Starting phenix.real_space_refine on Tue Feb 3 15:16:30 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8a7o_15222/02_2026/8a7o_15222.cif Found real_map, /net/cci-nas-00/data/ceres_data/8a7o_15222/02_2026/8a7o_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 { model { file = "/net/cci-nas-00/data/ceres_data/8a7o_15222/02_2026/8a7o_15222.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8a7o_15222/02_2026/8a7o_15222.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8a7o_15222/02_2026/8a7o_15222.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8a7o_15222/02_2026/8a7o_15222.map" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.004 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/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: 0.97, per 1000 atoms: 0.22 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: 0.35 Conformation dependent library (CDL) restraints added in 169.2 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: 0.21 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: 0.57 Time building geometry restraints manager: 0.47 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: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.080 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.100 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 6.150 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.320 ------------------------------------------------------------------------------- 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 4488 Z= 0.123 Angle : 0.548 5.776 6084 Z= 0.315 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 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: -3.59 (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 ARG 0.001 0.000 ARG A 81 TYR 0.006 0.001 TYR E 63 PHE 0.008 0.001 PHE B 22 TRP 0.002 0.001 TRP A 60 HIS 0.004 0.001 HIS E 13 Details of bonding type rmsd covalent geometry : bond 0.00240 ( 4482) covalent geometry : angle 0.54855 ( 6072) SS BOND : bond 0.00131 ( 6) SS BOND : angle 0.46166 ( 12) hydrogen bonds : bond 0.30173 ( 86) hydrogen bonds : angle 9.75660 ( 258) *********************** 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 : 0.177 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: 0.6577 (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: 0.9165 time to fit residues: 75.8407 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 : 0.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 24 optimal weight: 50.0000 chunk 26 optimal weight: 0.9990 chunk 2 optimal weight: 10.0000 chunk 16 optimal weight: 5.9990 chunk 32 optimal weight: 7.9990 chunk 31 optimal weight: 6.9990 chunk 25 optimal weight: 5.9990 chunk 19 optimal weight: 20.0000 chunk 30 optimal weight: 9.9990 chunk 22 optimal weight: 20.0000 chunk 37 optimal weight: 10.0000 overall best weight: 5.5990 ------------------------------------------------------------------------------- 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 = 0.3804 r_free = 0.3804 target = 0.086933 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.072040 restraints weight = 11106.724| |-----------------------------------------------------------------------------| r_work (start): 0.3534 rms_B_bonded: 2.31 r_work: 0.3450 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3370 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.3370 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8806 moved from start: 0.2564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 4488 Z= 0.180 Angle : 0.607 6.353 6084 Z= 0.337 Chirality : 0.047 0.146 642 Planarity : 0.004 0.041 780 Dihedral : 4.898 17.915 576 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 1.00 % Allowed : 8.84 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.55 (0.29), residues: 516 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.70 (0.22), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 45 TYR 0.014 0.002 TYR E 67 PHE 0.017 0.002 PHE D 22 TRP 0.006 0.001 TRP E 60 HIS 0.005 0.001 HIS A 13 Details of bonding type rmsd covalent geometry : bond 0.00441 ( 4482) covalent geometry : angle 0.60716 ( 6072) SS BOND : bond 0.00459 ( 6) SS BOND : angle 0.60484 ( 12) hydrogen bonds : bond 0.04152 ( 86) hydrogen bonds : angle 6.79345 ( 258) *********************** 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 60 residues out of total 498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 55 time to evaluate : 0.179 Fit side-chains REVERT: A 45 ARG cc_start: 0.8589 (mtt-85) cc_final: 0.7002 (ppt170) REVERT: A 67 TYR cc_start: 0.8615 (m-80) cc_final: 0.8291 (m-80) REVERT: B 91 LYS cc_start: 0.7398 (tttt) cc_final: 0.6986 (tttt) REVERT: C 50 GLU cc_start: 0.8684 (mt-10) cc_final: 0.8166 (mt-10) REVERT: D 12 ARG cc_start: 0.7455 (mtt180) cc_final: 0.7165 (mmt-90) REVERT: D 36 GLU cc_start: 0.8513 (tt0) cc_final: 0.8180 (tm-30) REVERT: D 91 LYS cc_start: 0.7258 (tttt) cc_final: 0.6798 (tttp) REVERT: E 6 MET cc_start: 0.8554 (mtp) cc_final: 0.8308 (mtm) REVERT: F 36 GLU cc_start: 0.8599 (tt0) cc_final: 0.8274 (tm-30) REVERT: F 44 GLU cc_start: 0.8485 (OUTLIER) cc_final: 0.7764 (tt0) REVERT: F 47 GLU cc_start: 0.8075 (tm-30) cc_final: 0.7702 (tm-30) REVERT: F 87 LEU cc_start: 0.8324 (OUTLIER) cc_final: 0.8034 (mt) outliers start: 5 outliers final: 2 residues processed: 60 average time/residue: 0.9893 time to fit residues: 60.6508 Evaluate side-chains 51 residues out of total 498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 47 time to evaluate : 0.179 ------------------------------------------------------------------------------- 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 87 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 41 optimal weight: 20.0000 chunk 34 optimal weight: 9.9990 chunk 12 optimal weight: 0.9980 chunk 29 optimal weight: 20.0000 chunk 42 optimal weight: 10.0000 chunk 28 optimal weight: 10.0000 chunk 37 optimal weight: 0.9990 chunk 39 optimal weight: 9.9990 chunk 21 optimal weight: 9.9990 chunk 22 optimal weight: 6.9990 chunk 23 optimal weight: 20.0000 overall best weight: 5.7988 ------------------------------------------------------------------------------- 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 = 0.3789 r_free = 0.3789 target = 0.086498 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.070498 restraints weight = 11595.975| |-----------------------------------------------------------------------------| r_work (start): 0.3527 rms_B_bonded: 2.36 r_work: 0.3441 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3361 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3361 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8810 moved from start: 0.2910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 4488 Z= 0.180 Angle : 0.595 4.518 6084 Z= 0.331 Chirality : 0.047 0.138 642 Planarity : 0.004 0.037 780 Dihedral : 4.992 17.092 576 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.40 % Favored : 93.60 % Rotamer: Outliers : 1.81 % Allowed : 9.04 % 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 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: -3.58 (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 ARG 0.003 0.000 ARG C 45 TYR 0.013 0.002 TYR E 67 PHE 0.017 0.002 PHE D 22 TRP 0.005 0.001 TRP E 60 HIS 0.004 0.001 HIS B 31 Details of bonding type rmsd covalent geometry : bond 0.00439 ( 4482) covalent geometry : angle 0.59518 ( 6072) SS BOND : bond 0.00471 ( 6) SS BOND : angle 0.60660 ( 12) hydrogen bonds : bond 0.03750 ( 86) hydrogen bonds : angle 6.38450 ( 258) *********************** 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 60 residues out of total 498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 51 time to evaluate : 0.176 Fit side-chains REVERT: A 45 ARG cc_start: 0.8473 (mtt-85) cc_final: 0.6959 (ppt170) REVERT: A 67 TYR cc_start: 0.8666 (m-80) cc_final: 0.8398 (m-80) REVERT: B 36 GLU cc_start: 0.8728 (OUTLIER) cc_final: 0.8448 (tt0) REVERT: C 50 GLU cc_start: 0.8672 (mt-10) cc_final: 0.8299 (mt-10) REVERT: C 69 GLU cc_start: 0.8076 (mp0) cc_final: 0.7870 (mp0) REVERT: D 12 ARG cc_start: 0.7530 (mtt180) cc_final: 0.7260 (mmt-90) REVERT: D 36 GLU cc_start: 0.8569 (tt0) cc_final: 0.8219 (tm-30) REVERT: D 91 LYS cc_start: 0.7132 (tttt) cc_final: 0.6628 (tttt) REVERT: E 6 MET cc_start: 0.8548 (mtp) cc_final: 0.8339 (mtm) REVERT: F 36 GLU cc_start: 0.8597 (tt0) cc_final: 0.8218 (tm-30) REVERT: F 44 GLU cc_start: 0.8560 (OUTLIER) cc_final: 0.7829 (tt0) REVERT: F 47 GLU cc_start: 0.8100 (tm-30) cc_final: 0.7463 (tm-30) REVERT: F 75 LYS cc_start: 0.7676 (mtpm) cc_final: 0.6703 (mmpt) REVERT: F 87 LEU cc_start: 0.8358 (OUTLIER) cc_final: 0.8101 (mt) outliers start: 9 outliers final: 3 residues processed: 59 average time/residue: 1.0001 time to fit residues: 60.3545 Evaluate side-chains 52 residues out of total 498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 46 time to evaluate : 0.221 ------------------------------------------------------------------------------- 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 85 VAL Chi-restraints excluded: chain F residue 87 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 34 optimal weight: 5.9990 chunk 26 optimal weight: 6.9990 chunk 6 optimal weight: 3.9990 chunk 25 optimal weight: 20.0000 chunk 12 optimal weight: 6.9990 chunk 7 optimal weight: 20.0000 chunk 47 optimal weight: 10.0000 chunk 23 optimal weight: 10.0000 chunk 40 optimal weight: 40.0000 chunk 41 optimal weight: 10.0000 chunk 36 optimal weight: 6.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- 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 = 0.3790 r_free = 0.3790 target = 0.084970 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.070232 restraints weight = 11184.119| |-----------------------------------------------------------------------------| r_work (start): 0.3503 rms_B_bonded: 2.24 r_work: 0.3428 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3348 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.3348 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8781 moved from start: 0.3141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.029 4488 Z= 0.188 Angle : 0.599 4.325 6084 Z= 0.332 Chirality : 0.047 0.137 642 Planarity : 0.004 0.032 780 Dihedral : 5.023 16.713 576 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.98 % Favored : 93.02 % Rotamer: Outliers : 1.61 % Allowed : 9.44 % Favored : 88.96 % 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: -3.53 (0.29), residues: 516 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.68 (0.22), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 45 TYR 0.016 0.002 TYR E 67 PHE 0.017 0.002 PHE D 22 TRP 0.004 0.001 TRP E 60 HIS 0.004 0.001 HIS B 31 Details of bonding type rmsd covalent geometry : bond 0.00460 ( 4482) covalent geometry : angle 0.59922 ( 6072) SS BOND : bond 0.00457 ( 6) SS BOND : angle 0.50531 ( 12) hydrogen bonds : bond 0.03503 ( 86) hydrogen bonds : angle 6.19690 ( 258) *********************** 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 53 residues out of total 498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 45 time to evaluate : 0.112 Fit side-chains REVERT: A 45 ARG cc_start: 0.8498 (mtt-85) cc_final: 0.7009 (ppt170) REVERT: A 67 TYR cc_start: 0.8713 (m-80) cc_final: 0.8508 (m-80) REVERT: B 36 GLU cc_start: 0.8727 (OUTLIER) cc_final: 0.8465 (tt0) REVERT: C 50 GLU cc_start: 0.8667 (mt-10) cc_final: 0.8197 (mt-10) REVERT: D 12 ARG cc_start: 0.7526 (mpt180) cc_final: 0.7107 (mmt-90) REVERT: D 36 GLU cc_start: 0.8517 (tt0) cc_final: 0.8263 (tt0) REVERT: D 74 GLU cc_start: 0.8128 (pt0) cc_final: 0.7593 (pt0) REVERT: F 36 GLU cc_start: 0.8501 (tt0) cc_final: 0.8078 (tm-30) REVERT: F 44 GLU cc_start: 0.8484 (OUTLIER) cc_final: 0.7730 (tt0) REVERT: F 47 GLU cc_start: 0.7980 (tm-30) cc_final: 0.7301 (tm-30) REVERT: F 75 LYS cc_start: 0.7550 (mtpm) cc_final: 0.6526 (mmpt) outliers start: 8 outliers final: 2 residues processed: 53 average time/residue: 0.9099 time to fit residues: 49.3111 Evaluate side-chains 47 residues out of total 498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 43 time to evaluate : 0.180 ------------------------------------------------------------------------------- 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 24 optimal weight: 40.0000 chunk 45 optimal weight: 9.9990 chunk 12 optimal weight: 20.0000 chunk 4 optimal weight: 20.0000 chunk 32 optimal weight: 9.9990 chunk 13 optimal weight: 10.0000 chunk 18 optimal weight: 7.9990 chunk 34 optimal weight: 9.9990 chunk 38 optimal weight: 0.5980 chunk 39 optimal weight: 10.0000 chunk 47 optimal weight: 20.0000 overall best weight: 7.7188 ------------------------------------------------------------------------------- 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 = 0.084596 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.069920 restraints weight = 11447.356| |-----------------------------------------------------------------------------| r_work (start): 0.3505 rms_B_bonded: 2.26 r_work: 0.3421 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3340 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.3340 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8852 moved from start: 0.3275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.033 4488 Z= 0.228 Angle : 0.633 4.690 6084 Z= 0.352 Chirality : 0.048 0.139 642 Planarity : 0.004 0.033 780 Dihedral : 5.132 16.508 576 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.75 % Favored : 92.25 % Rotamer: Outliers : 1.00 % Allowed : 10.44 % 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 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: -3.57 (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 ARG 0.002 0.000 ARG C 45 TYR 0.014 0.002 TYR E 67 PHE 0.018 0.002 PHE D 22 TRP 0.004 0.001 TRP C 60 HIS 0.005 0.001 HIS F 31 Details of bonding type rmsd covalent geometry : bond 0.00555 ( 4482) covalent geometry : angle 0.63301 ( 6072) SS BOND : bond 0.00522 ( 6) SS BOND : angle 0.55057 ( 12) hydrogen bonds : bond 0.03729 ( 86) hydrogen bonds : angle 6.18161 ( 258) *********************** 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: 5 poor density : 44 time to evaluate : 0.109 Fit side-chains revert: symmetry clash REVERT: A 45 ARG cc_start: 0.8501 (mtt-85) cc_final: 0.6993 (ppt170) REVERT: A 67 TYR cc_start: 0.8762 (m-80) cc_final: 0.8543 (m-80) REVERT: B 36 GLU cc_start: 0.8704 (OUTLIER) cc_final: 0.8415 (tt0) REVERT: C 47 GLU cc_start: 0.8008 (tm-30) cc_final: 0.7608 (tp30) REVERT: C 50 GLU cc_start: 0.8690 (mt-10) cc_final: 0.8152 (mt-10) REVERT: D 12 ARG cc_start: 0.7588 (mpt180) cc_final: 0.7251 (mmt-90) REVERT: D 74 GLU cc_start: 0.8203 (pt0) cc_final: 0.7721 (pt0) REVERT: E 50 GLU cc_start: 0.8778 (mt-10) cc_final: 0.8218 (mt-10) REVERT: F 44 GLU cc_start: 0.8639 (OUTLIER) cc_final: 0.7919 (tt0) REVERT: F 47 GLU cc_start: 0.8079 (OUTLIER) cc_final: 0.7354 (tm-30) REVERT: F 75 LYS cc_start: 0.7760 (mtpm) cc_final: 0.6696 (mmpt) outliers start: 5 outliers final: 2 residues processed: 49 average time/residue: 0.7923 time to fit residues: 39.7197 Evaluate side-chains 45 residues out of total 498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 40 time to evaluate : 0.169 ------------------------------------------------------------------------------- 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 12 optimal weight: 8.9990 chunk 15 optimal weight: 10.0000 chunk 5 optimal weight: 10.0000 chunk 34 optimal weight: 4.9990 chunk 37 optimal weight: 8.9990 chunk 36 optimal weight: 5.9990 chunk 8 optimal weight: 40.0000 chunk 30 optimal weight: 9.9990 chunk 32 optimal weight: 20.0000 chunk 43 optimal weight: 10.0000 chunk 17 optimal weight: 20.0000 overall best weight: 7.7990 ------------------------------------------------------------------------------- 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 = 0.084340 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.069703 restraints weight = 11608.759| |-----------------------------------------------------------------------------| r_work (start): 0.3495 rms_B_bonded: 2.26 r_work: 0.3414 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3338 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.3338 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8853 moved from start: 0.3371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.032 4488 Z= 0.228 Angle : 0.635 4.660 6084 Z= 0.353 Chirality : 0.048 0.140 642 Planarity : 0.004 0.032 780 Dihedral : 5.157 16.349 576 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.95 % Favored : 92.05 % Rotamer: Outliers : 1.61 % Allowed : 10.64 % Favored : 87.75 % 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: -3.60 (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 ARG 0.001 0.000 ARG C 45 TYR 0.015 0.002 TYR E 67 PHE 0.018 0.002 PHE D 22 TRP 0.003 0.001 TRP E 60 HIS 0.005 0.001 HIS F 31 Details of bonding type rmsd covalent geometry : bond 0.00557 ( 4482) covalent geometry : angle 0.63499 ( 6072) SS BOND : bond 0.00525 ( 6) SS BOND : angle 0.57719 ( 12) hydrogen bonds : bond 0.03728 ( 86) hydrogen bonds : angle 6.12945 ( 258) *********************** 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 49 residues out of total 498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 41 time to evaluate : 0.192 Fit side-chains REVERT: B 36 GLU cc_start: 0.8660 (OUTLIER) cc_final: 0.8373 (tt0) REVERT: C 50 GLU cc_start: 0.8675 (mt-10) cc_final: 0.8068 (mt-10) REVERT: D 6 MET cc_start: 0.7803 (ttp) cc_final: 0.7476 (ptm) REVERT: D 12 ARG cc_start: 0.7625 (mpt180) cc_final: 0.7343 (mmt-90) REVERT: D 36 GLU cc_start: 0.8672 (OUTLIER) cc_final: 0.8451 (tm-30) REVERT: D 74 GLU cc_start: 0.8163 (pt0) cc_final: 0.7699 (pt0) REVERT: E 47 GLU cc_start: 0.8111 (tm-30) cc_final: 0.7905 (tm-30) REVERT: E 48 LYS cc_start: 0.8576 (ttpt) cc_final: 0.8151 (ttpt) REVERT: E 50 GLU cc_start: 0.8775 (mt-10) cc_final: 0.8042 (mt-10) REVERT: F 44 GLU cc_start: 0.8627 (OUTLIER) cc_final: 0.7875 (tt0) REVERT: F 47 GLU cc_start: 0.8097 (OUTLIER) cc_final: 0.7327 (tm-30) REVERT: F 75 LYS cc_start: 0.7790 (mtpm) cc_final: 0.6732 (mmpt) outliers start: 8 outliers final: 2 residues processed: 48 average time/residue: 0.9191 time to fit residues: 45.1867 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 : 0.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 36 GLU Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain D residue 36 GLU 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 10 optimal weight: 10.0000 chunk 41 optimal weight: 20.0000 chunk 34 optimal weight: 9.9990 chunk 3 optimal weight: 8.9990 chunk 19 optimal weight: 7.9990 chunk 8 optimal weight: 40.0000 chunk 46 optimal weight: 6.9990 chunk 37 optimal weight: 10.0000 chunk 4 optimal weight: 6.9990 chunk 26 optimal weight: 0.9990 chunk 35 optimal weight: 7.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- 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 = 0.3779 r_free = 0.3779 target = 0.083931 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.069391 restraints weight = 11453.585| |-----------------------------------------------------------------------------| r_work (start): 0.3512 rms_B_bonded: 2.24 r_work: 0.3431 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3354 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.3354 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8841 moved from start: 0.3389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 4488 Z= 0.190 Angle : 0.618 5.769 6084 Z= 0.341 Chirality : 0.047 0.135 642 Planarity : 0.003 0.031 780 Dihedral : 5.085 16.227 576 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.75 % Favored : 92.25 % Rotamer: Outliers : 1.41 % Allowed : 11.85 % Favored : 86.75 % 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: -3.59 (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 ARG 0.001 0.000 ARG C 45 TYR 0.016 0.002 TYR E 67 PHE 0.018 0.002 PHE D 22 TRP 0.003 0.001 TRP E 60 HIS 0.004 0.001 HIS D 31 Details of bonding type rmsd covalent geometry : bond 0.00465 ( 4482) covalent geometry : angle 0.61766 ( 6072) SS BOND : bond 0.00447 ( 6) SS BOND : angle 0.54426 ( 12) hydrogen bonds : bond 0.03402 ( 86) hydrogen bonds : angle 5.98433 ( 258) *********************** 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 50 residues out of total 498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 43 time to evaluate : 0.182 Fit side-chains REVERT: A 45 ARG cc_start: 0.8481 (mtt-85) cc_final: 0.6956 (ppt170) REVERT: B 36 GLU cc_start: 0.8634 (OUTLIER) cc_final: 0.8336 (tt0) REVERT: C 47 GLU cc_start: 0.8036 (tm-30) cc_final: 0.7640 (tp30) REVERT: C 50 GLU cc_start: 0.8683 (mt-10) cc_final: 0.8101 (mt-10) REVERT: D 6 MET cc_start: 0.7803 (ttp) cc_final: 0.7503 (ptm) REVERT: D 36 GLU cc_start: 0.8648 (OUTLIER) cc_final: 0.8338 (tm-30) REVERT: D 74 GLU cc_start: 0.8112 (pt0) cc_final: 0.7638 (pt0) REVERT: E 47 GLU cc_start: 0.8139 (tm-30) cc_final: 0.7709 (tm-30) REVERT: E 48 LYS cc_start: 0.8550 (ttpt) cc_final: 0.8141 (ttpt) REVERT: E 50 GLU cc_start: 0.8818 (mt-10) cc_final: 0.8115 (mt-10) REVERT: F 44 GLU cc_start: 0.8612 (OUTLIER) cc_final: 0.7891 (tt0) REVERT: F 47 GLU cc_start: 0.8145 (OUTLIER) cc_final: 0.7440 (tm-30) REVERT: F 74 GLU cc_start: 0.8406 (pt0) cc_final: 0.7984 (pt0) REVERT: F 75 LYS cc_start: 0.7725 (mtpm) cc_final: 0.6673 (mmpt) outliers start: 7 outliers final: 2 residues processed: 49 average time/residue: 0.8303 time to fit residues: 41.5961 Evaluate side-chains 46 residues out of total 498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 40 time to evaluate : 0.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 36 GLU Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain D residue 36 GLU 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 44 optimal weight: 1.9990 chunk 4 optimal weight: 20.0000 chunk 34 optimal weight: 0.0270 chunk 2 optimal weight: 6.9990 chunk 13 optimal weight: 9.9990 chunk 42 optimal weight: 5.9990 chunk 20 optimal weight: 20.0000 chunk 19 optimal weight: 6.9990 chunk 36 optimal weight: 7.9990 chunk 11 optimal weight: 8.9990 chunk 12 optimal weight: 5.9990 overall best weight: 4.2046 ------------------------------------------------------------------------------- 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 = 0.3804 r_free = 0.3804 target = 0.085714 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.071179 restraints weight = 11383.987| |-----------------------------------------------------------------------------| r_work (start): 0.3533 rms_B_bonded: 2.24 r_work: 0.3452 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3374 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.3374 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8819 moved from start: 0.3400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 4488 Z= 0.144 Angle : 0.589 5.305 6084 Z= 0.323 Chirality : 0.046 0.132 642 Planarity : 0.003 0.030 780 Dihedral : 4.962 16.061 576 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.36 % Favored : 92.64 % Rotamer: Outliers : 1.20 % Allowed : 12.25 % Favored : 86.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -3.54 (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 ARG 0.002 0.000 ARG C 45 TYR 0.015 0.001 TYR E 67 PHE 0.018 0.002 PHE D 22 TRP 0.003 0.001 TRP E 60 HIS 0.004 0.001 HIS D 31 Details of bonding type rmsd covalent geometry : bond 0.00356 ( 4482) covalent geometry : angle 0.58924 ( 6072) SS BOND : bond 0.00346 ( 6) SS BOND : angle 0.46300 ( 12) hydrogen bonds : bond 0.02926 ( 86) hydrogen bonds : angle 5.80991 ( 258) *********************** 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 51 residues out of total 498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 45 time to evaluate : 0.202 Fit side-chains REVERT: A 6 MET cc_start: 0.8531 (mtp) cc_final: 0.8328 (mtp) REVERT: B 36 GLU cc_start: 0.8642 (OUTLIER) cc_final: 0.8358 (tt0) REVERT: C 50 GLU cc_start: 0.8678 (mt-10) cc_final: 0.8041 (mt-10) REVERT: D 6 MET cc_start: 0.7781 (ttp) cc_final: 0.7498 (ptm) REVERT: D 36 GLU cc_start: 0.8655 (OUTLIER) cc_final: 0.8441 (tm-30) REVERT: D 74 GLU cc_start: 0.8079 (pt0) cc_final: 0.7662 (pt0) REVERT: E 47 GLU cc_start: 0.8143 (tm-30) cc_final: 0.7868 (tm-30) REVERT: E 48 LYS cc_start: 0.8572 (ttpt) cc_final: 0.8133 (ttpt) REVERT: E 50 GLU cc_start: 0.8820 (mt-10) cc_final: 0.8073 (mp0) REVERT: F 12 ARG cc_start: 0.5010 (pmt170) cc_final: 0.4202 (pmt-80) REVERT: F 14 PRO cc_start: 0.5176 (Cg_exo) cc_final: 0.4923 (Cg_endo) REVERT: F 44 GLU cc_start: 0.8617 (OUTLIER) cc_final: 0.7891 (tt0) REVERT: F 74 GLU cc_start: 0.8339 (pt0) cc_final: 0.7926 (pt0) REVERT: F 75 LYS cc_start: 0.7615 (mtpm) cc_final: 0.6580 (mmpt) outliers start: 6 outliers final: 3 residues processed: 50 average time/residue: 0.9243 time to fit residues: 47.4133 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 : 0.218 ------------------------------------------------------------------------------- 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 D residue 36 GLU Chi-restraints excluded: chain E residue 71 THR Chi-restraints excluded: chain F residue 44 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 46 optimal weight: 9.9990 chunk 2 optimal weight: 8.9990 chunk 5 optimal weight: 1.9990 chunk 13 optimal weight: 9.9990 chunk 31 optimal weight: 0.6980 chunk 11 optimal weight: 20.0000 chunk 1 optimal weight: 0.6980 chunk 41 optimal weight: 20.0000 chunk 33 optimal weight: 1.9990 chunk 36 optimal weight: 0.6980 chunk 25 optimal weight: 10.0000 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 31 HIS D 31 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.089891 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.075654 restraints weight = 11263.351| |-----------------------------------------------------------------------------| r_work (start): 0.3620 rms_B_bonded: 2.23 r_work: 0.3544 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3471 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.3471 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8703 moved from start: 0.3508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 4488 Z= 0.097 Angle : 0.555 6.648 6084 Z= 0.299 Chirality : 0.044 0.128 642 Planarity : 0.003 0.028 780 Dihedral : 4.639 16.142 576 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 1.20 % Allowed : 12.65 % Favored : 86.14 % 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: -3.44 (0.30), residues: 516 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.61 (0.23), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 45 TYR 0.016 0.001 TYR E 67 PHE 0.018 0.001 PHE D 22 TRP 0.005 0.000 TRP F 60 HIS 0.004 0.001 HIS D 31 Details of bonding type rmsd covalent geometry : bond 0.00243 ( 4482) covalent geometry : angle 0.55505 ( 6072) SS BOND : bond 0.00111 ( 6) SS BOND : angle 0.35767 ( 12) hydrogen bonds : bond 0.02187 ( 86) hydrogen bonds : angle 5.31280 ( 258) *********************** 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 54 residues out of total 498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 48 time to evaluate : 0.140 Fit side-chains REVERT: C 50 GLU cc_start: 0.8587 (mt-10) cc_final: 0.8193 (mt-10) REVERT: D 6 MET cc_start: 0.7732 (ttp) cc_final: 0.7512 (ptm) REVERT: D 74 GLU cc_start: 0.8007 (pt0) cc_final: 0.7684 (pt0) REVERT: E 48 LYS cc_start: 0.8548 (ttpt) cc_final: 0.7379 (mmpt) REVERT: E 50 GLU cc_start: 0.8807 (mt-10) cc_final: 0.8233 (mp0) REVERT: F 12 ARG cc_start: 0.4909 (pmt170) cc_final: 0.4345 (pmt-80) REVERT: F 14 PRO cc_start: 0.5118 (Cg_exo) cc_final: 0.4869 (Cg_endo) REVERT: F 44 GLU cc_start: 0.8590 (OUTLIER) cc_final: 0.7776 (tt0) REVERT: F 47 GLU cc_start: 0.8092 (OUTLIER) cc_final: 0.7359 (tm-30) REVERT: F 74 GLU cc_start: 0.8248 (pt0) cc_final: 0.7873 (pt0) REVERT: F 75 LYS cc_start: 0.7245 (mtpm) cc_final: 0.6312 (mmpt) REVERT: F 91 LYS cc_start: 0.7992 (tttt) cc_final: 0.6093 (pmtt) outliers start: 6 outliers final: 3 residues processed: 53 average time/residue: 0.8472 time to fit residues: 45.9960 Evaluate side-chains 48 residues out of total 498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 43 time to evaluate : 0.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 ILE 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 15 optimal weight: 7.9990 chunk 25 optimal weight: 20.0000 chunk 46 optimal weight: 8.9990 chunk 8 optimal weight: 50.0000 chunk 34 optimal weight: 10.0000 chunk 12 optimal weight: 7.9990 chunk 31 optimal weight: 9.9990 chunk 11 optimal weight: 8.9990 chunk 40 optimal weight: 50.0000 chunk 38 optimal weight: 10.0000 chunk 7 optimal weight: 20.0000 overall best weight: 8.7990 ------------------------------------------------------------------------------- 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 = 0.3771 r_free = 0.3771 target = 0.083998 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.069308 restraints weight = 11469.892| |-----------------------------------------------------------------------------| r_work (start): 0.3492 rms_B_bonded: 2.27 r_work: 0.3409 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3330 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.3330 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8852 moved from start: 0.3567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.041 4488 Z= 0.257 Angle : 0.667 7.011 6084 Z= 0.368 Chirality : 0.048 0.137 642 Planarity : 0.003 0.030 780 Dihedral : 5.112 15.306 576 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.14 % Favored : 91.86 % Rotamer: Outliers : 1.41 % Allowed : 12.45 % Favored : 86.14 % 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: -3.53 (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 ARG 0.001 0.000 ARG D 12 TYR 0.018 0.002 TYR E 67 PHE 0.017 0.002 PHE D 22 TRP 0.004 0.001 TRP B 60 HIS 0.006 0.001 HIS F 31 Details of bonding type rmsd covalent geometry : bond 0.00627 ( 4482) covalent geometry : angle 0.66729 ( 6072) SS BOND : bond 0.00580 ( 6) SS BOND : angle 0.62235 ( 12) hydrogen bonds : bond 0.03676 ( 86) hydrogen bonds : angle 5.87387 ( 258) ********************** 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 49 residues out of total 498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 42 time to evaluate : 0.179 Fit side-chains REVERT: B 12 ARG cc_start: 0.6842 (mpt180) cc_final: 0.5898 (mmm160) REVERT: B 34 ASP cc_start: 0.8914 (t0) cc_final: 0.8682 (t70) REVERT: B 36 GLU cc_start: 0.8684 (OUTLIER) cc_final: 0.8358 (tt0) REVERT: C 47 GLU cc_start: 0.7862 (tm-30) cc_final: 0.7589 (tm-30) REVERT: C 50 GLU cc_start: 0.8660 (mt-10) cc_final: 0.8194 (mt-10) REVERT: D 74 GLU cc_start: 0.8107 (pt0) cc_final: 0.7660 (pt0) REVERT: E 47 GLU cc_start: 0.8134 (tm-30) cc_final: 0.7831 (tm-30) REVERT: E 50 GLU cc_start: 0.8819 (mt-10) cc_final: 0.8239 (mt-10) REVERT: F 12 ARG cc_start: 0.5040 (pmt170) cc_final: 0.4240 (pmt-80) REVERT: F 14 PRO cc_start: 0.5056 (Cg_exo) cc_final: 0.4823 (Cg_endo) REVERT: F 44 GLU cc_start: 0.8629 (OUTLIER) cc_final: 0.7932 (tt0) REVERT: F 47 GLU cc_start: 0.8114 (OUTLIER) cc_final: 0.7416 (tm-30) REVERT: F 74 GLU cc_start: 0.8418 (pt0) cc_final: 0.7982 (pt0) REVERT: F 75 LYS cc_start: 0.7776 (mtpm) cc_final: 0.6743 (mmpt) outliers start: 7 outliers final: 3 residues processed: 48 average time/residue: 0.9053 time to fit residues: 44.5386 Evaluate side-chains 47 residues out of total 498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 41 time to evaluate : 0.193 ------------------------------------------------------------------------------- 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 34 optimal weight: 0.4980 chunk 22 optimal weight: 20.0000 chunk 0 optimal weight: 10.0000 chunk 18 optimal weight: 6.9990 chunk 23 optimal weight: 20.0000 chunk 36 optimal weight: 0.1980 chunk 16 optimal weight: 20.0000 chunk 29 optimal weight: 10.0000 chunk 24 optimal weight: 9.9990 chunk 37 optimal weight: 9.9990 chunk 6 optimal weight: 8.9990 overall best weight: 5.3386 ------------------------------------------------------------------------------- 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 = 0.3793 r_free = 0.3793 target = 0.085020 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.070402 restraints weight = 11450.876| |-----------------------------------------------------------------------------| r_work (start): 0.3519 rms_B_bonded: 2.26 r_work: 0.3438 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3359 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.3359 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8808 moved from start: 0.3545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 4488 Z= 0.171 Angle : 0.618 6.671 6084 Z= 0.339 Chirality : 0.046 0.135 642 Planarity : 0.003 0.029 780 Dihedral : 5.022 15.515 576 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.98 % Favored : 93.02 % Rotamer: Outliers : 1.20 % Allowed : 12.65 % Favored : 86.14 % 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: -3.53 (0.29), residues: 516 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.68 (0.22), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 45 TYR 0.017 0.002 TYR E 67 PHE 0.018 0.002 PHE D 22 TRP 0.003 0.001 TRP E 60 HIS 0.004 0.001 HIS F 31 Details of bonding type rmsd covalent geometry : bond 0.00424 ( 4482) covalent geometry : angle 0.61824 ( 6072) SS BOND : bond 0.00406 ( 6) SS BOND : angle 0.51302 ( 12) hydrogen bonds : bond 0.03111 ( 86) hydrogen bonds : angle 5.73190 ( 258) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1675.01 seconds wall clock time: 29 minutes 20.44 seconds (1760.44 seconds total)