Starting phenix.real_space_refine on Wed Mar 5 16:40:59 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8bfa_16018/03_2025/8bfa_16018.cif Found real_map, /net/cci-nas-00/data/ceres_data/8bfa_16018/03_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8bfa_16018/03_2025/8bfa_16018.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8bfa_16018/03_2025/8bfa_16018.map" model { file = "/net/cci-nas-00/data/ceres_data/8bfa_16018/03_2025/8bfa_16018.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8bfa_16018/03_2025/8bfa_16018.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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: 2.25, per 1000 atoms: 0.79 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: 0.56 Conformation dependent library (CDL) restraints added in 335.2 milliseconds 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: 0.45 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: 0.62 Time building geometry restraints manager: 0.68 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' selection = chain 'G' selection = chain 'F' selection = chain 'I' selection = chain 'H' 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: 0.000 Normalize map: mean=0, sd=1: 1.080 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: 0.000 Extract box with map and model: 0.100 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 11.150 Find NCS groups from input model: 0.060 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:10.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.620 ------------------------------------------------------------------------------- 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= 0.171 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.13 (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 HIS 0.002 0.000 HIS B 6 PHE 0.006 0.001 PHE A 4 TYR 0.004 0.001 TYR C 10 ARG 0.001 0.000 ARG E 5 *********************** 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 : 0.311 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: 1.2909 time to fit residues: 66.1693 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 : 0.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 25 optimal weight: 9.9990 chunk 22 optimal weight: 10.0000 chunk 12 optimal weight: 20.0000 chunk 7 optimal weight: 10.0000 chunk 15 optimal weight: 20.0000 chunk 23 optimal weight: 10.0000 chunk 9 optimal weight: 3.9990 chunk 14 optimal weight: 10.0000 chunk 17 optimal weight: 4.9990 chunk 27 optimal weight: 9.9990 chunk 8 optimal weight: 1.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- 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 = 0.125781 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.106860 restraints weight = 3758.584| |-----------------------------------------------------------------------------| r_work (start): 0.3871 rms_B_bonded: 2.78 r_work: 0.3731 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3615 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3615 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8525 moved from start: 0.3331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.060 2920 Z= 0.648 Angle : 0.625 4.908 3900 Z= 0.342 Chirality : 0.054 0.139 390 Planarity : 0.004 0.027 520 Dihedral : 5.477 15.430 390 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 8.57 % Allowed : 8.21 % Favored : 83.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.77 (0.40), residues: 360 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.11 (0.30), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.002 HIS B 13 PHE 0.017 0.003 PHE F 4 TYR 0.013 0.003 TYR C 10 ARG 0.002 0.001 ARG D 5 *********************** 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 65 residues out of total 280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 41 time to evaluate : 0.314 Fit side-chains REVERT: A 1 ASP cc_start: 0.6955 (m-30) cc_final: 0.6547 (t0) REVERT: B 1 ASP cc_start: 0.7021 (m-30) cc_final: 0.6451 (t0) REVERT: B 28 LYS cc_start: 0.9159 (OUTLIER) cc_final: 0.8813 (mtpt) REVERT: C 1 ASP cc_start: 0.6672 (m-30) cc_final: 0.5857 (OUTLIER) REVERT: C 5 ARG cc_start: 0.7389 (mtp180) cc_final: 0.6936 (tmt90) REVERT: C 28 LYS cc_start: 0.9025 (OUTLIER) cc_final: 0.8673 (mtpt) REVERT: D 1 ASP cc_start: 0.6728 (m-30) cc_final: 0.5888 (t0) REVERT: E 1 ASP cc_start: 0.6940 (m-30) cc_final: 0.5858 (t0) REVERT: F 1 ASP cc_start: 0.6807 (m-30) cc_final: 0.5882 (t0) REVERT: F 5 ARG cc_start: 0.7522 (mtp180) cc_final: 0.7077 (ttt90) REVERT: G 1 ASP cc_start: 0.7012 (m-30) cc_final: 0.6067 (t0) REVERT: G 5 ARG cc_start: 0.7306 (mtp180) cc_final: 0.6992 (tmt90) REVERT: H 1 ASP cc_start: 0.6812 (m-30) cc_final: 0.5881 (t0) REVERT: I 1 ASP cc_start: 0.7188 (m-30) cc_final: 0.6226 (t0) REVERT: J 1 ASP cc_start: 0.6992 (m-30) cc_final: 0.6004 (t0) outliers start: 24 outliers final: 10 residues processed: 63 average time/residue: 1.3587 time to fit residues: 87.5555 Evaluate side-chains 45 residues out of total 280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 34 time to evaluate : 0.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 SER Chi-restraints excluded: chain B residue 28 LYS Chi-restraints excluded: chain C residue 28 LYS 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 29 optimal weight: 0.6980 chunk 16 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 9 optimal weight: 9.9990 chunk 11 optimal weight: 0.9990 chunk 28 optimal weight: 5.9990 chunk 12 optimal weight: 9.9990 chunk 8 optimal weight: 0.8980 chunk 23 optimal weight: 0.9990 chunk 27 optimal weight: 9.9990 chunk 1 optimal weight: 3.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- 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 = 0.4183 r_free = 0.4183 target = 0.133420 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.115553 restraints weight = 3586.489| |-----------------------------------------------------------------------------| r_work (start): 0.3983 rms_B_bonded: 2.72 r_work: 0.3840 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3727 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3727 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8440 moved from start: 0.3248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 2920 Z= 0.150 Angle : 0.368 2.774 3900 Z= 0.211 Chirality : 0.051 0.129 390 Planarity : 0.001 0.005 520 Dihedral : 4.080 11.424 390 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.11 % Favored : 98.89 % Rotamer: Outliers : 3.93 % Allowed : 14.29 % Favored : 81.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.69 (0.39), residues: 360 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.04 (0.30), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.000 HIS B 13 PHE 0.007 0.001 PHE D 4 TYR 0.009 0.001 TYR I 10 ARG 0.000 0.000 ARG J 5 *********************** 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 : 0.297 Fit side-chains REVERT: A 5 ARG cc_start: 0.7906 (mtp180) cc_final: 0.7657 (tmt90) REVERT: B 1 ASP cc_start: 0.6804 (m-30) cc_final: 0.6350 (t0) REVERT: B 5 ARG cc_start: 0.7972 (mtp180) cc_final: 0.7666 (tmt90) REVERT: B 35 MET cc_start: 0.8164 (OUTLIER) cc_final: 0.7953 (ttp) REVERT: C 1 ASP cc_start: 0.6427 (m-30) cc_final: 0.5881 (t0) REVERT: C 5 ARG cc_start: 0.7360 (mtp180) cc_final: 0.6887 (tmt90) REVERT: D 1 ASP cc_start: 0.6487 (m-30) cc_final: 0.5774 (t0) REVERT: D 11 GLU cc_start: 0.8306 (tt0) cc_final: 0.7842 (tt0) REVERT: F 1 ASP cc_start: 0.6512 (m-30) cc_final: 0.5809 (t0) REVERT: F 5 ARG cc_start: 0.7480 (mtp180) cc_final: 0.7076 (tmt90) REVERT: G 1 ASP cc_start: 0.6512 (m-30) cc_final: 0.5917 (t0) REVERT: G 5 ARG cc_start: 0.7371 (mtp180) cc_final: 0.7075 (tmt90) REVERT: H 1 ASP cc_start: 0.6641 (m-30) cc_final: 0.5811 (t0) outliers start: 11 outliers final: 6 residues processed: 54 average time/residue: 1.4710 time to fit residues: 81.2462 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 : 0.316 ------------------------------------------------------------------------------- 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 22 optimal weight: 4.9990 chunk 19 optimal weight: 9.9990 chunk 2 optimal weight: 10.0000 chunk 12 optimal weight: 20.0000 chunk 14 optimal weight: 8.9990 chunk 29 optimal weight: 6.9990 chunk 13 optimal weight: 2.9990 chunk 16 optimal weight: 0.9980 chunk 15 optimal weight: 10.0000 chunk 5 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 overall best weight: 3.9988 ------------------------------------------------------------------------------- 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 = 0.4126 r_free = 0.4126 target = 0.128094 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.109652 restraints weight = 3708.795| |-----------------------------------------------------------------------------| r_work (start): 0.3907 rms_B_bonded: 2.73 r_work: 0.3773 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3663 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3663 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8518 moved from start: 0.3766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.036 2920 Z= 0.414 Angle : 0.512 5.038 3900 Z= 0.275 Chirality : 0.052 0.133 390 Planarity : 0.002 0.006 520 Dihedral : 5.027 13.955 390 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 4.64 % Allowed : 15.00 % Favored : 80.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.64 (0.40), residues: 360 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.01 (0.31), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS E 14 PHE 0.012 0.002 PHE D 4 TYR 0.008 0.002 TYR C 10 ARG 0.001 0.000 ARG F 5 *********************** 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 55 residues out of total 280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 42 time to evaluate : 0.303 Fit side-chains REVERT: A 1 ASP cc_start: 0.6953 (m-30) cc_final: 0.6516 (t0) REVERT: B 1 ASP cc_start: 0.6970 (m-30) cc_final: 0.6473 (t0) REVERT: B 3 GLU cc_start: 0.8212 (mt-10) cc_final: 0.7900 (tt0) REVERT: B 35 MET cc_start: 0.8367 (OUTLIER) cc_final: 0.8091 (ttp) REVERT: C 1 ASP cc_start: 0.6680 (m-30) cc_final: 0.6035 (t0) REVERT: C 5 ARG cc_start: 0.7327 (mtp180) cc_final: 0.6903 (tmt90) REVERT: E 11 GLU cc_start: 0.8513 (tt0) cc_final: 0.8027 (tt0) REVERT: F 1 ASP cc_start: 0.6865 (m-30) cc_final: 0.6210 (t0) REVERT: F 3 GLU cc_start: 0.7758 (mt-10) cc_final: 0.6741 (tm-30) REVERT: F 28 LYS cc_start: 0.8872 (mtpt) cc_final: 0.8481 (mttt) REVERT: G 3 GLU cc_start: 0.7735 (mt-10) cc_final: 0.7151 (tm-30) REVERT: H 1 ASP cc_start: 0.6848 (m-30) cc_final: 0.6038 (t0) REVERT: I 1 ASP cc_start: 0.7205 (m-30) cc_final: 0.6436 (t0) outliers start: 13 outliers final: 6 residues processed: 54 average time/residue: 1.4333 time to fit residues: 79.1115 Evaluate side-chains 48 residues out of total 280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 41 time to evaluate : 0.355 ------------------------------------------------------------------------------- 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 18 optimal weight: 20.0000 chunk 9 optimal weight: 10.0000 chunk 14 optimal weight: 3.9990 chunk 8 optimal weight: 4.9990 chunk 11 optimal weight: 8.9990 chunk 12 optimal weight: 2.9990 chunk 3 optimal weight: 6.9990 chunk 22 optimal weight: 8.9990 chunk 10 optimal weight: 4.9990 chunk 2 optimal weight: 0.9990 chunk 24 optimal weight: 1.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- 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 = 0.4161 r_free = 0.4161 target = 0.127275 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.109052 restraints weight = 3629.982| |-----------------------------------------------------------------------------| r_work (start): 0.3958 rms_B_bonded: 2.67 r_work: 0.3811 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3695 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3695 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8518 moved from start: 0.3991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 2920 Z= 0.317 Angle : 0.456 4.045 3900 Z= 0.248 Chirality : 0.052 0.135 390 Planarity : 0.002 0.007 520 Dihedral : 4.766 12.972 390 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 4.29 % Allowed : 15.36 % Favored : 80.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.57 (0.41), residues: 360 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.95 (0.31), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS E 14 PHE 0.010 0.002 PHE D 4 TYR 0.007 0.001 TYR G 10 ARG 0.002 0.000 ARG G 5 *********************** 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 60 residues out of total 280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 48 time to evaluate : 0.324 Fit side-chains REVERT: A 3 GLU cc_start: 0.8115 (mt-10) cc_final: 0.7744 (tm-30) REVERT: B 3 GLU cc_start: 0.8262 (mt-10) cc_final: 0.7746 (tm-30) REVERT: C 5 ARG cc_start: 0.7310 (mtp180) cc_final: 0.6879 (tmt90) REVERT: D 11 GLU cc_start: 0.8302 (tt0) cc_final: 0.7983 (tt0) REVERT: E 28 LYS cc_start: 0.8939 (mtpt) cc_final: 0.8665 (mtpt) REVERT: F 3 GLU cc_start: 0.7823 (mt-10) cc_final: 0.7017 (tm-30) REVERT: F 5 ARG cc_start: 0.7827 (OUTLIER) cc_final: 0.7088 (tmt90) REVERT: G 3 GLU cc_start: 0.7791 (mt-10) cc_final: 0.6946 (tm-30) REVERT: G 28 LYS cc_start: 0.9021 (OUTLIER) cc_final: 0.8702 (mttt) REVERT: H 28 LYS cc_start: 0.8997 (OUTLIER) cc_final: 0.8749 (mttt) outliers start: 12 outliers final: 5 residues processed: 55 average time/residue: 1.6216 time to fit residues: 90.9556 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 : 0.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 26 SER Chi-restraints excluded: chain F residue 5 ARG Chi-restraints excluded: chain F residue 26 SER Chi-restraints excluded: chain G residue 28 LYS Chi-restraints excluded: chain H 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 27 optimal weight: 9.9990 chunk 8 optimal weight: 9.9990 chunk 14 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 15 optimal weight: 20.0000 chunk 16 optimal weight: 6.9990 chunk 17 optimal weight: 0.9980 chunk 13 optimal weight: 2.9990 chunk 25 optimal weight: 7.9990 chunk 21 optimal weight: 3.9990 chunk 24 optimal weight: 8.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- 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 = 0.126843 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.108761 restraints weight = 3659.233| |-----------------------------------------------------------------------------| r_work (start): 0.3953 rms_B_bonded: 2.65 r_work: 0.3807 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3688 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3688 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8526 moved from start: 0.4197 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= 0.337 Angle : 0.475 4.613 3900 Z= 0.255 Chirality : 0.052 0.133 390 Planarity : 0.002 0.006 520 Dihedral : 4.838 13.287 390 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 5.36 % Allowed : 16.43 % Favored : 78.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.47 (0.41), residues: 360 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.88 (0.32), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS E 14 PHE 0.010 0.002 PHE J 4 TYR 0.007 0.001 TYR I 10 ARG 0.002 0.000 ARG G 5 *********************** 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 61 residues out of total 280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 46 time to evaluate : 0.313 Fit side-chains REVERT: A 3 GLU cc_start: 0.8172 (mt-10) cc_final: 0.7710 (tm-30) REVERT: B 3 GLU cc_start: 0.8323 (mt-10) cc_final: 0.7563 (tm-30) REVERT: C 26 SER cc_start: 0.9394 (OUTLIER) cc_final: 0.9045 (p) REVERT: D 11 GLU cc_start: 0.8304 (tt0) cc_final: 0.7921 (tt0) REVERT: D 26 SER cc_start: 0.9378 (OUTLIER) cc_final: 0.9021 (p) REVERT: E 11 GLU cc_start: 0.8605 (tt0) cc_final: 0.8182 (tt0) REVERT: F 3 GLU cc_start: 0.7923 (mt-10) cc_final: 0.7085 (tm-30) REVERT: F 5 ARG cc_start: 0.7836 (OUTLIER) cc_final: 0.7086 (tmt90) REVERT: G 3 GLU cc_start: 0.7874 (mt-10) cc_final: 0.6997 (tm-30) REVERT: G 28 LYS cc_start: 0.8999 (OUTLIER) cc_final: 0.8718 (mttt) REVERT: H 28 LYS cc_start: 0.9013 (OUTLIER) cc_final: 0.8671 (mttt) REVERT: J 1 ASP cc_start: 0.7080 (m-30) cc_final: 0.6820 (m-30) outliers start: 15 outliers final: 6 residues processed: 57 average time/residue: 1.2435 time to fit residues: 72.5717 Evaluate side-chains 55 residues out of total 280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 44 time to evaluate : 0.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 26 SER Chi-restraints excluded: chain D residue 26 SER Chi-restraints excluded: chain E residue 26 SER Chi-restraints excluded: chain F residue 5 ARG Chi-restraints excluded: chain F residue 26 SER Chi-restraints excluded: chain G residue 26 SER Chi-restraints excluded: chain G residue 28 LYS Chi-restraints excluded: chain H 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 20 optimal weight: 7.9990 chunk 28 optimal weight: 3.9990 chunk 4 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 chunk 16 optimal weight: 10.0000 chunk 8 optimal weight: 9.9990 chunk 3 optimal weight: 10.0000 chunk 23 optimal weight: 10.0000 chunk 14 optimal weight: 0.9980 chunk 18 optimal weight: 20.0000 chunk 0 optimal weight: 10.0000 overall best weight: 3.7988 ------------------------------------------------------------------------------- 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 = 0.4138 r_free = 0.4138 target = 0.125885 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.107815 restraints weight = 3696.289| |-----------------------------------------------------------------------------| r_work (start): 0.3936 rms_B_bonded: 2.64 r_work: 0.3793 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3672 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3672 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8539 moved from start: 0.4356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.037 2920 Z= 0.393 Angle : 0.508 4.960 3900 Z= 0.271 Chirality : 0.052 0.133 390 Planarity : 0.002 0.006 520 Dihedral : 5.035 13.549 390 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 5.00 % Allowed : 17.50 % Favored : 77.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 HIS 0.003 0.001 HIS E 14 PHE 0.011 0.002 PHE J 4 TYR 0.006 0.002 TYR I 10 ARG 0.002 0.001 ARG H 5 *********************** 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 57 residues out of total 280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 43 time to evaluate : 0.311 Fit side-chains REVERT: A 3 GLU cc_start: 0.8284 (mt-10) cc_final: 0.7722 (tm-30) REVERT: B 3 GLU cc_start: 0.8352 (mt-10) cc_final: 0.7633 (tm-30) REVERT: C 26 SER cc_start: 0.9428 (OUTLIER) cc_final: 0.9104 (p) REVERT: D 11 GLU cc_start: 0.8309 (tt0) cc_final: 0.7923 (tt0) REVERT: F 3 GLU cc_start: 0.7938 (mt-10) cc_final: 0.7111 (tm-30) REVERT: F 5 ARG cc_start: 0.7839 (OUTLIER) cc_final: 0.7036 (tmt90) REVERT: G 3 GLU cc_start: 0.7956 (mt-10) cc_final: 0.7059 (tm-30) REVERT: G 28 LYS cc_start: 0.8992 (OUTLIER) cc_final: 0.8678 (mttt) REVERT: H 28 LYS cc_start: 0.9050 (OUTLIER) cc_final: 0.8799 (mttt) REVERT: J 26 SER cc_start: 0.9154 (OUTLIER) cc_final: 0.8655 (p) outliers start: 14 outliers final: 5 residues processed: 54 average time/residue: 1.3668 time to fit residues: 75.6144 Evaluate side-chains 51 residues out of total 280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 41 time to evaluate : 0.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 26 SER Chi-restraints excluded: chain D residue 26 SER Chi-restraints excluded: chain E residue 26 SER Chi-restraints excluded: chain F residue 5 ARG Chi-restraints excluded: chain F residue 26 SER Chi-restraints excluded: chain G residue 28 LYS Chi-restraints excluded: chain H 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 7 optimal weight: 8.9990 chunk 23 optimal weight: 6.9990 chunk 20 optimal weight: 5.9990 chunk 19 optimal weight: 5.9990 chunk 29 optimal weight: 2.9990 chunk 18 optimal weight: 9.9990 chunk 2 optimal weight: 5.9990 chunk 13 optimal weight: 3.9990 chunk 24 optimal weight: 3.9990 chunk 14 optimal weight: 0.9990 chunk 8 optimal weight: 2.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 13 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4147 r_free = 0.4147 target = 0.127097 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.109249 restraints weight = 3718.967| |-----------------------------------------------------------------------------| r_work (start): 0.3954 rms_B_bonded: 2.64 r_work: 0.3809 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3689 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3689 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8525 moved from start: 0.4380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 2920 Z= 0.320 Angle : 0.468 4.291 3900 Z= 0.253 Chirality : 0.052 0.134 390 Planarity : 0.002 0.005 520 Dihedral : 4.857 13.945 390 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 4.64 % Allowed : 18.21 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.37 (0.42), residues: 360 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.80 (0.32), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS C 14 PHE 0.010 0.002 PHE J 4 TYR 0.007 0.001 TYR H 10 ARG 0.001 0.000 ARG G 5 *********************** 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 56 residues out of total 280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 43 time to evaluate : 0.309 Fit side-chains REVERT: A 3 GLU cc_start: 0.8289 (mt-10) cc_final: 0.7699 (tm-30) REVERT: B 3 GLU cc_start: 0.8350 (mt-10) cc_final: 0.7574 (tm-30) REVERT: C 26 SER cc_start: 0.9417 (OUTLIER) cc_final: 0.9093 (p) REVERT: D 11 GLU cc_start: 0.8299 (tt0) cc_final: 0.7998 (tt0) REVERT: D 26 SER cc_start: 0.9394 (OUTLIER) cc_final: 0.9033 (p) REVERT: F 3 GLU cc_start: 0.7928 (mt-10) cc_final: 0.7049 (tm-30) REVERT: F 5 ARG cc_start: 0.7856 (OUTLIER) cc_final: 0.7094 (tmt90) REVERT: G 3 GLU cc_start: 0.7973 (mt-10) cc_final: 0.7135 (tm-30) REVERT: H 28 LYS cc_start: 0.9027 (OUTLIER) cc_final: 0.8776 (mttt) REVERT: J 26 SER cc_start: 0.9154 (OUTLIER) cc_final: 0.8667 (p) outliers start: 13 outliers final: 4 residues processed: 53 average time/residue: 1.2876 time to fit residues: 69.9570 Evaluate side-chains 50 residues out of total 280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 41 time to evaluate : 0.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 26 SER Chi-restraints excluded: chain D residue 26 SER Chi-restraints excluded: chain E residue 26 SER Chi-restraints excluded: chain F residue 5 ARG Chi-restraints excluded: chain F residue 26 SER Chi-restraints excluded: chain H 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 5 optimal weight: 10.0000 chunk 22 optimal weight: 0.0870 chunk 0 optimal weight: 10.0000 chunk 23 optimal weight: 2.9990 chunk 11 optimal weight: 0.9980 chunk 8 optimal weight: 8.9990 chunk 2 optimal weight: 0.9990 chunk 29 optimal weight: 2.9990 chunk 7 optimal weight: 1.9990 chunk 10 optimal weight: 9.9990 chunk 1 optimal weight: 3.9990 overall best weight: 1.4164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 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 = 0.4200 r_free = 0.4200 target = 0.131261 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.113573 restraints weight = 3598.683| |-----------------------------------------------------------------------------| r_work (start): 0.4014 rms_B_bonded: 2.63 r_work: 0.3873 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3754 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3754 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8486 moved from start: 0.4383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 2920 Z= 0.176 Angle : 0.403 3.454 3900 Z= 0.222 Chirality : 0.051 0.134 390 Planarity : 0.001 0.006 520 Dihedral : 4.354 13.044 390 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 1.79 % Allowed : 20.00 % Favored : 78.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.35 (0.42), residues: 360 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.78 (0.32), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 13 PHE 0.007 0.001 PHE H 4 TYR 0.010 0.001 TYR I 10 ARG 0.001 0.000 ARG G 5 *********************** 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 54 residues out of total 280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 49 time to evaluate : 0.288 Fit side-chains REVERT: A 3 GLU cc_start: 0.8260 (mt-10) cc_final: 0.7728 (tm-30) REVERT: B 3 GLU cc_start: 0.8270 (mt-10) cc_final: 0.7546 (tm-30) REVERT: B 28 LYS cc_start: 0.9071 (mtpp) cc_final: 0.7587 (mmpt) REVERT: C 26 SER cc_start: 0.9382 (OUTLIER) cc_final: 0.9076 (p) REVERT: D 11 GLU cc_start: 0.8212 (tt0) cc_final: 0.7988 (tt0) REVERT: F 3 GLU cc_start: 0.7898 (mt-10) cc_final: 0.7106 (tm-30) REVERT: G 3 GLU cc_start: 0.7882 (mt-10) cc_final: 0.7041 (tm-30) REVERT: G 28 LYS cc_start: 0.8914 (mtpt) cc_final: 0.8689 (mtmt) REVERT: H 28 LYS cc_start: 0.9004 (mtpt) cc_final: 0.8775 (mttt) REVERT: J 26 SER cc_start: 0.9115 (p) cc_final: 0.8608 (p) outliers start: 5 outliers final: 3 residues processed: 54 average time/residue: 1.3549 time to fit residues: 74.8370 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 : 0.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 26 SER Chi-restraints excluded: chain D residue 26 SER Chi-restraints excluded: chain E residue 26 SER Chi-restraints excluded: chain F residue 26 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 13 optimal weight: 10.0000 chunk 27 optimal weight: 10.0000 chunk 15 optimal weight: 20.0000 chunk 26 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 4 optimal weight: 2.9990 chunk 20 optimal weight: 7.9990 chunk 11 optimal weight: 6.9990 chunk 16 optimal weight: 2.9990 chunk 8 optimal weight: 9.9990 chunk 19 optimal weight: 0.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4138 r_free = 0.4138 target = 0.126238 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.108375 restraints weight = 3714.518| |-----------------------------------------------------------------------------| r_work (start): 0.3941 rms_B_bonded: 2.63 r_work: 0.3799 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3675 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3675 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8531 moved from start: 0.4524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 2920 Z= 0.382 Angle : 0.502 4.518 3900 Z= 0.268 Chirality : 0.052 0.132 390 Planarity : 0.002 0.006 520 Dihedral : 4.982 14.052 390 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 2.14 % Allowed : 20.00 % Favored : 77.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.33 (0.42), residues: 360 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.76 (0.32), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS C 14 PHE 0.011 0.002 PHE J 4 TYR 0.007 0.002 TYR J 10 ARG 0.002 0.001 ARG H 5 ********************** 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 50 residues out of total 280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 44 time to evaluate : 0.290 Fit side-chains REVERT: A 3 GLU cc_start: 0.8313 (mt-10) cc_final: 0.7712 (tm-30) REVERT: B 3 GLU cc_start: 0.8334 (mt-10) cc_final: 0.7563 (tm-30) REVERT: C 26 SER cc_start: 0.9418 (OUTLIER) cc_final: 0.9110 (p) REVERT: D 11 GLU cc_start: 0.8279 (tt0) cc_final: 0.7937 (tt0) REVERT: F 3 GLU cc_start: 0.7937 (mt-10) cc_final: 0.7038 (tm-30) REVERT: F 5 ARG cc_start: 0.7861 (OUTLIER) cc_final: 0.7165 (tmt90) REVERT: G 3 GLU cc_start: 0.7979 (mt-10) cc_final: 0.7141 (tm-30) REVERT: G 28 LYS cc_start: 0.9018 (mtpt) cc_final: 0.8787 (mtmt) REVERT: H 28 LYS cc_start: 0.9080 (mtpt) cc_final: 0.8746 (mttt) REVERT: J 26 SER cc_start: 0.9153 (p) cc_final: 0.8671 (p) outliers start: 6 outliers final: 3 residues processed: 49 average time/residue: 1.3235 time to fit residues: 66.4442 Evaluate side-chains 49 residues out of total 280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 44 time to evaluate : 0.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 26 SER Chi-restraints excluded: chain D residue 26 SER Chi-restraints excluded: chain E residue 26 SER Chi-restraints excluded: chain F residue 5 ARG Chi-restraints excluded: chain F residue 26 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 26 optimal weight: 0.3980 chunk 10 optimal weight: 7.9990 chunk 13 optimal weight: 6.9990 chunk 25 optimal weight: 0.6980 chunk 7 optimal weight: 1.9990 chunk 14 optimal weight: 4.9990 chunk 21 optimal weight: 9.9990 chunk 24 optimal weight: 0.7980 chunk 3 optimal weight: 0.8980 chunk 29 optimal weight: 1.9990 chunk 20 optimal weight: 8.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 13 HIS I 13 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4218 r_free = 0.4218 target = 0.132517 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.114927 restraints weight = 3582.228| |-----------------------------------------------------------------------------| r_work (start): 0.4039 rms_B_bonded: 2.64 r_work: 0.3895 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3775 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3775 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8471 moved from start: 0.4459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 2920 Z= 0.138 Angle : 0.391 3.497 3900 Z= 0.218 Chirality : 0.051 0.132 390 Planarity : 0.001 0.009 520 Dihedral : 4.225 13.036 390 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 1.07 % Allowed : 22.50 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.36 (0.41), residues: 360 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.79 (0.31), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS B 13 PHE 0.007 0.001 PHE H 4 TYR 0.012 0.001 TYR I 10 ARG 0.002 0.000 ARG B 5 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2382.91 seconds wall clock time: 41 minutes 28.26 seconds (2488.26 seconds total)