 63 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N LEU F 65 " --> pdb=" O LEU D 64 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N TYR D 66 " --> pdb=" O LEU F 65 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 69 through 70 Processing sheet with id=AC3, first strand: chain 'B' and resid 73 through 78 Processing sheet with id=AC4, first strand: chain 'B' and resid 81 through 83 removed outlier: 6.639A pdb=" N VAL B 82 " --> pdb=" O ASN D 83 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N VAL D 82 " --> pdb=" O ASN F 83 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC4 Processing sheet with id=AC5, first strand: chain 'B' and resid 86 through 88 removed outlier: 6.475A pdb=" N LEU B 87 " --> pdb=" O SER D 88 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N LEU D 87 " --> pdb=" O SER F 88 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'B' and resid 91 through 92 removed outlier: 6.740A pdb=" N LYS B 91 " --> pdb=" O ILE D 92 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N LYS D 91 " --> pdb=" O ILE F 92 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 86 hydrogen bonds defined for protein. 258 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.17 Time building geometry restraints manager: 1.26 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1392 1.34 - 1.46: 977 1.46 - 1.58: 2089 1.58 - 1.69: 0 1.69 - 1.81: 24 Bond restraints: 4482 Sorted by residual: bond pdb=" C THR C 71 " pdb=" N PRO C 72 " ideal model delta sigma weight residual 1.333 1.342 -0.009 1.20e-02 6.94e+03 5.69e-01 bond pdb=" C ASN F 42 " pdb=" N GLY F 43 " ideal model delta sigma weight residual 1.322 1.332 -0.010 1.41e-02 5.03e+03 5.30e-01 bond pdb=" C TYR F 78 " pdb=" N ALA F 79 " ideal model delta sigma weight residual 1.333 1.342 -0.009 1.30e-02 5.92e+03 5.09e-01 bond pdb=" C THR A 71 " pdb=" N PRO A 72 " ideal model delta sigma weight residual 1.333 1.341 -0.008 1.20e-02 6.94e+03 5.00e-01 bond pdb=" C ASN D 42 " pdb=" N GLY D 43 " ideal model delta sigma weight residual 1.322 1.332 -0.010 1.41e-02 5.03e+03 4.77e-01 ... (remaining 4477 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.16: 5823 1.16 - 2.31: 190 2.31 - 3.47: 41 3.47 - 4.62: 15 4.62 - 5.78: 3 Bond angle restraints: 6072 Sorted by residual: angle pdb=" N LYS D 48 " pdb=" CA LYS D 48 " pdb=" C LYS D 48 " ideal model delta sigma weight residual 108.13 111.44 -3.31 1.72e+00 3.38e-01 3.69e+00 angle pdb=" N LYS F 48 " pdb=" CA LYS F 48 " pdb=" C LYS F 48 " ideal model delta sigma weight residual 108.13 111.41 -3.28 1.72e+00 3.38e-01 3.64e+00 angle pdb=" N LYS B 48 " pdb=" CA LYS B 48 " pdb=" C LYS B 48 " ideal model delta sigma weight residual 108.13 111.40 -3.27 1.72e+00 3.38e-01 3.61e+00 angle pdb=" C LYS F 19 " pdb=" N SER F 20 " pdb=" CA SER F 20 " ideal model delta sigma weight residual 121.62 118.42 3.20 1.83e+00 2.99e-01 3.07e+00 angle pdb=" C LYS B 19 " pdb=" N SER B 20 " pdb=" CA SER B 20 " ideal model delta sigma weight residual 121.62 118.46 3.16 1.83e+00 2.99e-01 2.98e+00 ... (remaining 6067 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.02: 2477 13.02 - 26.03: 142 26.03 - 39.05: 24 39.05 - 52.07: 15 52.07 - 65.08: 18 Dihedral angle restraints: 2676 sinusoidal: 1098 harmonic: 1578 Sorted by residual: dihedral pdb=" CA ARG D 12 " pdb=" CB ARG D 12 " pdb=" CG ARG D 12 " pdb=" CD ARG D 12 " ideal model delta sinusoidal sigma weight residual 180.00 125.74 54.26 3 1.50e+01 4.44e-03 9.27e+00 dihedral pdb=" CA ARG F 12 " pdb=" CB ARG F 12 " pdb=" CG ARG F 12 " pdb=" CD ARG F 12 " ideal model delta sinusoidal sigma weight residual 180.00 125.80 54.20 3 1.50e+01 4.44e-03 9.26e+00 dihedral pdb=" CA ARG B 12 " pdb=" CB ARG B 12 " pdb=" CG ARG B 12 " pdb=" CD ARG B 12 " ideal model delta sinusoidal sigma weight residual 180.00 125.83 54.17 3 1.50e+01 4.44e-03 9.26e+00 ... (remaining 2673 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 303 0.026 - 0.052: 226 0.052 - 0.078: 53 0.078 - 0.104: 19 0.104 - 0.130: 41 Chirality restraints: 642 Sorted by residual: chirality pdb=" CA VAL E 49 " pdb=" N VAL E 49 " pdb=" C VAL E 49 " pdb=" CB VAL E 49 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.23e-01 chirality pdb=" CA VAL A 49 " pdb=" N VAL A 49 " pdb=" C VAL A 49 " pdb=" CB VAL A 49 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.17e-01 chirality pdb=" CA PRO F 14 " pdb=" N PRO F 14 " pdb=" C PRO F 14 " pdb=" CB PRO F 14 " both_signs ideal model delta sigma weight residual False 2.72 2.59 0.13 2.00e-01 2.50e+01 4.06e-01 ... (remaining 639 not shown) Planarity restraints: 780 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C HIS D 13 " 0.029 5.00e-02 4.00e+02 4.44e-02 3.15e+00 pdb=" N PRO D 14 " -0.077 5.00e-02 4.00e+02 pdb=" CA PRO D 14 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO D 14 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS B 13 " 0.029 5.00e-02 4.00e+02 4.43e-02 3.14e+00 pdb=" N PRO B 14 " -0.077 5.00e-02 4.00e+02 pdb=" CA PRO B 14 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO B 14 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS F 13 " 0.029 5.00e-02 4.00e+02 4.39e-02 3.09e+00 pdb=" N PRO F 14 " -0.076 5.00e-02 4.00e+02 pdb=" CA PRO F 14 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO F 14 " 0.025 5.00e-02 4.00e+02 ... (remaining 777 not shown) Histogram of nonbonded interaction distances: 2.42 - 2.91: 1549 2.91 - 3.41: 3409 3.41 - 3.91: 7113 3.91 - 4.40: 6917 4.40 - 4.90: 12418 Nonbonded interactions: 31406 Sorted by model distance: nonbonded pdb=" O LYS B 58 " pdb=" N LYS D 58 " model vdw 2.418 3.120 nonbonded pdb=" O LYS D 58 " pdb=" N LYS F 58 " model vdw 2.419 3.120 nonbonded pdb=" OE2 GLU A 16 " pdb=" NH2 ARG A 81 " model vdw 2.595 3.120 nonbonded pdb=" OE2 GLU E 16 " pdb=" NH2 ARG E 81 " model vdw 2.595 3.120 nonbonded pdb=" OE2 GLU C 16 " pdb=" NH2 ARG C 81 " model vdw 2.596 3.120 ... (remaining 31401 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' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.640 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: 0.190 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 16.530 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:15.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8454 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 0.020 4482 Z= 0.159 Angle : 0.549 5.776 6072 Z= 0.316 Chirality : 0.045 0.130 642 Planarity : 0.004 0.044 780 Dihedral : 11.280 65.084 1638 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.59 (0.29), residues: 516 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.73 (0.22), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP A 60 HIS 0.004 0.001 HIS E 13 PHE 0.008 0.001 PHE B 22 TYR 0.006 0.001 TYR E 63 ARG 0.001 0.000 ARG A 81 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1032 Ramachandran restraints generated. 516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1032 Ramachandran restraints generated. 516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 81 time to evaluate : 0.559 Fit side-chains REVERT: A 45 ARG cc_start: 0.7959 (mtt-85) cc_final: 0.6058 (tmm160) REVERT: B 12 ARG cc_start: 0.7181 (mtt180) cc_final: 0.6096 (tpm170) REVERT: B 34 ASP cc_start: 0.6576 (m-30) cc_final: 0.6303 (m-30) REVERT: B 91 LYS cc_start: 0.7899 (tttt) cc_final: 0.7432 (tttt) REVERT: C 50 GLU cc_start: 0.8053 (mt-10) cc_final: 0.7810 (mt-10) REVERT: D 36 GLU cc_start: 0.7948 (tt0) cc_final: 0.7743 (tm-30) REVERT: D 91 LYS cc_start: 0.7892 (tttt) cc_final: 0.7435 (tttp) REVERT: E 6 MET cc_start: 0.8252 (mtp) cc_final: 0.7935 (mtm) REVERT: F 36 GLU cc_start: 0.8002 (tt0) cc_final: 0.7748 (tm-30) outliers start: 0 outliers final: 0 residues processed: 81 average time/residue: 1.9647 time to fit residues: 163.3366 Evaluate side-chains 45 residues out of total 498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 45 time to evaluate : 0.786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 40 optimal weight: 30.0000 chunk 36 optimal weight: 0.1980 chunk 20 optimal weight: 20.0000 chunk 12 optimal weight: 9.9990 chunk 24 optimal weight: 30.0000 chunk 19 optimal weight: 9.9990 chunk 37 optimal weight: 10.0000 chunk 14 optimal weight: 5.9990 chunk 22 optimal weight: 20.0000 chunk 28 optimal weight: 6.9990 chunk 43 optimal weight: 9.9990 overall best weight: 6.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 8 GLN A 13 HIS A 31 HIS A 42 ASN B 13 HIS B 89 GLN C 8 GLN C 13 HIS C 31 HIS C 42 ASN D 89 GLN E 8 GLN E 13 HIS E 42 ASN F 89 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.084760 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.070045 restraints weight = 11102.919| |-----------------------------------------------------------------------------| r_work (start): 0.3521 rms_B_bonded: 2.26 r_work: 0.3437 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3356 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.3356 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8817 moved from start: 0.2639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 4482 Z= 0.320 Angle : 0.622 6.345 6072 Z= 0.347 Chirality : 0.048 0.147 642 Planarity : 0.004 0.042 780 Dihedral : 4.972 17.765 576 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.81 % Favored : 94.19 % Rotamer: Outliers : 1.61 % Allowed : 8.23 % Favored : 90.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.57 (0.29), residues: 516 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.71 (0.22), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 60 HIS 0.005 0.001 HIS A 13 PHE 0.017 0.002 PHE D 22 TYR 0.014 0.002 TYR E 67 ARG 0.003 0.000 ARG C 45 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1032 Ramachandran restraints generated. 516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1032 Ramachandran restraints generated. 516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 56 time to evaluate : 0.559 Fit side-chains REVERT: A 45 ARG cc_start: 0.8595 (mtt-85) cc_final: 0.7000 (ppt170) REVERT: A 67 TYR cc_start: 0.8641 (m-80) cc_final: 0.8333 (m-80) REVERT: B 91 LYS cc_start: 0.7414 (tttt) cc_final: 0.7005 (tttt) REVERT: C 50 GLU cc_start: 0.8682 (mt-10) cc_final: 0.8240 (mt-10) REVERT: D 12 ARG cc_start: 0.7444 (mtt180) cc_final: 0.7152 (mmt-90) REVERT: D 36 GLU cc_start: 0.8507 (tt0) cc_final: 0.8188 (tm-30) REVERT: D 91 LYS cc_start: 0.7260 (tttt) cc_final: 0.6813 (tttp) REVERT: E 6 MET cc_start: 0.8590 (mtp) cc_final: 0.8370 (mtm) REVERT: F 36 GLU cc_start: 0.8612 (tt0) cc_final: 0.8302 (tm-30) REVERT: F 44 GLU cc_start: 0.8493 (OUTLIER) cc_final: 0.7784 (tt0) REVERT: F 47 GLU cc_start: 0.8063 (tm-30) cc_final: 0.7714 (tm-30) REVERT: F 75 LYS cc_start: 0.7732 (mtpm) cc_final: 0.6699 (mmpt) REVERT: F 87 LEU cc_start: 0.8376 (OUTLIER) cc_final: 0.8123 (mt) outliers start: 8 outliers final: 3 residues processed: 63 average time/residue: 2.7566 time to fit residues: 178.2245 Evaluate side-chains 51 residues out of total 498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 46 time to evaluate : 1.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain E residue 71 THR Chi-restraints excluded: chain F residue 44 GLU Chi-restraints excluded: chain F residue 85 VAL Chi-restraints excluded: chain F residue 87 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 35 optimal weight: 9.9990 chunk 2 optimal weight: 5.9990 chunk 45 optimal weight: 9.9990 chunk 47 optimal weight: 9.9990 chunk 43 optimal weight: 8.9990 chunk 42 optimal weight: 20.0000 chunk 28 optimal weight: 10.0000 chunk 40 optimal weight: 50.0000 chunk 8 optimal weight: 50.0000 chunk 22 optimal weight: 20.0000 chunk 1 optimal weight: 4.9990 overall best weight: 7.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 84 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.084216 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.069264 restraints weight = 11160.093| |-----------------------------------------------------------------------------| r_work (start): 0.3486 rms_B_bonded: 2.26 r_work: 0.3412 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3329 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.3329 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8801 moved from start: 0.3052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.035 4482 Z= 0.371 Angle : 0.642 4.638 6072 Z= 0.358 Chirality : 0.048 0.142 642 Planarity : 0.004 0.038 780 Dihedral : 5.163 17.095 576 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.98 % Favored : 93.02 % Rotamer: Outliers : 1.61 % Allowed : 9.24 % Favored : 89.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.62 (0.29), residues: 516 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.75 (0.22), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP E 60 HIS 0.005 0.001 HIS F 31 PHE 0.018 0.002 PHE D 22 TYR 0.015 0.002 TYR E 67 ARG 0.003 0.000 ARG C 45 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1032 Ramachandran restraints generated. 516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1032 Ramachandran restraints generated. 516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 47 time to evaluate : 1.625 Fit side-chains REVERT: A 67 TYR cc_start: 0.8697 (m-80) cc_final: 0.8449 (m-80) REVERT: B 36 GLU cc_start: 0.8750 (OUTLIER) cc_final: 0.8461 (tt0) REVERT: C 50 GLU cc_start: 0.8663 (mt-10) cc_final: 0.8267 (mt-10) REVERT: D 12 ARG cc_start: 0.7532 (mtt180) cc_final: 0.7052 (mmt-90) REVERT: D 36 GLU cc_start: 0.8528 (tt0) cc_final: 0.8264 (tt0) REVERT: E 6 MET cc_start: 0.8569 (mtp) cc_final: 0.8253 (mtm) REVERT: F 36 GLU cc_start: 0.8505 (tt0) cc_final: 0.8059 (tm-30) REVERT: F 44 GLU cc_start: 0.8513 (OUTLIER) cc_final: 0.7786 (tt0) REVERT: F 47 GLU cc_start: 0.8006 (tm-30) cc_final: 0.7389 (tm-30) REVERT: F 75 LYS cc_start: 0.7648 (mtpm) cc_final: 0.6632 (mmpt) outliers start: 8 outliers final: 2 residues processed: 55 average time/residue: 1.8981 time to fit residues: 107.8291 Evaluate side-chains 46 residues out of total 498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 42 time to evaluate : 0.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 36 GLU Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain E residue 71 THR Chi-restraints excluded: chain F residue 44 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 35 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 6 optimal weight: 5.9990 chunk 41 optimal weight: 30.0000 chunk 32 optimal weight: 9.9990 chunk 34 optimal weight: 8.9990 chunk 13 optimal weight: 10.0000 chunk 21 optimal weight: 9.9990 chunk 23 optimal weight: 10.0000 chunk 5 optimal weight: 1.9990 chunk 8 optimal weight: 50.0000 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.084290 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.069463 restraints weight = 11238.778| |-----------------------------------------------------------------------------| r_work (start): 0.3499 rms_B_bonded: 2.26 r_work: 0.3410 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3332 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.3332 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8842 moved from start: 0.3226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.031 4482 Z= 0.339 Angle : 0.623 4.552 6072 Z= 0.346 Chirality : 0.047 0.140 642 Planarity : 0.004 0.034 780 Dihedral : 5.141 16.815 576 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.36 % Favored : 92.64 % Rotamer: Outliers : 1.20 % Allowed : 10.24 % Favored : 88.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.59 (0.29), residues: 516 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.73 (0.22), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP E 60 HIS 0.005 0.001 HIS F 31 PHE 0.018 0.002 PHE D 22 TYR 0.015 0.002 TYR E 67 ARG 0.002 0.000 ARG C 45 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1032 Ramachandran restraints generated. 516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1032 Ramachandran restraints generated. 516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 42 time to evaluate : 0.532 Fit side-chains REVERT: A 45 ARG cc_start: 0.8485 (mtt-85) cc_final: 0.6993 (ppt170) REVERT: A 67 TYR cc_start: 0.8772 (m-80) cc_final: 0.8563 (m-80) REVERT: B 36 GLU cc_start: 0.8678 (OUTLIER) cc_final: 0.8387 (tt0) REVERT: C 50 GLU cc_start: 0.8734 (mt-10) cc_final: 0.8354 (mt-10) REVERT: D 12 ARG cc_start: 0.7597 (mpt180) cc_final: 0.7229 (mmt-90) REVERT: D 74 GLU cc_start: 0.8185 (pt0) cc_final: 0.7678 (pt0) REVERT: E 6 MET cc_start: 0.8557 (mtp) cc_final: 0.8352 (mtm) REVERT: F 44 GLU cc_start: 0.8583 (OUTLIER) cc_final: 0.7827 (tt0) REVERT: F 75 LYS cc_start: 0.7785 (mtpm) cc_final: 0.6772 (mmpt) outliers start: 6 outliers final: 2 residues processed: 48 average time/residue: 1.9662 time to fit residues: 96.8025 Evaluate side-chains 42 residues out of total 498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 38 time to evaluate : 0.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 36 GLU Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain E residue 71 THR Chi-restraints excluded: chain F residue 44 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 2 optimal weight: 5.9990 chunk 17 optimal weight: 10.0000 chunk 8 optimal weight: 50.0000 chunk 32 optimal weight: 9.9990 chunk 31 optimal weight: 5.9990 chunk 12 optimal weight: 20.0000 chunk 0 optimal weight: 10.0000 chunk 38 optimal weight: 0.0050 chunk 1 optimal weight: 1.9990 chunk 46 optimal weight: 7.9990 chunk 41 optimal weight: 20.0000 overall best weight: 4.4002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.085688 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.071070 restraints weight = 11518.580| |-----------------------------------------------------------------------------| r_work (start): 0.3527 rms_B_bonded: 2.29 r_work: 0.3447 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3369 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.3369 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8808 moved from start: 0.3243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 4482 Z= 0.235 Angle : 0.577 4.722 6072 Z= 0.318 Chirality : 0.046 0.134 642 Planarity : 0.003 0.031 780 Dihedral : 4.993 16.673 576 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.36 % Favored : 92.64 % Rotamer: Outliers : 1.20 % Allowed : 10.84 % Favored : 87.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.55 (0.29), residues: 516 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.69 (0.22), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP E 60 HIS 0.004 0.001 HIS B 31 PHE 0.018 0.002 PHE D 22 TYR 0.014 0.001 TYR E 67 ARG 0.002 0.000 ARG C 45 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1032 Ramachandran restraints generated. 516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1032 Ramachandran restraints generated. 516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 43 time to evaluate : 0.491 Fit side-chains REVERT: A 45 ARG cc_start: 0.8453 (mtt-85) cc_final: 0.6960 (ppt170) REVERT: B 36 GLU cc_start: 0.8658 (OUTLIER) cc_final: 0.8351 (tt0) REVERT: C 47 GLU cc_start: 0.8007 (tm-30) cc_final: 0.7588 (tp30) REVERT: C 50 GLU cc_start: 0.8688 (mt-10) cc_final: 0.8180 (mt-10) REVERT: D 12 ARG cc_start: 0.7568 (mpt180) cc_final: 0.7215 (mmt-90) REVERT: D 74 GLU cc_start: 0.8149 (pt0) cc_final: 0.7664 (pt0) REVERT: E 47 GLU cc_start: 0.8119 (tm-30) cc_final: 0.7739 (tm-30) REVERT: F 44 GLU cc_start: 0.8563 (OUTLIER) cc_final: 0.7790 (tt0) REVERT: F 47 GLU cc_start: 0.8072 (OUTLIER) cc_final: 0.7291 (tm-30) REVERT: F 75 LYS cc_start: 0.7604 (mtpm) cc_final: 0.6568 (mmpt) outliers start: 6 outliers final: 2 residues processed: 49 average time/residue: 1.9227 time to fit residues: 96.7110 Evaluate side-chains 46 residues out of total 498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 41 time to evaluate : 0.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 36 GLU Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain E residue 71 THR Chi-restraints excluded: chain F residue 44 GLU Chi-restraints excluded: chain F residue 47 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 23 optimal weight: 9.9990 chunk 14 optimal weight: 9.9990 chunk 24 optimal weight: 20.0000 chunk 0 optimal weight: 20.0000 chunk 17 optimal weight: 8.9990 chunk 26 optimal weight: 7.9990 chunk 46 optimal weight: 9.9990 chunk 33 optimal weight: 5.9990 chunk 20 optimal weight: 30.0000 chunk 8 optimal weight: 7.9990 chunk 45 optimal weight: 5.9990 overall best weight: 7.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.082996 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.068618 restraints weight = 11325.747| |-----------------------------------------------------------------------------| r_work (start): 0.3505 rms_B_bonded: 2.22 r_work: 0.3422 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3342 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.3342 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8851 moved from start: 0.3369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.031 4482 Z= 0.345 Angle : 0.621 4.502 6072 Z= 0.345 Chirality : 0.047 0.138 642 Planarity : 0.003 0.032 780 Dihedral : 5.100 16.335 576 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.95 % Favored : 92.05 % Rotamer: Outliers : 1.41 % Allowed : 11.45 % Favored : 87.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.58 (0.29), residues: 516 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.72 (0.22), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP C 60 HIS 0.005 0.001 HIS F 31 PHE 0.017 0.002 PHE D 22 TYR 0.015 0.002 TYR E 67 ARG 0.001 0.000 ARG C 45 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1032 Ramachandran restraints generated. 516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1032 Ramachandran restraints generated. 516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 43 time to evaluate : 0.555 Fit side-chains REVERT: B 36 GLU cc_start: 0.8698 (OUTLIER) cc_final: 0.8400 (tt0) REVERT: C 50 GLU cc_start: 0.8660 (mt-10) cc_final: 0.8242 (mt-10) REVERT: D 12 ARG cc_start: 0.7612 (mpt180) cc_final: 0.7328 (mmt-90) REVERT: D 74 GLU cc_start: 0.8142 (pt0) cc_final: 0.7656 (pt0) REVERT: E 47 GLU cc_start: 0.8145 (tm-30) cc_final: 0.7930 (tm-30) REVERT: F 36 GLU cc_start: 0.8670 (OUTLIER) cc_final: 0.8435 (tt0) REVERT: F 44 GLU cc_start: 0.8608 (OUTLIER) cc_final: 0.7845 (tt0) REVERT: F 47 GLU cc_start: 0.8114 (OUTLIER) cc_final: 0.7317 (tm-30) REVERT: F 75 LYS cc_start: 0.7742 (mtpm) cc_final: 0.6678 (mmpt) outliers start: 7 outliers final: 3 residues processed: 49 average time/residue: 1.8811 time to fit residues: 94.6801 Evaluate side-chains 47 residues out of total 498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 40 time to evaluate : 0.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 ILE Chi-restraints excluded: chain B residue 36 GLU Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain E residue 71 THR Chi-restraints excluded: chain F residue 36 GLU Chi-restraints excluded: chain F residue 44 GLU Chi-restraints excluded: chain F residue 47 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 38 optimal weight: 8.9990 chunk 33 optimal weight: 9.9990 chunk 12 optimal weight: 9.9990 chunk 37 optimal weight: 9.9990 chunk 8 optimal weight: 40.0000 chunk 26 optimal weight: 6.9990 chunk 23 optimal weight: 20.0000 chunk 24 optimal weight: 8.9990 chunk 15 optimal weight: 5.9990 chunk 18 optimal weight: 5.9990 chunk 30 optimal weight: 4.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.083707 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.069235 restraints weight = 11389.221| |-----------------------------------------------------------------------------| r_work (start): 0.3505 rms_B_bonded: 2.24 r_work: 0.3425 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3348 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.3348 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8843 moved from start: 0.3401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 4482 Z= 0.316 Angle : 0.626 6.130 6072 Z= 0.346 Chirality : 0.047 0.137 642 Planarity : 0.003 0.032 780 Dihedral : 5.086 16.147 576 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.95 % Favored : 92.05 % Rotamer: Outliers : 1.61 % Allowed : 12.05 % Favored : 86.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.61 (0.29), residues: 516 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.74 (0.22), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP E 60 HIS 0.004 0.001 HIS F 31 PHE 0.018 0.002 PHE D 22 TYR 0.015 0.002 TYR E 67 ARG 0.001 0.000 ARG C 45 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1032 Ramachandran restraints generated. 516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1032 Ramachandran restraints generated. 516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 41 time to evaluate : 0.592 Fit side-chains REVERT: B 36 GLU cc_start: 0.8668 (OUTLIER) cc_final: 0.8373 (tt0) REVERT: C 47 GLU cc_start: 0.8084 (tm-30) cc_final: 0.7683 (tp30) REVERT: C 50 GLU cc_start: 0.8661 (mt-10) cc_final: 0.8236 (mt-10) REVERT: D 74 GLU cc_start: 0.8129 (pt0) cc_final: 0.7635 (pt0) REVERT: E 47 GLU cc_start: 0.8153 (tm-30) cc_final: 0.7687 (tm-30) REVERT: F 44 GLU cc_start: 0.8594 (OUTLIER) cc_final: 0.7815 (tt0) REVERT: F 47 GLU cc_start: 0.8135 (OUTLIER) cc_final: 0.7403 (tm-30) REVERT: F 74 GLU cc_start: 0.8430 (pt0) cc_final: 0.7991 (pt0) REVERT: F 75 LYS cc_start: 0.7714 (mtpm) cc_final: 0.6646 (mmpt) outliers start: 8 outliers final: 3 residues processed: 47 average time/residue: 2.1051 time to fit residues: 101.5583 Evaluate side-chains 45 residues out of total 498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 39 time to evaluate : 0.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 ILE Chi-restraints excluded: chain B residue 36 GLU Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain E residue 71 THR Chi-restraints excluded: chain F residue 44 GLU Chi-restraints excluded: chain F residue 47 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 30 optimal weight: 7.9990 chunk 27 optimal weight: 6.9990 chunk 1 optimal weight: 3.9990 chunk 4 optimal weight: 10.0000 chunk 5 optimal weight: 9.9990 chunk 11 optimal weight: 10.0000 chunk 25 optimal weight: 20.0000 chunk 20 optimal weight: 9.9990 chunk 36 optimal weight: 2.9990 chunk 35 optimal weight: 0.9990 chunk 24 optimal weight: 40.0000 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.085406 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.070897 restraints weight = 11214.585| |-----------------------------------------------------------------------------| r_work (start): 0.3525 rms_B_bonded: 2.23 r_work: 0.3444 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3367 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.3367 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8793 moved from start: 0.3410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 4482 Z= 0.243 Angle : 0.596 5.032 6072 Z= 0.327 Chirality : 0.046 0.133 642 Planarity : 0.003 0.031 780 Dihedral : 4.990 16.024 576 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.75 % Favored : 92.25 % Rotamer: Outliers : 1.41 % Allowed : 12.25 % Favored : 86.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.57 (0.29), residues: 516 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.71 (0.22), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP C 60 HIS 0.004 0.001 HIS D 31 PHE 0.018 0.002 PHE D 22 TYR 0.015 0.001 TYR E 67 ARG 0.001 0.000 ARG C 45 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1032 Ramachandran restraints generated. 516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1032 Ramachandran restraints generated. 516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 41 time to evaluate : 0.545 Fit side-chains REVERT: B 36 GLU cc_start: 0.8683 (OUTLIER) cc_final: 0.8411 (tt0) REVERT: C 47 GLU cc_start: 0.8006 (tm-30) cc_final: 0.7578 (tp30) REVERT: C 50 GLU cc_start: 0.8592 (mt-10) cc_final: 0.8093 (mt-10) REVERT: D 74 GLU cc_start: 0.8065 (pt0) cc_final: 0.7559 (pt0) REVERT: E 47 GLU cc_start: 0.8126 (tm-30) cc_final: 0.7595 (tm-30) REVERT: E 50 GLU cc_start: 0.8744 (mt-10) cc_final: 0.8302 (pm20) REVERT: F 6 MET cc_start: 0.7838 (ttp) cc_final: 0.7309 (tpp) REVERT: F 12 ARG cc_start: 0.4899 (pmt170) cc_final: 0.4115 (pmt-80) REVERT: F 14 PRO cc_start: 0.5186 (Cg_exo) cc_final: 0.4936 (Cg_endo) REVERT: F 36 GLU cc_start: 0.8610 (OUTLIER) cc_final: 0.8331 (tm-30) REVERT: F 44 GLU cc_start: 0.8556 (OUTLIER) cc_final: 0.7786 (tt0) REVERT: F 47 GLU cc_start: 0.8109 (OUTLIER) cc_final: 0.7358 (tm-30) REVERT: F 74 GLU cc_start: 0.8377 (pt0) cc_final: 0.7915 (pt0) REVERT: F 75 LYS cc_start: 0.7517 (mtpm) cc_final: 0.6468 (mmpt) outliers start: 7 outliers final: 3 residues processed: 47 average time/residue: 1.7900 time to fit residues: 86.5129 Evaluate side-chains 47 residues out of total 498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 40 time to evaluate : 0.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 ILE Chi-restraints excluded: chain B residue 36 GLU Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain E residue 71 THR Chi-restraints excluded: chain F residue 36 GLU Chi-restraints excluded: chain F residue 44 GLU Chi-restraints excluded: chain F residue 47 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 9 optimal weight: 20.0000 chunk 16 optimal weight: 20.0000 chunk 21 optimal weight: 20.0000 chunk 28 optimal weight: 30.0000 chunk 6 optimal weight: 6.9990 chunk 2 optimal weight: 10.0000 chunk 19 optimal weight: 10.0000 chunk 34 optimal weight: 4.9990 chunk 39 optimal weight: 10.0000 chunk 45 optimal weight: 9.9990 chunk 11 optimal weight: 5.9990 overall best weight: 7.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.084225 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.069622 restraints weight = 11537.066| |-----------------------------------------------------------------------------| r_work (start): 0.3499 rms_B_bonded: 2.26 r_work: 0.3418 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3338 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.3338 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8854 moved from start: 0.3483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.039 4482 Z= 0.356 Angle : 0.651 6.160 6072 Z= 0.360 Chirality : 0.047 0.138 642 Planarity : 0.003 0.031 780 Dihedral : 5.117 15.847 576 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.53 % Favored : 91.47 % Rotamer: Outliers : 1.41 % Allowed : 12.85 % Favored : 85.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.62 (0.28), residues: 516 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.75 (0.22), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 60 HIS 0.005 0.001 HIS F 31 PHE 0.017 0.002 PHE D 22 TYR 0.019 0.002 TYR E 67 ARG 0.001 0.000 ARG D 12 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1032 Ramachandran restraints generated. 516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1032 Ramachandran restraints generated. 516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 40 time to evaluate : 0.501 Fit side-chains REVERT: B 36 GLU cc_start: 0.8698 (OUTLIER) cc_final: 0.8401 (tt0) REVERT: C 47 GLU cc_start: 0.8020 (tm-30) cc_final: 0.7565 (tp30) REVERT: C 50 GLU cc_start: 0.8653 (mt-10) cc_final: 0.8132 (mt-10) REVERT: D 74 GLU cc_start: 0.8109 (pt0) cc_final: 0.7606 (pt0) REVERT: E 47 GLU cc_start: 0.8198 (tm-30) cc_final: 0.7636 (tm-30) REVERT: F 12 ARG cc_start: 0.5155 (pmt170) cc_final: 0.4311 (pmt-80) REVERT: F 14 PRO cc_start: 0.5174 (Cg_exo) cc_final: 0.4930 (Cg_endo) REVERT: F 36 GLU cc_start: 0.8639 (OUTLIER) cc_final: 0.8424 (tt0) REVERT: F 44 GLU cc_start: 0.8606 (OUTLIER) cc_final: 0.7856 (tt0) REVERT: F 47 GLU cc_start: 0.8127 (OUTLIER) cc_final: 0.7388 (tm-30) REVERT: F 74 GLU cc_start: 0.8427 (pt0) cc_final: 0.7961 (pt0) REVERT: F 75 LYS cc_start: 0.7761 (mtpm) cc_final: 0.6727 (mmpt) outliers start: 7 outliers final: 3 residues processed: 46 average time/residue: 1.7956 time to fit residues: 84.8706 Evaluate side-chains 45 residues out of total 498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 38 time to evaluate : 0.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 ILE Chi-restraints excluded: chain B residue 36 GLU Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain E residue 71 THR Chi-restraints excluded: chain F residue 36 GLU Chi-restraints excluded: chain F residue 44 GLU Chi-restraints excluded: chain F residue 47 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 37 optimal weight: 9.9990 chunk 24 optimal weight: 6.9990 chunk 6 optimal weight: 10.0000 chunk 34 optimal weight: 0.6980 chunk 5 optimal weight: 7.9990 chunk 46 optimal weight: 9.9990 chunk 16 optimal weight: 20.0000 chunk 26 optimal weight: 5.9990 chunk 23 optimal weight: 20.0000 chunk 27 optimal weight: 10.0000 chunk 40 optimal weight: 9.9990 overall best weight: 6.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 8 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.084619 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.070109 restraints weight = 11234.757| |-----------------------------------------------------------------------------| r_work (start): 0.3509 rms_B_bonded: 2.22 r_work: 0.3430 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3352 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.3352 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8842 moved from start: 0.3491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 4482 Z= 0.308 Angle : 0.632 6.129 6072 Z= 0.348 Chirality : 0.047 0.137 642 Planarity : 0.003 0.031 780 Dihedral : 5.089 15.758 576 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.75 % Favored : 92.25 % Rotamer: Outliers : 1.41 % Allowed : 12.85 % Favored : 85.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.61 (0.28), residues: 516 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.74 (0.22), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 60 HIS 0.005 0.001 HIS D 31 PHE 0.018 0.002 PHE D 22 TYR 0.017 0.002 TYR E 67 ARG 0.001 0.000 ARG C 45 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1032 Ramachandran restraints generated. 516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1032 Ramachandran restraints generated. 516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 39 time to evaluate : 0.509 Fit side-chains REVERT: B 12 ARG cc_start: 0.6872 (mpt180) cc_final: 0.5965 (mmm160) REVERT: B 36 GLU cc_start: 0.8677 (OUTLIER) cc_final: 0.8387 (tt0) REVERT: C 50 GLU cc_start: 0.8571 (mt-10) cc_final: 0.8251 (mt-10) REVERT: D 74 GLU cc_start: 0.8087 (pt0) cc_final: 0.7584 (pt0) REVERT: E 47 GLU cc_start: 0.8156 (tm-30) cc_final: 0.7858 (tm-30) REVERT: F 12 ARG cc_start: 0.5077 (pmt170) cc_final: 0.4261 (pmt-80) REVERT: F 14 PRO cc_start: 0.5200 (Cg_exo) cc_final: 0.4945 (Cg_endo) REVERT: F 36 GLU cc_start: 0.8626 (OUTLIER) cc_final: 0.8410 (tt0) REVERT: F 44 GLU cc_start: 0.8586 (OUTLIER) cc_final: 0.7852 (tt0) REVERT: F 47 GLU cc_start: 0.8134 (OUTLIER) cc_final: 0.7393 (tm-30) REVERT: F 74 GLU cc_start: 0.8378 (pt0) cc_final: 0.7920 (pt0) REVERT: F 75 LYS cc_start: 0.7781 (mtpm) cc_final: 0.6769 (mmpt) outliers start: 7 outliers final: 3 residues processed: 45 average time/residue: 1.8891 time to fit residues: 87.3166 Evaluate side-chains 45 residues out of total 498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 38 time to evaluate : 0.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 ILE Chi-restraints excluded: chain B residue 36 GLU Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain E residue 71 THR Chi-restraints excluded: chain F residue 36 GLU Chi-restraints excluded: chain F residue 44 GLU Chi-restraints excluded: chain F residue 47 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 32 optimal weight: 20.0000 chunk 24 optimal weight: 50.0000 chunk 21 optimal weight: 10.0000 chunk 15 optimal weight: 30.0000 chunk 12 optimal weight: 10.0000 chunk 4 optimal weight: 6.9990 chunk 7 optimal weight: 6.9990 chunk 41 optimal weight: 20.0000 chunk 23 optimal weight: 6.9990 chunk 6 optimal weight: 9.9990 chunk 26 optimal weight: 5.9990 overall best weight: 7.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.083074 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.068584 restraints weight = 11343.604| |-----------------------------------------------------------------------------| r_work (start): 0.3502 rms_B_bonded: 2.22 r_work: 0.3420 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3341 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.3341 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8818 moved from start: 0.3518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 4482 Z= 0.349 Angle : 0.658 7.357 6072 Z= 0.362 Chirality : 0.047 0.137 642 Planarity : 0.003 0.031 780 Dihedral : 5.162 15.696 576 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.53 % Favored : 91.47 % Rotamer: Outliers : 1.41 % Allowed : 13.05 % Favored : 85.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.63 (0.28), residues: 516 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.76 (0.22), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 60 HIS 0.005 0.001 HIS F 31 PHE 0.017 0.002 PHE D 22 TYR 0.017 0.002 TYR E 67 ARG 0.001 0.000 ARG D 12 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3476.39 seconds wall clock time: 61 minutes 26.34 seconds (3686.34 seconds total)