Starting phenix.real_space_refine on Fri Aug 22 13:00:36 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8bfa_16018/08_2025/8bfa_16018.cif Found real_map, /net/cci-nas-00/data/ceres_data/8bfa_16018/08_2025/8bfa_16018.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/8bfa_16018/08_2025/8bfa_16018.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8bfa_16018/08_2025/8bfa_16018.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8bfa_16018/08_2025/8bfa_16018.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8bfa_16018/08_2025/8bfa_16018.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= 0.000 sd= 0.002 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 10 5.16 5 C 1810 2.51 5 N 510 2.21 5 O 530 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 30 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 2860 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 286 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 286 Classifications: {'peptide': 38} Link IDs: {'TRANS': 37} Chain: "B" Number of atoms: 286 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 286 Classifications: {'peptide': 38} Link IDs: {'TRANS': 37} Chain: "C" Number of atoms: 286 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 286 Classifications: {'peptide': 38} Link IDs: {'TRANS': 37} Chain: "D" Number of atoms: 286 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 286 Classifications: {'peptide': 38} Link IDs: {'TRANS': 37} Chain: "E" Number of atoms: 286 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 286 Classifications: {'peptide': 38} Link IDs: {'TRANS': 37} Chain: "F" Number of atoms: 286 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 286 Classifications: {'peptide': 38} Link IDs: {'TRANS': 37} Chain: "G" Number of atoms: 286 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 286 Classifications: {'peptide': 38} Link IDs: {'TRANS': 37} Chain: "H" Number of atoms: 286 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 286 Classifications: {'peptide': 38} Link IDs: {'TRANS': 37} Chain: "I" Number of atoms: 286 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 286 Classifications: {'peptide': 38} Link IDs: {'TRANS': 37} Chain: "J" Number of atoms: 286 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 286 Classifications: {'peptide': 38} Link IDs: {'TRANS': 37} Time building chain proxies: 0.93, per 1000 atoms: 0.33 Number of scatterers: 2860 At special positions: 0 Unit cell: (90.47, 67.23, 39.84, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 10 16.00 O 530 8.00 N 510 7.00 C 1810 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.19 Conformation dependent library (CDL) restraints added in 108.7 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 620 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 10 sheets defined 0.0% alpha, 52.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.14 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 3 through 7 removed outlier: 6.163A pdb=" N PHE E 4 " --> pdb=" O ARG G 5 " (cutoff:3.500A) removed outlier: 7.746A pdb=" N ASP G 7 " --> pdb=" O PHE E 4 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N HIS E 6 " --> pdb=" O ASP G 7 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 10 through 16 removed outlier: 6.385A pdb=" N GLU A 11 " --> pdb=" O VAL C 12 " (cutoff:3.500A) removed outlier: 7.843A pdb=" N HIS C 14 " --> pdb=" O GLU A 11 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N HIS A 13 " --> pdb=" O HIS C 14 " (cutoff:3.500A) removed outlier: 7.990A pdb=" N LYS C 16 " --> pdb=" O HIS A 13 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N GLN A 15 " --> pdb=" O LYS C 16 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N GLU E 11 " --> pdb=" O VAL G 12 " (cutoff:3.500A) removed outlier: 7.837A pdb=" N HIS G 14 " --> pdb=" O GLU E 11 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N HIS E 13 " --> pdb=" O HIS G 14 " (cutoff:3.500A) removed outlier: 7.983A pdb=" N LYS G 16 " --> pdb=" O HIS E 13 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N GLN E 15 " --> pdb=" O LYS G 16 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N GLU G 11 " --> pdb=" O VAL I 12 " (cutoff:3.500A) removed outlier: 7.864A pdb=" N HIS I 14 " --> pdb=" O GLU G 11 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N HIS G 13 " --> pdb=" O HIS I 14 " (cutoff:3.500A) removed outlier: 8.007A pdb=" N LYS I 16 " --> pdb=" O HIS G 13 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N GLN G 15 " --> pdb=" O LYS I 16 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 20 through 21 Processing sheet with id=AA4, first strand: chain 'A' and resid 24 through 27 removed outlier: 6.818A pdb=" N SER C 26 " --> pdb=" O GLY A 25 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N ASN A 27 " --> pdb=" O SER C 26 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N SER E 26 " --> pdb=" O GLY C 25 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N ASN C 27 " --> pdb=" O SER E 26 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N SER G 26 " --> pdb=" O GLY E 25 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N ASN E 27 " --> pdb=" O SER G 26 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N SER I 26 " --> pdb=" O GLY G 25 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N ASN G 27 " --> pdb=" O SER I 26 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 30 through 36 removed outlier: 6.398A pdb=" N ALA A 30 " --> pdb=" O ILE C 31 " (cutoff:3.500A) removed outlier: 7.720A pdb=" N GLY C 33 " --> pdb=" O ALA A 30 " (cutoff:3.500A) removed outlier: 9.029A pdb=" N ILE A 32 " --> pdb=" O GLY C 33 " (cutoff:3.500A) removed outlier: 7.264A pdb=" N MET C 35 " --> pdb=" O ILE A 32 " (cutoff:3.500A) removed outlier: 9.274A pdb=" N LEU A 34 " --> pdb=" O MET C 35 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N ALA C 30 " --> pdb=" O ILE E 31 " (cutoff:3.500A) removed outlier: 7.725A pdb=" N GLY E 33 " --> pdb=" O ALA C 30 " (cutoff:3.500A) removed outlier: 9.036A pdb=" N ILE C 32 " --> pdb=" O GLY E 33 " (cutoff:3.500A) removed outlier: 7.277A pdb=" N MET E 35 " --> pdb=" O ILE C 32 " (cutoff:3.500A) removed outlier: 9.286A pdb=" N LEU C 34 " --> pdb=" O MET E 35 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N ALA E 30 " --> pdb=" O ILE G 31 " (cutoff:3.500A) removed outlier: 7.713A pdb=" N GLY G 33 " --> pdb=" O ALA E 30 " (cutoff:3.500A) removed outlier: 9.025A pdb=" N ILE E 32 " --> pdb=" O GLY G 33 " (cutoff:3.500A) removed outlier: 7.259A pdb=" N MET G 35 " --> pdb=" O ILE E 32 " (cutoff:3.500A) removed outlier: 9.274A pdb=" N LEU E 34 " --> pdb=" O MET G 35 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N ALA G 30 " --> pdb=" O ILE I 31 " (cutoff:3.500A) removed outlier: 7.732A pdb=" N GLY I 33 " --> pdb=" O ALA G 30 " (cutoff:3.500A) removed outlier: 9.034A pdb=" N ILE G 32 " --> pdb=" O GLY I 33 " (cutoff:3.500A) removed outlier: 7.271A pdb=" N MET I 35 " --> pdb=" O ILE G 32 " (cutoff:3.500A) removed outlier: 9.275A pdb=" N LEU G 34 " --> pdb=" O MET I 35 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'B' and resid 3 through 7 removed outlier: 6.150A pdb=" N PHE D 4 " --> pdb=" O ARG F 5 " (cutoff:3.500A) removed outlier: 7.736A pdb=" N ASP F 7 " --> pdb=" O PHE D 4 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N HIS D 6 " --> pdb=" O ASP F 7 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 10 through 16 removed outlier: 6.393A pdb=" N GLU B 11 " --> pdb=" O VAL D 12 " (cutoff:3.500A) removed outlier: 7.851A pdb=" N HIS D 14 " --> pdb=" O GLU B 11 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N HIS B 13 " --> pdb=" O HIS D 14 " (cutoff:3.500A) removed outlier: 7.994A pdb=" N LYS D 16 " --> pdb=" O HIS B 13 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N GLN B 15 " --> pdb=" O LYS D 16 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N GLU D 11 " --> pdb=" O VAL F 12 " (cutoff:3.500A) removed outlier: 7.828A pdb=" N HIS F 14 " --> pdb=" O GLU D 11 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N HIS D 13 " --> pdb=" O HIS F 14 " (cutoff:3.500A) removed outlier: 7.974A pdb=" N LYS F 16 " --> pdb=" O HIS D 13 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N GLN D 15 " --> pdb=" O LYS F 16 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N GLU F 11 " --> pdb=" O VAL H 12 " (cutoff:3.500A) removed outlier: 7.854A pdb=" N HIS H 14 " --> pdb=" O GLU F 11 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N HIS F 13 " --> pdb=" O HIS H 14 " (cutoff:3.500A) removed outlier: 7.999A pdb=" N LYS H 16 " --> pdb=" O HIS F 13 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N GLN F 15 " --> pdb=" O LYS H 16 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N GLU H 11 " --> pdb=" O VAL J 12 " (cutoff:3.500A) removed outlier: 7.870A pdb=" N HIS J 14 " --> pdb=" O GLU H 11 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N HIS H 13 " --> pdb=" O HIS J 14 " (cutoff:3.500A) removed outlier: 8.013A pdb=" N LYS J 16 " --> pdb=" O HIS H 13 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N GLN H 15 " --> pdb=" O LYS J 16 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'B' and resid 20 through 21 Processing sheet with id=AA9, first strand: chain 'B' and resid 24 through 27 removed outlier: 6.835A pdb=" N SER D 26 " --> pdb=" O GLY B 25 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N ASN B 27 " --> pdb=" O SER D 26 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N SER F 26 " --> pdb=" O GLY D 25 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N ASN D 27 " --> pdb=" O SER F 26 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N SER H 26 " --> pdb=" O GLY F 25 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N ASN F 27 " --> pdb=" O SER H 26 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N SER J 26 " --> pdb=" O GLY H 25 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N ASN H 27 " --> pdb=" O SER J 26 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 30 through 36 removed outlier: 6.406A pdb=" N ALA B 30 " --> pdb=" O ILE D 31 " (cutoff:3.500A) removed outlier: 7.726A pdb=" N GLY D 33 " --> pdb=" O ALA B 30 " (cutoff:3.500A) removed outlier: 9.034A pdb=" N ILE B 32 " --> pdb=" O GLY D 33 " (cutoff:3.500A) removed outlier: 7.269A pdb=" N MET D 35 " --> pdb=" O ILE B 32 " (cutoff:3.500A) removed outlier: 9.279A pdb=" N LEU B 34 " --> pdb=" O MET D 35 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N ALA D 30 " --> pdb=" O ILE F 31 " (cutoff:3.500A) removed outlier: 7.705A pdb=" N GLY F 33 " --> pdb=" O ALA D 30 " (cutoff:3.500A) removed outlier: 9.013A pdb=" N ILE D 32 " --> pdb=" O GLY F 33 " (cutoff:3.500A) removed outlier: 7.247A pdb=" N MET F 35 " --> pdb=" O ILE D 32 " (cutoff:3.500A) removed outlier: 9.261A pdb=" N LEU D 34 " --> pdb=" O MET F 35 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N ALA F 30 " --> pdb=" O ILE H 31 " (cutoff:3.500A) removed outlier: 7.724A pdb=" N GLY H 33 " --> pdb=" O ALA F 30 " (cutoff:3.500A) removed outlier: 9.031A pdb=" N ILE F 32 " --> pdb=" O GLY H 33 " (cutoff:3.500A) removed outlier: 7.270A pdb=" N MET H 35 " --> pdb=" O ILE F 32 " (cutoff:3.500A) removed outlier: 9.278A pdb=" N LEU F 34 " --> pdb=" O MET H 35 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N ALA H 30 " --> pdb=" O ILE J 31 " (cutoff:3.500A) removed outlier: 7.736A pdb=" N GLY J 33 " --> pdb=" O ALA H 30 " (cutoff:3.500A) removed outlier: 9.044A pdb=" N ILE H 32 " --> pdb=" O GLY J 33 " (cutoff:3.500A) removed outlier: 7.282A pdb=" N MET J 35 " --> pdb=" O ILE H 32 " (cutoff:3.500A) removed outlier: 9.290A pdb=" N LEU H 34 " --> pdb=" O MET J 35 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 46 hydrogen bonds defined for protein. 138 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: 0.39 Time building geometry restraints manager: 0.26 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: 980 1.34 - 1.46: 648 1.46 - 1.57: 1272 1.57 - 1.69: 0 1.69 - 1.80: 20 Bond restraints: 2920 Sorted by residual: bond pdb=" N ARG J 5 " pdb=" CA ARG J 5 " ideal model delta sigma weight residual 1.458 1.486 -0.028 1.19e-02 7.06e+03 5.65e+00 bond pdb=" N ARG B 5 " pdb=" CA ARG B 5 " ideal model delta sigma weight residual 1.458 1.486 -0.028 1.19e-02 7.06e+03 5.55e+00 bond pdb=" N ARG I 5 " pdb=" CA ARG I 5 " ideal model delta sigma weight residual 1.458 1.486 -0.028 1.19e-02 7.06e+03 5.54e+00 bond pdb=" N ARG E 5 " pdb=" CA ARG E 5 " ideal model delta sigma weight residual 1.458 1.486 -0.028 1.19e-02 7.06e+03 5.45e+00 bond pdb=" N ARG C 5 " pdb=" CA ARG C 5 " ideal model delta sigma weight residual 1.458 1.486 -0.028 1.19e-02 7.06e+03 5.43e+00 ... (remaining 2915 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.54: 3433 0.54 - 1.08: 392 1.08 - 1.61: 45 1.61 - 2.15: 20 2.15 - 2.69: 10 Bond angle restraints: 3900 Sorted by residual: angle pdb=" CA ARG A 5 " pdb=" C ARG A 5 " pdb=" O ARG A 5 " ideal model delta sigma weight residual 120.24 118.31 1.93 1.06e+00 8.90e-01 3.33e+00 angle pdb=" CA ARG B 5 " pdb=" C ARG B 5 " pdb=" O ARG B 5 " ideal model delta sigma weight residual 120.24 118.32 1.92 1.06e+00 8.90e-01 3.27e+00 angle pdb=" CA ARG G 5 " pdb=" C ARG G 5 " pdb=" O ARG G 5 " ideal model delta sigma weight residual 120.24 118.34 1.90 1.06e+00 8.90e-01 3.22e+00 angle pdb=" CA ARG F 5 " pdb=" C ARG F 5 " pdb=" O ARG F 5 " ideal model delta sigma weight residual 120.24 118.34 1.90 1.06e+00 8.90e-01 3.21e+00 angle pdb=" CA ARG I 5 " pdb=" C ARG I 5 " pdb=" O ARG I 5 " ideal model delta sigma weight residual 120.24 118.35 1.89 1.06e+00 8.90e-01 3.19e+00 ... (remaining 3895 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.04: 1440 13.04 - 26.08: 90 26.08 - 39.13: 40 39.13 - 52.17: 30 52.17 - 65.21: 10 Dihedral angle restraints: 1610 sinusoidal: 610 harmonic: 1000 Sorted by residual: dihedral pdb=" CA LEU E 34 " pdb=" CB LEU E 34 " pdb=" CG LEU E 34 " pdb=" CD1 LEU E 34 " ideal model delta sinusoidal sigma weight residual 180.00 139.97 40.03 3 1.50e+01 4.44e-03 7.12e+00 dihedral pdb=" CA LEU I 34 " pdb=" CB LEU I 34 " pdb=" CG LEU I 34 " pdb=" CD1 LEU I 34 " ideal model delta sinusoidal sigma weight residual 180.00 140.02 39.98 3 1.50e+01 4.44e-03 7.11e+00 dihedral pdb=" CA LEU H 34 " pdb=" CB LEU H 34 " pdb=" CG LEU H 34 " pdb=" CD1 LEU H 34 " ideal model delta sinusoidal sigma weight residual 180.00 140.03 39.97 3 1.50e+01 4.44e-03 7.10e+00 ... (remaining 1607 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.024: 149 0.024 - 0.049: 133 0.049 - 0.073: 48 0.073 - 0.098: 3 0.098 - 0.122: 57 Chirality restraints: 390 Sorted by residual: chirality pdb=" CA ARG H 5 " pdb=" N ARG H 5 " pdb=" C ARG H 5 " pdb=" CB ARG H 5 " both_signs ideal model delta sigma weight residual False 2.51 2.63 -0.12 2.00e-01 2.50e+01 3.72e-01 chirality pdb=" CA ARG E 5 " pdb=" N ARG E 5 " pdb=" C ARG E 5 " pdb=" CB ARG E 5 " both_signs ideal model delta sigma weight residual False 2.51 2.63 -0.12 2.00e-01 2.50e+01 3.59e-01 chirality pdb=" CA ARG F 5 " pdb=" N ARG F 5 " pdb=" C ARG F 5 " pdb=" CB ARG F 5 " both_signs ideal model delta sigma weight residual False 2.51 2.63 -0.12 2.00e-01 2.50e+01 3.56e-01 ... (remaining 387 not shown) Planarity restraints: 520 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 4 " -0.003 2.00e-02 2.50e+03 2.70e-03 1.28e-01 pdb=" CG PHE A 4 " 0.006 2.00e-02 2.50e+03 pdb=" CD1 PHE A 4 " -0.002 2.00e-02 2.50e+03 pdb=" CD2 PHE A 4 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 PHE A 4 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE A 4 " -0.000 2.00e-02 2.50e+03 pdb=" CZ PHE A 4 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE G 4 " -0.002 2.00e-02 2.50e+03 2.51e-03 1.11e-01 pdb=" CG PHE G 4 " 0.006 2.00e-02 2.50e+03 pdb=" CD1 PHE G 4 " -0.001 2.00e-02 2.50e+03 pdb=" CD2 PHE G 4 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 PHE G 4 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE G 4 " 0.000 2.00e-02 2.50e+03 pdb=" CZ PHE G 4 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE C 4 " -0.002 2.00e-02 2.50e+03 2.50e-03 1.10e-01 pdb=" CG PHE C 4 " 0.006 2.00e-02 2.50e+03 pdb=" CD1 PHE C 4 " -0.001 2.00e-02 2.50e+03 pdb=" CD2 PHE C 4 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 PHE C 4 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE C 4 " 0.000 2.00e-02 2.50e+03 pdb=" CZ PHE C 4 " -0.000 2.00e-02 2.50e+03 ... (remaining 517 not shown) Histogram of nonbonded interaction distances: 2.59 - 3.05: 1663 3.05 - 3.51: 2612 3.51 - 3.98: 4531 3.98 - 4.44: 4981 4.44 - 4.90: 10405 Nonbonded interactions: 24192 Sorted by model distance: nonbonded pdb=" NZ LYS G 28 " pdb=" OE2 GLU H 11 " model vdw 2.592 3.120 nonbonded pdb=" NZ LYS E 28 " pdb=" OE2 GLU F 11 " model vdw 2.603 3.120 nonbonded pdb=" NZ LYS F 28 " pdb=" OE2 GLU G 11 " model vdw 2.609 3.120 nonbonded pdb=" NZ LYS I 28 " pdb=" OE2 GLU J 11 " model vdw 2.618 3.120 nonbonded pdb=" NZ LYS H 28 " pdb=" OE2 GLU I 11 " model vdw 2.618 3.120 ... (remaining 24187 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' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' } 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: 0.010 Normalize map: mean=0, sd=1: 1.800 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.060 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 4.660 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.480 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7853 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 0.028 2920 Z= 0.172 Angle : 0.386 2.691 3900 Z= 0.246 Chirality : 0.052 0.122 390 Planarity : 0.001 0.003 520 Dihedral : 13.944 65.212 990 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.00 % Allowed : 7.14 % Favored : 92.86 % 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 aren not related in a simple way. whole: -3.13 (0.34), residues: 360 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.38 (0.26), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG E 5 TYR 0.004 0.001 TYR C 10 PHE 0.006 0.001 PHE A 4 HIS 0.002 0.000 HIS B 6 Details of bonding type rmsd covalent geometry : bond 0.00244 ( 2920) covalent geometry : angle 0.38634 ( 3900) hydrogen bonds : bond 0.08351 ( 46) hydrogen bonds : angle 8.49138 ( 138) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 50 time to evaluate : 0.137 Fit side-chains REVERT: G 28 LYS cc_start: 0.8369 (mttt) cc_final: 0.8006 (mttt) REVERT: H 28 LYS cc_start: 0.8370 (mttt) cc_final: 0.8099 (mttt) REVERT: I 35 MET cc_start: 0.8337 (mtt) cc_final: 0.8137 (mtm) REVERT: J 23 ASP cc_start: 0.7789 (m-30) cc_final: 0.7255 (p0) outliers start: 0 outliers final: 0 residues processed: 50 average time/residue: 0.6401 time to fit residues: 32.7443 Evaluate side-chains 32 residues out of total 280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 32 time to evaluate : 0.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 27 optimal weight: 9.9990 chunk 12 optimal weight: 20.0000 chunk 24 optimal weight: 10.0000 chunk 28 optimal weight: 2.9990 chunk 13 optimal weight: 10.0000 chunk 1 optimal weight: 0.9980 chunk 8 optimal weight: 9.9990 chunk 16 optimal weight: 10.0000 chunk 15 optimal weight: 20.0000 chunk 29 optimal weight: 10.0000 chunk 25 optimal weight: 3.9990 overall best weight: 5.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 27 ASN B 13 HIS B 27 ASN C 27 ASN D 27 ASN E 13 HIS E 27 ASN F 27 ASN G 27 ASN H 27 ASN I 27 ASN J 27 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.126093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.107302 restraints weight = 3760.594| |-----------------------------------------------------------------------------| r_work (start): 0.3887 rms_B_bonded: 2.79 r_work: 0.3738 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3620 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3620 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8505 moved from start: 0.3094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.055 2920 Z= 0.362 Angle : 0.576 4.532 3900 Z= 0.318 Chirality : 0.053 0.131 390 Planarity : 0.004 0.025 520 Dihedral : 5.188 14.603 390 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.11 % Favored : 98.89 % Rotamer: Outliers : 8.57 % Allowed : 7.50 % Favored : 83.93 % 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 aren not related in a simple way. whole: -2.80 (0.40), residues: 360 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.12 (0.30), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG D 5 TYR 0.012 0.003 TYR C 10 PHE 0.015 0.003 PHE F 4 HIS 0.005 0.002 HIS B 13 Details of bonding type rmsd covalent geometry : bond 0.00822 ( 2920) covalent geometry : angle 0.57616 ( 3900) hydrogen bonds : bond 0.02386 ( 46) hydrogen bonds : angle 5.45659 ( 138) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 42 time to evaluate : 0.067 Fit side-chains REVERT: A 1 ASP cc_start: 0.6910 (m-30) cc_final: 0.6678 (t0) REVERT: B 1 ASP cc_start: 0.6982 (m-30) cc_final: 0.6396 (t0) REVERT: B 35 MET cc_start: 0.8359 (OUTLIER) cc_final: 0.8102 (ttp) REVERT: C 1 ASP cc_start: 0.6717 (m-30) cc_final: 0.5659 (t0) REVERT: C 5 ARG cc_start: 0.7347 (mtp180) cc_final: 0.6962 (tmt90) REVERT: C 35 MET cc_start: 0.8455 (ttm) cc_final: 0.8244 (mtm) REVERT: D 1 ASP cc_start: 0.6652 (m-30) cc_final: 0.5785 (t0) REVERT: E 1 ASP cc_start: 0.6824 (m-30) cc_final: 0.5809 (t0) REVERT: F 1 ASP cc_start: 0.6749 (m-30) cc_final: 0.5854 (t0) REVERT: F 5 ARG cc_start: 0.7519 (mtp180) cc_final: 0.7118 (tmt90) REVERT: G 1 ASP cc_start: 0.6846 (m-30) cc_final: 0.5930 (t0) REVERT: G 5 ARG cc_start: 0.7215 (mtp180) cc_final: 0.6951 (tmt90) REVERT: H 1 ASP cc_start: 0.6705 (m-30) cc_final: 0.5790 (t0) REVERT: I 1 ASP cc_start: 0.7093 (m-30) cc_final: 0.6262 (t0) REVERT: J 1 ASP cc_start: 0.6961 (m-30) cc_final: 0.5992 (t0) outliers start: 24 outliers final: 9 residues processed: 63 average time/residue: 0.6178 time to fit residues: 39.7466 Evaluate side-chains 46 residues out of total 280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 36 time to evaluate : 0.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 SER Chi-restraints excluded: chain B residue 35 MET Chi-restraints excluded: chain D residue 26 SER Chi-restraints excluded: chain E residue 26 SER Chi-restraints excluded: chain F residue 26 SER Chi-restraints excluded: chain G residue 26 SER Chi-restraints excluded: chain H residue 26 SER Chi-restraints excluded: chain I residue 26 SER Chi-restraints excluded: chain J residue 26 SER Chi-restraints excluded: chain J residue 28 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 16 optimal weight: 1.9990 chunk 25 optimal weight: 0.7980 chunk 2 optimal weight: 4.9990 chunk 22 optimal weight: 2.9990 chunk 14 optimal weight: 4.9990 chunk 7 optimal weight: 0.9980 chunk 24 optimal weight: 8.9990 chunk 28 optimal weight: 7.9990 chunk 21 optimal weight: 10.0000 chunk 4 optimal weight: 3.9990 chunk 19 optimal weight: 0.9980 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 13 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4168 r_free = 0.4168 target = 0.132727 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.114653 restraints weight = 3648.932| |-----------------------------------------------------------------------------| r_work (start): 0.3966 rms_B_bonded: 2.76 r_work: 0.3823 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3707 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3707 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8451 moved from start: 0.3136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 2920 Z= 0.117 Angle : 0.380 3.659 3900 Z= 0.216 Chirality : 0.051 0.128 390 Planarity : 0.001 0.006 520 Dihedral : 4.183 11.784 390 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 3.93 % Allowed : 13.93 % Favored : 82.14 % 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 aren not related in a simple way. whole: -2.73 (0.39), residues: 360 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.07 (0.30), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG D 5 TYR 0.004 0.001 TYR E 10 PHE 0.008 0.001 PHE D 4 HIS 0.002 0.001 HIS F 13 Details of bonding type rmsd covalent geometry : bond 0.00272 ( 2920) covalent geometry : angle 0.38024 ( 3900) hydrogen bonds : bond 0.01291 ( 46) hydrogen bonds : angle 5.04166 ( 138) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 46 time to evaluate : 0.111 Fit side-chains REVERT: A 1 ASP cc_start: 0.6830 (m-30) cc_final: 0.6378 (t0) REVERT: A 5 ARG cc_start: 0.7909 (mtp180) cc_final: 0.7666 (tmt90) REVERT: B 1 ASP cc_start: 0.6833 (m-30) cc_final: 0.6375 (t0) REVERT: B 5 ARG cc_start: 0.7964 (mtp180) cc_final: 0.7696 (tmt90) REVERT: B 35 MET cc_start: 0.8162 (OUTLIER) cc_final: 0.7943 (ttp) REVERT: C 1 ASP cc_start: 0.6426 (m-30) cc_final: 0.5734 (t0) REVERT: C 5 ARG cc_start: 0.7346 (mtp180) cc_final: 0.6895 (tmt90) REVERT: D 1 ASP cc_start: 0.6527 (m-30) cc_final: 0.5783 (t0) REVERT: D 11 GLU cc_start: 0.8340 (tt0) cc_final: 0.7840 (tt0) REVERT: F 1 ASP cc_start: 0.6490 (m-30) cc_final: 0.5715 (t0) REVERT: F 5 ARG cc_start: 0.7481 (mtp180) cc_final: 0.7092 (tmt90) REVERT: G 1 ASP cc_start: 0.6549 (m-30) cc_final: 0.5894 (t0) REVERT: G 5 ARG cc_start: 0.7346 (mtp180) cc_final: 0.7059 (tmt90) REVERT: H 1 ASP cc_start: 0.6572 (m-30) cc_final: 0.5780 (t0) outliers start: 11 outliers final: 6 residues processed: 54 average time/residue: 0.6917 time to fit residues: 38.1099 Evaluate side-chains 47 residues out of total 280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 40 time to evaluate : 0.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 35 MET Chi-restraints excluded: chain D residue 26 SER Chi-restraints excluded: chain E residue 26 SER Chi-restraints excluded: chain F residue 26 SER Chi-restraints excluded: chain H residue 26 SER Chi-restraints excluded: chain I residue 26 SER Chi-restraints excluded: chain J residue 26 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 15 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 14 optimal weight: 9.9990 chunk 5 optimal weight: 9.9990 chunk 7 optimal weight: 5.9990 chunk 11 optimal weight: 6.9990 chunk 3 optimal weight: 10.0000 chunk 27 optimal weight: 9.9990 chunk 20 optimal weight: 4.9990 chunk 1 optimal weight: 2.9990 chunk 12 optimal weight: 20.0000 overall best weight: 4.3988 ------------------------------------------------------------------------------- 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 = 0.4119 r_free = 0.4119 target = 0.127560 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.109099 restraints weight = 3680.227| |-----------------------------------------------------------------------------| r_work (start): 0.3899 rms_B_bonded: 2.72 r_work: 0.3764 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3653 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3653 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8525 moved from start: 0.3861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.039 2920 Z= 0.282 Angle : 0.525 4.548 3900 Z= 0.285 Chirality : 0.053 0.134 390 Planarity : 0.002 0.008 520 Dihedral : 5.190 14.315 390 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 6.07 % Allowed : 14.29 % Favored : 79.64 % 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 aren not related in a simple way. whole: -2.68 (0.40), residues: 360 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.03 (0.30), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG F 5 TYR 0.008 0.002 TYR C 10 PHE 0.012 0.002 PHE D 4 HIS 0.004 0.001 HIS E 14 Details of bonding type rmsd covalent geometry : bond 0.00628 ( 2920) covalent geometry : angle 0.52528 ( 3900) hydrogen bonds : bond 0.01869 ( 46) hydrogen bonds : angle 4.91487 ( 138) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 42 time to evaluate : 0.072 Fit side-chains REVERT: A 1 ASP cc_start: 0.6966 (m-30) cc_final: 0.6498 (t0) REVERT: A 3 GLU cc_start: 0.8119 (mt-10) cc_final: 0.7795 (tm-30) REVERT: B 1 ASP cc_start: 0.6975 (m-30) cc_final: 0.6495 (t0) REVERT: B 3 GLU cc_start: 0.8225 (mt-10) cc_final: 0.7826 (tm-30) REVERT: B 35 MET cc_start: 0.8377 (OUTLIER) cc_final: 0.8111 (ttp) REVERT: C 1 ASP cc_start: 0.6631 (m-30) cc_final: 0.5895 (t0) REVERT: C 5 ARG cc_start: 0.7322 (mtp180) cc_final: 0.6892 (tmt90) REVERT: D 11 GLU cc_start: 0.8377 (tt0) cc_final: 0.7858 (tt0) REVERT: F 1 ASP cc_start: 0.6894 (m-30) cc_final: 0.6201 (t0) REVERT: F 3 GLU cc_start: 0.7770 (mt-10) cc_final: 0.6744 (tm-30) REVERT: G 3 GLU cc_start: 0.7718 (mt-10) cc_final: 0.7105 (tm-30) REVERT: H 1 ASP cc_start: 0.6962 (m-30) cc_final: 0.6101 (t0) REVERT: I 1 ASP cc_start: 0.7211 (m-30) cc_final: 0.6444 (t0) outliers start: 17 outliers final: 6 residues processed: 58 average time/residue: 0.6627 time to fit residues: 39.2479 Evaluate side-chains 47 residues out of total 280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 40 time to evaluate : 0.110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 35 MET Chi-restraints excluded: chain D residue 26 SER Chi-restraints excluded: chain E residue 26 SER Chi-restraints excluded: chain G residue 26 SER Chi-restraints excluded: chain H residue 26 SER Chi-restraints excluded: chain I residue 26 SER Chi-restraints excluded: chain J residue 26 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 8 optimal weight: 0.9990 chunk 25 optimal weight: 2.9990 chunk 4 optimal weight: 0.8980 chunk 10 optimal weight: 1.9990 chunk 13 optimal weight: 8.9990 chunk 3 optimal weight: 10.0000 chunk 23 optimal weight: 8.9990 chunk 27 optimal weight: 10.0000 chunk 12 optimal weight: 9.9990 chunk 22 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 13 HIS J 13 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4198 r_free = 0.4198 target = 0.130319 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.112350 restraints weight = 3574.283| |-----------------------------------------------------------------------------| r_work (start): 0.4004 rms_B_bonded: 2.66 r_work: 0.3856 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3741 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3741 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8477 moved from start: 0.3926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 2920 Z= 0.120 Angle : 0.397 3.228 3900 Z= 0.220 Chirality : 0.051 0.132 390 Planarity : 0.001 0.005 520 Dihedral : 4.401 12.502 390 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 2.14 % Allowed : 17.86 % Favored : 80.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.62 (0.40), residues: 360 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.99 (0.31), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG G 5 TYR 0.008 0.001 TYR I 10 PHE 0.007 0.001 PHE J 4 HIS 0.003 0.001 HIS B 13 Details of bonding type rmsd covalent geometry : bond 0.00271 ( 2920) covalent geometry : angle 0.39723 ( 3900) hydrogen bonds : bond 0.01196 ( 46) hydrogen bonds : angle 4.64294 ( 138) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 48 time to evaluate : 0.113 Fit side-chains REVERT: A 3 GLU cc_start: 0.8108 (mt-10) cc_final: 0.7723 (tm-30) REVERT: B 3 GLU cc_start: 0.8194 (mt-10) cc_final: 0.7667 (tm-30) REVERT: C 5 ARG cc_start: 0.7295 (mtp180) cc_final: 0.6904 (tmt90) REVERT: D 11 GLU cc_start: 0.8299 (tt0) cc_final: 0.7964 (tt0) REVERT: D 26 SER cc_start: 0.9347 (OUTLIER) cc_final: 0.9009 (p) REVERT: F 3 GLU cc_start: 0.7776 (mt-10) cc_final: 0.6993 (tm-30) REVERT: F 11 GLU cc_start: 0.8214 (tt0) cc_final: 0.7873 (tt0) REVERT: G 3 GLU cc_start: 0.7735 (mt-10) cc_final: 0.6899 (tm-30) REVERT: G 28 LYS cc_start: 0.8942 (mtpt) cc_final: 0.8680 (mtmt) REVERT: H 28 LYS cc_start: 0.8967 (mtpt) cc_final: 0.8700 (mttt) outliers start: 6 outliers final: 3 residues processed: 52 average time/residue: 0.7407 time to fit residues: 39.2736 Evaluate side-chains 50 residues out of total 280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 46 time to evaluate : 0.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 26 SER Chi-restraints excluded: chain F residue 26 SER Chi-restraints excluded: chain H residue 26 SER Chi-restraints excluded: chain I residue 26 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 14 optimal weight: 10.0000 chunk 2 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 8 optimal weight: 0.9980 chunk 25 optimal weight: 8.9990 chunk 5 optimal weight: 8.9990 chunk 11 optimal weight: 0.8980 chunk 15 optimal weight: 8.9990 chunk 7 optimal weight: 9.9990 chunk 6 optimal weight: 9.9990 chunk 9 optimal weight: 6.9990 overall best weight: 5.3786 ------------------------------------------------------------------------------- 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 = 0.4116 r_free = 0.4116 target = 0.124382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.106303 restraints weight = 3744.671| |-----------------------------------------------------------------------------| r_work (start): 0.3912 rms_B_bonded: 2.64 r_work: 0.3767 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3649 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3649 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8554 moved from start: 0.4457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.050 2920 Z= 0.341 Angle : 0.585 5.448 3900 Z= 0.311 Chirality : 0.054 0.132 390 Planarity : 0.003 0.014 520 Dihedral : 5.366 14.350 390 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 4.64 % Allowed : 19.29 % Favored : 76.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.49 (0.42), residues: 360 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.89 (0.32), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG H 5 TYR 0.007 0.002 TYR C 10 PHE 0.014 0.002 PHE J 4 HIS 0.005 0.002 HIS C 14 Details of bonding type rmsd covalent geometry : bond 0.00755 ( 2920) covalent geometry : angle 0.58494 ( 3900) hydrogen bonds : bond 0.02072 ( 46) hydrogen bonds : angle 4.81829 ( 138) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 45 time to evaluate : 0.115 Fit side-chains REVERT: A 3 GLU cc_start: 0.8220 (mt-10) cc_final: 0.7726 (tm-30) REVERT: B 3 GLU cc_start: 0.8369 (mt-10) cc_final: 0.7603 (tm-30) REVERT: C 26 SER cc_start: 0.9434 (OUTLIER) cc_final: 0.9102 (p) REVERT: D 11 GLU cc_start: 0.8350 (tt0) cc_final: 0.7937 (tt0) REVERT: E 11 GLU cc_start: 0.8570 (tt0) cc_final: 0.8055 (tt0) REVERT: F 3 GLU cc_start: 0.7964 (mt-10) cc_final: 0.7090 (tm-30) REVERT: G 3 GLU cc_start: 0.7923 (mt-10) cc_final: 0.7087 (tm-30) REVERT: G 28 LYS cc_start: 0.9017 (OUTLIER) cc_final: 0.8774 (mttt) REVERT: J 1 ASP cc_start: 0.7168 (m-30) cc_final: 0.6906 (m-30) outliers start: 13 outliers final: 5 residues processed: 56 average time/residue: 0.6089 time to fit residues: 34.8142 Evaluate side-chains 49 residues out of total 280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 42 time to evaluate : 0.065 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 26 SER Chi-restraints excluded: chain D residue 26 SER Chi-restraints excluded: chain G residue 28 LYS Chi-restraints excluded: chain H residue 26 SER Chi-restraints excluded: chain I residue 26 SER Chi-restraints excluded: chain J residue 26 SER Chi-restraints excluded: chain J residue 28 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 21 optimal weight: 10.0000 chunk 13 optimal weight: 3.9990 chunk 10 optimal weight: 3.9990 chunk 8 optimal weight: 0.9990 chunk 1 optimal weight: 5.9990 chunk 7 optimal weight: 5.9990 chunk 19 optimal weight: 3.9990 chunk 29 optimal weight: 5.9990 chunk 25 optimal weight: 3.9990 chunk 16 optimal weight: 2.9990 chunk 9 optimal weight: 9.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- 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 = 0.4150 r_free = 0.4150 target = 0.127064 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.108960 restraints weight = 3624.589| |-----------------------------------------------------------------------------| r_work (start): 0.3950 rms_B_bonded: 2.65 r_work: 0.3809 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3689 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3689 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8528 moved from start: 0.4397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 2920 Z= 0.213 Angle : 0.486 4.473 3900 Z= 0.261 Chirality : 0.052 0.133 390 Planarity : 0.002 0.006 520 Dihedral : 4.977 13.377 390 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 3.57 % Allowed : 19.64 % Favored : 76.79 % 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 aren not related in a simple way. whole: -2.44 (0.42), residues: 360 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.85 (0.32), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 5 TYR 0.007 0.001 TYR H 10 PHE 0.010 0.002 PHE J 4 HIS 0.003 0.001 HIS B 14 Details of bonding type rmsd covalent geometry : bond 0.00476 ( 2920) covalent geometry : angle 0.48631 ( 3900) hydrogen bonds : bond 0.01636 ( 46) hydrogen bonds : angle 4.73216 ( 138) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 42 time to evaluate : 0.084 Fit side-chains REVERT: A 3 GLU cc_start: 0.8279 (mt-10) cc_final: 0.7725 (tm-30) REVERT: B 3 GLU cc_start: 0.8350 (mt-10) cc_final: 0.7562 (tm-30) REVERT: B 26 SER cc_start: 0.9420 (OUTLIER) cc_final: 0.9131 (p) REVERT: C 26 SER cc_start: 0.9419 (OUTLIER) cc_final: 0.9109 (p) REVERT: D 11 GLU cc_start: 0.8307 (tt0) cc_final: 0.7938 (tt0) REVERT: D 26 SER cc_start: 0.9385 (OUTLIER) cc_final: 0.8993 (p) REVERT: E 11 GLU cc_start: 0.8440 (tt0) cc_final: 0.8051 (tt0) REVERT: F 3 GLU cc_start: 0.7925 (mt-10) cc_final: 0.7085 (tm-30) REVERT: G 3 GLU cc_start: 0.7969 (mt-10) cc_final: 0.7007 (tm-30) REVERT: G 28 LYS cc_start: 0.8952 (OUTLIER) cc_final: 0.8731 (mttt) REVERT: H 28 LYS cc_start: 0.8995 (mtpt) cc_final: 0.8768 (mttt) REVERT: J 1 ASP cc_start: 0.7175 (m-30) cc_final: 0.6940 (m-30) REVERT: J 26 SER cc_start: 0.9150 (OUTLIER) cc_final: 0.8644 (p) outliers start: 10 outliers final: 2 residues processed: 51 average time/residue: 0.5927 time to fit residues: 30.8871 Evaluate side-chains 47 residues out of total 280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 40 time to evaluate : 0.105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 26 SER Chi-restraints excluded: chain C residue 26 SER Chi-restraints excluded: chain D residue 26 SER Chi-restraints excluded: chain G residue 28 LYS Chi-restraints excluded: chain H residue 26 SER Chi-restraints excluded: chain I residue 26 SER Chi-restraints excluded: chain J residue 26 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 26 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 17 optimal weight: 5.9990 chunk 5 optimal weight: 10.0000 chunk 3 optimal weight: 9.9990 chunk 11 optimal weight: 0.9990 chunk 7 optimal weight: 1.9990 chunk 18 optimal weight: 20.0000 chunk 9 optimal weight: 10.0000 chunk 28 optimal weight: 2.9990 chunk 6 optimal weight: 9.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- 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 = 0.4176 r_free = 0.4176 target = 0.129296 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.111174 restraints weight = 3649.531| |-----------------------------------------------------------------------------| r_work (start): 0.3976 rms_B_bonded: 2.67 r_work: 0.3840 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3725 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3725 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8512 moved from start: 0.4337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 2920 Z= 0.152 Angle : 0.430 3.400 3900 Z= 0.234 Chirality : 0.051 0.132 390 Planarity : 0.001 0.006 520 Dihedral : 4.604 13.262 390 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 2.86 % Allowed : 20.71 % Favored : 76.43 % 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 aren not related in a simple way. whole: -2.41 (0.42), residues: 360 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.83 (0.32), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG G 5 TYR 0.003 0.001 TYR C 10 PHE 0.008 0.001 PHE J 4 HIS 0.002 0.001 HIS B 13 Details of bonding type rmsd covalent geometry : bond 0.00341 ( 2920) covalent geometry : angle 0.42959 ( 3900) hydrogen bonds : bond 0.01369 ( 46) hydrogen bonds : angle 4.59783 ( 138) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 46 time to evaluate : 0.107 Fit side-chains REVERT: A 3 GLU cc_start: 0.8267 (mt-10) cc_final: 0.7726 (tm-30) REVERT: B 3 GLU cc_start: 0.8303 (mt-10) cc_final: 0.7580 (tm-30) REVERT: B 26 SER cc_start: 0.9442 (OUTLIER) cc_final: 0.9152 (p) REVERT: B 28 LYS cc_start: 0.9081 (mtpp) cc_final: 0.7589 (mmpt) REVERT: C 26 SER cc_start: 0.9418 (OUTLIER) cc_final: 0.9120 (p) REVERT: D 11 GLU cc_start: 0.8314 (tt0) cc_final: 0.8047 (tt0) REVERT: D 26 SER cc_start: 0.9386 (OUTLIER) cc_final: 0.8984 (p) REVERT: E 11 GLU cc_start: 0.8497 (tt0) cc_final: 0.8291 (tt0) REVERT: F 3 GLU cc_start: 0.7938 (mt-10) cc_final: 0.7136 (tm-30) REVERT: G 3 GLU cc_start: 0.7916 (mt-10) cc_final: 0.6992 (tm-30) REVERT: H 28 LYS cc_start: 0.8994 (OUTLIER) cc_final: 0.8760 (mttt) REVERT: J 26 SER cc_start: 0.9157 (OUTLIER) cc_final: 0.8650 (p) outliers start: 8 outliers final: 1 residues processed: 52 average time/residue: 0.6785 time to fit residues: 36.0685 Evaluate side-chains 50 residues out of total 280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 44 time to evaluate : 0.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 26 SER Chi-restraints excluded: chain C residue 26 SER Chi-restraints excluded: chain D residue 26 SER Chi-restraints excluded: chain H residue 28 LYS Chi-restraints excluded: chain I residue 26 SER Chi-restraints excluded: chain J residue 26 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 3 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 23 optimal weight: 3.9990 chunk 10 optimal weight: 9.9990 chunk 15 optimal weight: 10.0000 chunk 18 optimal weight: 20.0000 chunk 29 optimal weight: 0.9980 chunk 4 optimal weight: 5.9990 chunk 28 optimal weight: 0.7980 chunk 22 optimal weight: 2.9990 chunk 25 optimal weight: 0.0070 overall best weight: 1.7602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 13 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4198 r_free = 0.4198 target = 0.130369 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.112506 restraints weight = 3671.886| |-----------------------------------------------------------------------------| r_work (start): 0.4011 rms_B_bonded: 2.67 r_work: 0.3865 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3746 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3746 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8495 moved from start: 0.4445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 2920 Z= 0.125 Angle : 0.406 3.205 3900 Z= 0.223 Chirality : 0.051 0.132 390 Planarity : 0.001 0.006 520 Dihedral : 4.386 13.412 390 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 2.14 % Allowed : 20.71 % Favored : 77.14 % 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 aren not related in a simple way. whole: -2.36 (0.42), residues: 360 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.79 (0.32), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 5 TYR 0.009 0.001 TYR I 10 PHE 0.008 0.001 PHE C 4 HIS 0.003 0.001 HIS B 13 Details of bonding type rmsd covalent geometry : bond 0.00281 ( 2920) covalent geometry : angle 0.40555 ( 3900) hydrogen bonds : bond 0.01232 ( 46) hydrogen bonds : angle 4.51633 ( 138) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 47 time to evaluate : 0.066 Fit side-chains REVERT: A 3 GLU cc_start: 0.8236 (mt-10) cc_final: 0.7718 (tm-30) REVERT: B 3 GLU cc_start: 0.8280 (mt-10) cc_final: 0.7549 (tm-30) REVERT: C 26 SER cc_start: 0.9391 (OUTLIER) cc_final: 0.9094 (p) REVERT: D 11 GLU cc_start: 0.8338 (tt0) cc_final: 0.8051 (tt0) REVERT: F 3 GLU cc_start: 0.7892 (mt-10) cc_final: 0.7094 (tm-30) REVERT: G 3 GLU cc_start: 0.7880 (mt-10) cc_final: 0.7022 (tm-30) REVERT: H 28 LYS cc_start: 0.9079 (mtpt) cc_final: 0.8790 (mttt) REVERT: J 26 SER cc_start: 0.9117 (OUTLIER) cc_final: 0.8596 (p) outliers start: 6 outliers final: 3 residues processed: 52 average time/residue: 0.6166 time to fit residues: 32.7804 Evaluate side-chains 50 residues out of total 280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 45 time to evaluate : 0.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 26 SER Chi-restraints excluded: chain D residue 26 SER Chi-restraints excluded: chain H residue 26 SER Chi-restraints excluded: chain I residue 26 SER Chi-restraints excluded: chain J residue 26 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 5 optimal weight: 0.0980 chunk 22 optimal weight: 0.9990 chunk 20 optimal weight: 8.9990 chunk 17 optimal weight: 8.9990 chunk 12 optimal weight: 9.9990 chunk 6 optimal weight: 9.9990 chunk 16 optimal weight: 0.9990 chunk 18 optimal weight: 9.9990 chunk 26 optimal weight: 0.8980 chunk 25 optimal weight: 10.0000 chunk 21 optimal weight: 10.0000 overall best weight: 2.3986 ------------------------------------------------------------------------------- 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 = 0.4180 r_free = 0.4180 target = 0.129039 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.111067 restraints weight = 3686.238| |-----------------------------------------------------------------------------| r_work (start): 0.3982 rms_B_bonded: 2.66 r_work: 0.3845 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3727 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3727 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8512 moved from start: 0.4443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 2920 Z= 0.164 Angle : 0.443 5.058 3900 Z= 0.237 Chirality : 0.052 0.133 390 Planarity : 0.002 0.007 520 Dihedral : 4.595 13.880 390 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 2.14 % Allowed : 20.71 % Favored : 77.14 % 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 aren not related in a simple way. whole: -2.38 (0.41), residues: 360 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.81 (0.32), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 5 TYR 0.009 0.001 TYR J 10 PHE 0.009 0.001 PHE C 4 HIS 0.002 0.001 HIS B 13 Details of bonding type rmsd covalent geometry : bond 0.00370 ( 2920) covalent geometry : angle 0.44349 ( 3900) hydrogen bonds : bond 0.01427 ( 46) hydrogen bonds : angle 4.58881 ( 138) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 42 time to evaluate : 0.071 Fit side-chains REVERT: A 3 GLU cc_start: 0.8239 (mt-10) cc_final: 0.7699 (tm-30) REVERT: A 35 MET cc_start: 0.8663 (ptp) cc_final: 0.8384 (ptp) REVERT: B 3 GLU cc_start: 0.8275 (mt-10) cc_final: 0.7554 (tm-30) REVERT: B 26 SER cc_start: 0.9421 (OUTLIER) cc_final: 0.9126 (p) REVERT: B 28 LYS cc_start: 0.9022 (mtpp) cc_final: 0.7574 (mmpt) REVERT: C 26 SER cc_start: 0.9413 (OUTLIER) cc_final: 0.9121 (p) REVERT: D 11 GLU cc_start: 0.8302 (tt0) cc_final: 0.8017 (tt0) REVERT: E 11 GLU cc_start: 0.8432 (tt0) cc_final: 0.8030 (tt0) REVERT: F 3 GLU cc_start: 0.7875 (mt-10) cc_final: 0.7045 (tm-30) REVERT: G 3 GLU cc_start: 0.7911 (mt-10) cc_final: 0.6980 (tm-30) REVERT: H 28 LYS cc_start: 0.9075 (mtpt) cc_final: 0.8830 (mttt) REVERT: J 26 SER cc_start: 0.9130 (OUTLIER) cc_final: 0.8620 (p) outliers start: 6 outliers final: 3 residues processed: 47 average time/residue: 0.5719 time to fit residues: 27.5277 Evaluate side-chains 47 residues out of total 280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 41 time to evaluate : 0.065 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 26 SER Chi-restraints excluded: chain C residue 26 SER Chi-restraints excluded: chain D residue 26 SER Chi-restraints excluded: chain H residue 26 SER Chi-restraints excluded: chain I residue 26 SER Chi-restraints excluded: chain J residue 26 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 3 optimal weight: 10.0000 chunk 28 optimal weight: 2.9990 chunk 26 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 23 optimal weight: 3.9990 chunk 7 optimal weight: 1.9990 chunk 21 optimal weight: 9.9990 chunk 4 optimal weight: 4.9990 chunk 13 optimal weight: 2.9990 chunk 6 optimal weight: 5.9990 chunk 16 optimal weight: 9.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- 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 = 0.4156 r_free = 0.4156 target = 0.127384 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.109185 restraints weight = 3613.062| |-----------------------------------------------------------------------------| r_work (start): 0.3959 rms_B_bonded: 2.64 r_work: 0.3813 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3694 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3694 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8527 moved from start: 0.4622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 2920 Z= 0.212 Angle : 0.485 5.433 3900 Z= 0.258 Chirality : 0.052 0.132 390 Planarity : 0.002 0.006 520 Dihedral : 4.880 15.679 390 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 2.50 % Allowed : 20.36 % Favored : 77.14 % 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 aren not related in a simple way. whole: -2.36 (0.42), residues: 360 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.79 (0.32), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG G 5 TYR 0.008 0.002 TYR I 10 PHE 0.011 0.002 PHE J 4 HIS 0.003 0.001 HIS C 14 Details of bonding type rmsd covalent geometry : bond 0.00477 ( 2920) covalent geometry : angle 0.48510 ( 3900) hydrogen bonds : bond 0.01623 ( 46) hydrogen bonds : angle 4.64668 ( 138) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1163.25 seconds wall clock time: 20 minutes 28.97 seconds (1228.97 seconds total)