Starting phenix.real_space_refine on Mon Feb 10 21:42:21 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8bfa_16018/02_2025/8bfa_16018.cif Found real_map, /net/cci-nas-00/data/ceres_data/8bfa_16018/02_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_16018/02_2025/8bfa_16018.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8bfa_16018/02_2025/8bfa_16018.map" model { file = "/net/cci-nas-00/data/ceres_data/8bfa_16018/02_2025/8bfa_16018.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8bfa_16018/02_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-5592/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: 2.94, per 1000 atoms: 1.03 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: 0.69 Conformation dependent library (CDL) restraints added in 362.6 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: 0.53 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: 0.77 Time building geometry restraints manager: 0.81 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: 1.220 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: 0.090 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 13.590 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:13.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.110 ------------------------------------------------------------------------------- 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 : 0.327 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: 1.3652 time to fit residues: 69.8887 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 : 0.321 ------------------------------------------------------------------------------- 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 = 34)----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.106858 restraints weight = 3758.585| |-----------------------------------------------------------------------------| 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 : 0.334 Fit side-chains REVERT: A 1 ASP cc_start: 0.6955 (m-30) cc_final: 0.6548 (t0) REVERT: B 1 ASP cc_start: 0.7020 (m-30) cc_final: 0.6452 (t0) REVERT: B 28 LYS cc_start: 0.9160 (OUTLIER) cc_final: 0.8813 (mtpt) REVERT: C 1 ASP cc_start: 0.6672 (m-30) cc_final: 0.5859 (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: 0.8674 (mtpt) REVERT: D 1 ASP cc_start: 0.6729 (m-30) cc_final: 0.5890 (t0) REVERT: E 1 ASP cc_start: 0.6940 (m-30) cc_final: 0.5860 (t0) REVERT: F 1 ASP cc_start: 0.6808 (m-30) cc_final: 0.5884 (t0) REVERT: F 5 ARG cc_start: 0.7521 (mtp180) cc_final: 0.7076 (ttt90) REVERT: G 1 ASP cc_start: 0.7012 (m-30) cc_final: 0.6068 (t0) REVERT: G 5 ARG cc_start: 0.7305 (mtp180) cc_final: 0.6991 (tmt90) REVERT: H 1 ASP cc_start: 0.6813 (m-30) cc_final: 0.5883 (t0) REVERT: I 1 ASP cc_start: 0.7187 (m-30) cc_final: 0.6226 (t0) REVERT: J 1 ASP cc_start: 0.6990 (m-30) cc_final: 0.6004 (t0) outliers start: 24 outliers final: 10 residues processed: 63 average time/residue: 1.4015 time to fit residues: 90.3327 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 : 0.321 ------------------------------------------------------------------------------- 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: 0.9990 chunk 16 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 9 optimal weight: 10.0000 chunk 11 optimal weight: 0.8980 chunk 28 optimal weight: 4.9990 chunk 12 optimal weight: 10.0000 chunk 8 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 27 optimal weight: 0.2980 chunk 1 optimal weight: 3.9990 overall best weight: 1.2386 ------------------------------------------------------------------------------- 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 = 0.4181 r_free = 0.4181 target = 0.133112 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.115248 restraints weight = 3604.081| |-----------------------------------------------------------------------------| r_work (start): 0.3979 rms_B_bonded: 2.72 r_work: 0.3837 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3724 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3724 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8445 moved from start: 0.3260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 2920 Z= 0.162 Angle : 0.369 2.828 3900 Z= 0.212 Chirality : 0.051 0.129 390 Planarity : 0.001 0.005 520 Dihedral : 4.117 11.390 390 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 4.49 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: -2.68 (0.39), 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 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 D 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 : 0.342 Fit side-chains REVERT: A 5 ARG cc_start: 0.7910 (mtp180) cc_final: 0.7651 (tmt90) REVERT: B 1 ASP cc_start: 0.6812 (m-30) cc_final: 0.6357 (t0) REVERT: B 5 ARG cc_start: 0.7956 (mtp180) cc_final: 0.7661 (tmt90) REVERT: B 35 MET cc_start: 0.8165 (OUTLIER) cc_final: 0.7926 (ttp) REVERT: C 1 ASP cc_start: 0.6403 (m-30) cc_final: 0.5861 (t0) REVERT: C 5 ARG cc_start: 0.7359 (mtp180) cc_final: 0.6890 (tmt90) REVERT: D 1 ASP cc_start: 0.6499 (m-30) cc_final: 0.5782 (t0) REVERT: D 11 GLU cc_start: 0.8310 (tt0) cc_final: 0.7836 (tt0) REVERT: F 1 ASP cc_start: 0.6526 (m-30) cc_final: 0.5761 (t0) REVERT: F 5 ARG cc_start: 0.7471 (mtp180) cc_final: 0.7072 (tmt90) REVERT: G 1 ASP cc_start: 0.6523 (m-30) cc_final: 0.5916 (t0) REVERT: G 5 ARG cc_start: 0.7376 (mtp180) cc_final: 0.7075 (tmt90) REVERT: H 1 ASP cc_start: 0.6656 (m-30) cc_final: 0.5855 (t0) outliers start: 11 outliers final: 6 residues processed: 54 average time/residue: 1.5390 time to fit residues: 85.0693 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 : 0.325 ------------------------------------------------------------------------------- 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: 3.9990 chunk 19 optimal weight: 10.0000 chunk 2 optimal weight: 8.9990 chunk 12 optimal weight: 20.0000 chunk 14 optimal weight: 8.9990 chunk 29 optimal weight: 5.9990 chunk 13 optimal weight: 6.9990 chunk 16 optimal weight: 1.9990 chunk 15 optimal weight: 9.9990 chunk 5 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 overall best weight: 5.5990 ------------------------------------------------------------------------------- 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 = 0.4113 r_free = 0.4113 target = 0.126978 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.108498 restraints weight = 3731.172| |-----------------------------------------------------------------------------| r_work (start): 0.3895 rms_B_bonded: 2.71 r_work: 0.3752 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3638 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3638 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8539 moved from start: 0.3915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.045 2920 Z= 0.538 Angle : 0.575 5.179 3900 Z= 0.310 Chirality : 0.054 0.133 390 Planarity : 0.002 0.006 520 Dihedral : 5.348 14.415 390 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 5.36 % Allowed : 15.71 % Favored : 78.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -2.63 (0.40), residues: 360 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.00 (0.31), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS D 14 PHE 0.014 0.002 PHE D 4 TYR 0.008 0.002 TYR C 10 ARG 0.002 0.001 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 59 residues out of total 280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 44 time to evaluate : 0.336 Fit side-chains REVERT: A 1 ASP cc_start: 0.6993 (m-30) cc_final: 0.6490 (t0) REVERT: A 3 GLU cc_start: 0.8159 (mt-10) cc_final: 0.7733 (tm-30) REVERT: B 1 ASP cc_start: 0.7040 (m-30) cc_final: 0.6507 (t0) REVERT: B 3 GLU cc_start: 0.8282 (mt-10) cc_final: 0.7762 (tm-30) REVERT: D 1 ASP cc_start: 0.6742 (m-30) cc_final: 0.5841 (t0) REVERT: F 1 ASP cc_start: 0.6911 (m-30) cc_final: 0.5965 (t0) REVERT: F 3 GLU cc_start: 0.7853 (mt-10) cc_final: 0.6807 (tm-30) REVERT: F 28 LYS cc_start: 0.8940 (mtpt) cc_final: 0.8736 (mttt) REVERT: G 1 ASP cc_start: 0.7071 (m-30) cc_final: 0.6241 (t0) REVERT: G 3 GLU cc_start: 0.7781 (mt-10) cc_final: 0.7085 (tm-30) REVERT: G 28 LYS cc_start: 0.8979 (mtpt) cc_final: 0.8701 (mttt) REVERT: H 1 ASP cc_start: 0.6894 (m-30) cc_final: 0.5996 (t0) REVERT: I 1 ASP cc_start: 0.7234 (m-30) cc_final: 0.6167 (t0) outliers start: 15 outliers final: 5 residues processed: 58 average time/residue: 1.4394 time to fit residues: 85.3611 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 : 0.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 26 SER Chi-restraints excluded: chain E 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: 9.9990 chunk 9 optimal weight: 9.9990 chunk 14 optimal weight: 0.9980 chunk 8 optimal weight: 4.9990 chunk 11 optimal weight: 6.9990 chunk 12 optimal weight: 10.0000 chunk 3 optimal weight: 6.9990 chunk 22 optimal weight: 0.9980 chunk 10 optimal weight: 4.9990 chunk 2 optimal weight: 0.9980 chunk 24 optimal weight: 4.9990 overall best weight: 2.5984 ------------------------------------------------------------------------------- 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 = 0.4170 r_free = 0.4170 target = 0.127941 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.109580 restraints weight = 3633.731| |-----------------------------------------------------------------------------| r_work (start): 0.3970 rms_B_bonded: 2.69 r_work: 0.3825 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3705 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3705 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8515 moved from start: 0.4041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 2920 Z= 0.287 Angle : 0.455 4.046 3900 Z= 0.247 Chirality : 0.052 0.138 390 Planarity : 0.002 0.006 520 Dihedral : 4.772 12.820 390 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 2.86 % Allowed : 18.21 % Favored : 78.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -2.53 (0.41), residues: 360 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.92 (0.31), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS E 14 PHE 0.009 0.002 PHE D 4 TYR 0.007 0.001 TYR G 10 ARG 0.001 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 53 residues out of total 280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 45 time to evaluate : 0.297 Fit side-chains REVERT: A 3 GLU cc_start: 0.8134 (mt-10) cc_final: 0.7720 (tm-30) REVERT: B 3 GLU cc_start: 0.8258 (mt-10) cc_final: 0.7747 (tm-30) REVERT: C 5 ARG cc_start: 0.7310 (mtp180) cc_final: 0.6871 (tmt90) REVERT: D 26 SER cc_start: 0.9368 (OUTLIER) cc_final: 0.9023 (p) REVERT: E 11 GLU cc_start: 0.8477 (tt0) cc_final: 0.8101 (tt0) REVERT: F 3 GLU cc_start: 0.7860 (mt-10) cc_final: 0.7017 (tm-30) REVERT: F 5 ARG cc_start: 0.7735 (OUTLIER) cc_final: 0.7220 (tmt90) REVERT: G 3 GLU cc_start: 0.7799 (mt-10) cc_final: 0.6915 (tm-30) REVERT: G 28 LYS cc_start: 0.9002 (mtpt) cc_final: 0.8727 (mttt) REVERT: H 28 LYS cc_start: 0.9011 (mtpt) cc_final: 0.8764 (mttt) outliers start: 8 outliers final: 5 residues processed: 51 average time/residue: 1.6689 time to fit residues: 86.8137 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 : 0.334 ------------------------------------------------------------------------------- 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 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=3.00 ------------------------------------------------------------------------------- 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: 0.9980 chunk 0 optimal weight: 10.0000 chunk 15 optimal weight: 9.9990 chunk 16 optimal weight: 6.9990 chunk 17 optimal weight: 7.9990 chunk 13 optimal weight: 0.9980 chunk 25 optimal weight: 2.9990 chunk 21 optimal weight: 10.0000 chunk 24 optimal weight: 0.0980 overall best weight: 2.4184 ------------------------------------------------------------------------------- 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 = 0.4178 r_free = 0.4178 target = 0.128645 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.110331 restraints weight = 3625.176| |-----------------------------------------------------------------------------| r_work (start): 0.3968 rms_B_bonded: 2.67 r_work: 0.3831 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3716 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3716 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8518 moved from start: 0.4185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 2920 Z= 0.260 Angle : 0.441 4.136 3900 Z= 0.237 Chirality : 0.052 0.133 390 Planarity : 0.001 0.006 520 Dihedral : 4.604 13.104 390 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 2.86 % Allowed : 20.36 % 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 (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: -2.49 (0.41), residues: 360 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.89 (0.31), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 13 PHE 0.009 0.001 PHE H 4 TYR 0.008 0.001 TYR H 10 ARG 0.001 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 54 residues out of total 280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 46 time to evaluate : 0.302 Fit side-chains REVERT: A 3 GLU cc_start: 0.8129 (mt-10) cc_final: 0.7750 (tm-30) REVERT: B 3 GLU cc_start: 0.8257 (mt-10) cc_final: 0.7585 (tm-30) REVERT: C 5 ARG cc_start: 0.7315 (mtp180) cc_final: 0.6862 (tmt90) REVERT: F 3 GLU cc_start: 0.7895 (mt-10) cc_final: 0.7085 (tm-30) REVERT: G 3 GLU cc_start: 0.7752 (mt-10) cc_final: 0.6895 (tm-30) REVERT: G 28 LYS cc_start: 0.8964 (mtpt) cc_final: 0.8712 (mttt) REVERT: H 28 LYS cc_start: 0.9008 (OUTLIER) cc_final: 0.8736 (mttt) REVERT: J 1 ASP cc_start: 0.7041 (m-30) cc_final: 0.6771 (m-30) REVERT: J 26 SER cc_start: 0.9204 (OUTLIER) cc_final: 0.8691 (p) outliers start: 8 outliers final: 3 residues processed: 52 average time/residue: 1.5888 time to fit residues: 84.3375 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 : 0.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 20 optimal weight: 3.9990 chunk 28 optimal weight: 2.9990 chunk 4 optimal weight: 5.9990 chunk 13 optimal weight: 9.9990 chunk 16 optimal weight: 8.9990 chunk 8 optimal weight: 8.9990 chunk 3 optimal weight: 10.0000 chunk 23 optimal weight: 10.0000 chunk 14 optimal weight: 0.9980 chunk 18 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 overall best weight: 4.5988 ------------------------------------------------------------------------------- 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 = 0.4117 r_free = 0.4117 target = 0.125072 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.107127 restraints weight = 3711.538| |-----------------------------------------------------------------------------| r_work (start): 0.3918 rms_B_bonded: 2.63 r_work: 0.3773 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3655 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3655 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8547 moved from start: 0.4415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.043 2920 Z= 0.463 Angle : 0.538 5.202 3900 Z= 0.288 Chirality : 0.053 0.133 390 Planarity : 0.002 0.010 520 Dihedral : 5.193 13.813 390 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 3.57 % Allowed : 18.93 % 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: -2.43 (0.42), residues: 360 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.84 (0.32), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS D 13 PHE 0.013 0.002 PHE D 4 TYR 0.006 0.002 TYR C 10 ARG 0.002 0.001 ARG E 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 52 residues out of total 280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 42 time to evaluate : 0.331 Fit side-chains REVERT: A 3 GLU cc_start: 0.8256 (mt-10) cc_final: 0.7698 (tm-30) REVERT: B 3 GLU cc_start: 0.8358 (mt-10) cc_final: 0.7620 (tm-30) REVERT: F 3 GLU cc_start: 0.7962 (mt-10) cc_final: 0.7102 (tm-30) REVERT: G 3 GLU cc_start: 0.7954 (mt-10) cc_final: 0.7071 (tm-30) REVERT: G 28 LYS cc_start: 0.9024 (mtpt) cc_final: 0.8806 (mttt) REVERT: H 28 LYS cc_start: 0.9044 (OUTLIER) cc_final: 0.8752 (mttt) REVERT: J 1 ASP cc_start: 0.7161 (m-30) cc_final: 0.6913 (m-30) outliers start: 10 outliers final: 5 residues processed: 50 average time/residue: 1.3791 time to fit residues: 70.6038 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 : 0.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D 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 Chi-restraints excluded: chain J residue 28 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 7 optimal weight: 2.9990 chunk 23 optimal weight: 4.9990 chunk 20 optimal weight: 5.9990 chunk 19 optimal weight: 0.9990 chunk 29 optimal weight: 1.9990 chunk 18 optimal weight: 9.9990 chunk 2 optimal weight: 6.9990 chunk 13 optimal weight: 5.9990 chunk 24 optimal weight: 7.9990 chunk 14 optimal weight: 0.9980 chunk 8 optimal weight: 2.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- 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 = 0.4173 r_free = 0.4173 target = 0.129001 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.111088 restraints weight = 3675.315| |-----------------------------------------------------------------------------| r_work (start): 0.3972 rms_B_bonded: 2.65 r_work: 0.3838 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3719 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3719 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8512 moved from start: 0.4327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 2920 Z= 0.229 Angle : 0.426 3.723 3900 Z= 0.233 Chirality : 0.051 0.134 390 Planarity : 0.001 0.007 520 Dihedral : 4.565 13.220 390 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % 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 (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 0.004 0.001 HIS D 13 PHE 0.008 0.001 PHE J 4 TYR 0.008 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 52 residues out of total 280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 45 time to evaluate : 0.314 Fit side-chains REVERT: A 3 GLU cc_start: 0.8210 (mt-10) cc_final: 0.7721 (tm-30) REVERT: B 3 GLU cc_start: 0.8322 (mt-10) cc_final: 0.7566 (tm-30) REVERT: B 28 LYS cc_start: 0.9065 (mtpp) cc_final: 0.7571 (mmpt) REVERT: D 26 SER cc_start: 0.9368 (OUTLIER) cc_final: 0.8999 (p) REVERT: F 3 GLU cc_start: 0.7921 (mt-10) cc_final: 0.7110 (tm-30) REVERT: G 3 GLU cc_start: 0.7894 (mt-10) cc_final: 0.6974 (tm-30) REVERT: G 28 LYS cc_start: 0.9043 (mtpt) cc_final: 0.8820 (mttt) REVERT: H 28 LYS cc_start: 0.9000 (OUTLIER) cc_final: 0.8745 (mttt) REVERT: J 26 SER cc_start: 0.9158 (p) cc_final: 0.8656 (p) outliers start: 7 outliers final: 3 residues processed: 50 average time/residue: 1.5424 time to fit residues: 78.7604 Evaluate side-chains 48 residues out of total 280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 43 time to evaluate : 0.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 26 SER Chi-restraints excluded: chain E 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 5 optimal weight: 7.9990 chunk 22 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 23 optimal weight: 1.9990 chunk 11 optimal weight: 3.9990 chunk 8 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 7 optimal weight: 1.9990 chunk 10 optimal weight: 0.8980 chunk 1 optimal weight: 0.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 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 = 0.4194 r_free = 0.4194 target = 0.130691 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.113213 restraints weight = 3608.726| |-----------------------------------------------------------------------------| r_work (start): 0.4011 rms_B_bonded: 2.62 r_work: 0.3863 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3745 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3745 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8490 moved from start: 0.4401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 2920 Z= 0.188 Angle : 0.400 3.272 3900 Z= 0.220 Chirality : 0.051 0.134 390 Planarity : 0.001 0.006 520 Dihedral : 4.291 13.113 390 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 1.43 % Allowed : 21.07 % 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: -2.35 (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 HIS 0.004 0.001 HIS D 13 PHE 0.007 0.001 PHE H 4 TYR 0.010 0.001 TYR I 10 ARG 0.002 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 52 residues out of total 280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 48 time to evaluate : 0.273 Fit side-chains REVERT: A 3 GLU cc_start: 0.8230 (mt-10) cc_final: 0.7755 (tm-30) REVERT: B 3 GLU cc_start: 0.8302 (mt-10) cc_final: 0.7537 (tm-30) REVERT: B 28 LYS cc_start: 0.9001 (mtpp) cc_final: 0.7511 (mmtt) REVERT: F 3 GLU cc_start: 0.7874 (mt-10) cc_final: 0.7072 (tm-30) REVERT: G 3 GLU cc_start: 0.7867 (mt-10) cc_final: 0.7055 (tm-30) REVERT: G 28 LYS cc_start: 0.9038 (mtpt) cc_final: 0.8772 (mttt) REVERT: H 28 LYS cc_start: 0.9026 (OUTLIER) cc_final: 0.8755 (mttt) REVERT: J 26 SER cc_start: 0.9097 (OUTLIER) cc_final: 0.8590 (p) outliers start: 4 outliers final: 1 residues processed: 50 average time/residue: 1.4725 time to fit residues: 75.2228 Evaluate side-chains 50 residues out of total 280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 47 time to evaluate : 0.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 26 SER Chi-restraints excluded: chain H residue 28 LYS 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 13 optimal weight: 0.9990 chunk 27 optimal weight: 0.7980 chunk 15 optimal weight: 9.9990 chunk 26 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 4 optimal weight: 4.9990 chunk 20 optimal weight: 8.9990 chunk 11 optimal weight: 0.7980 chunk 16 optimal weight: 1.9990 chunk 8 optimal weight: 9.9990 chunk 19 optimal weight: 3.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 13 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4190 r_free = 0.4190 target = 0.130303 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.112706 restraints weight = 3634.702| |-----------------------------------------------------------------------------| r_work (start): 0.3999 rms_B_bonded: 2.61 r_work: 0.3857 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3738 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3738 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8498 moved from start: 0.4395 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= 0.204 Angle : 0.408 3.561 3900 Z= 0.223 Chirality : 0.051 0.134 390 Planarity : 0.001 0.007 520 Dihedral : 4.261 12.653 390 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 1.07 % Allowed : 21.79 % 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: -2.33 (0.42), residues: 360 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.77 (0.32), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS E 13 PHE 0.008 0.001 PHE H 4 TYR 0.009 0.001 TYR J 10 ARG 0.001 0.000 ARG B 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 49 residues out of total 280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 46 time to evaluate : 0.309 Fit side-chains REVERT: A 3 GLU cc_start: 0.8205 (mt-10) cc_final: 0.7723 (tm-30) REVERT: B 3 GLU cc_start: 0.8292 (mt-10) cc_final: 0.7544 (tm-30) REVERT: C 26 SER cc_start: 0.9378 (OUTLIER) cc_final: 0.9086 (p) REVERT: E 11 GLU cc_start: 0.8677 (tt0) cc_final: 0.8392 (tt0) REVERT: F 3 GLU cc_start: 0.7884 (mt-10) cc_final: 0.7094 (tm-30) REVERT: G 3 GLU cc_start: 0.7863 (mt-10) cc_final: 0.7057 (tm-30) REVERT: G 28 LYS cc_start: 0.9066 (mtpt) cc_final: 0.8790 (mttt) REVERT: H 28 LYS cc_start: 0.9088 (mtpt) cc_final: 0.8849 (mttt) REVERT: J 26 SER cc_start: 0.9127 (p) cc_final: 0.8615 (p) outliers start: 3 outliers final: 2 residues processed: 49 average time/residue: 1.3238 time to fit residues: 66.4734 Evaluate side-chains 49 residues out of total 280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 46 time to evaluate : 0.290 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 26 optimal weight: 8.9990 chunk 10 optimal weight: 0.0170 chunk 13 optimal weight: 7.9990 chunk 25 optimal weight: 4.9990 chunk 7 optimal weight: 5.9990 chunk 14 optimal weight: 2.9990 chunk 21 optimal weight: 20.0000 chunk 24 optimal weight: 0.0870 chunk 3 optimal weight: 8.9990 chunk 29 optimal weight: 6.9990 chunk 20 optimal weight: 6.9990 overall best weight: 2.8202 ------------------------------------------------------------------------------- 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 = 0.4155 r_free = 0.4155 target = 0.127899 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.110041 restraints weight = 3618.607| |-----------------------------------------------------------------------------| r_work (start): 0.3959 rms_B_bonded: 2.61 r_work: 0.3813 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3696 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3696 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8520 moved from start: 0.4522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 2920 Z= 0.307 Angle : 0.454 3.968 3900 Z= 0.245 Chirality : 0.051 0.132 390 Planarity : 0.002 0.007 520 Dihedral : 4.614 13.195 390 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 1.43 % Allowed : 22.14 % 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: -2.30 (0.42), residues: 360 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.74 (0.32), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS E 13 PHE 0.010 0.002 PHE J 4 TYR 0.008 0.002 TYR I 10 ARG 0.001 0.000 ARG G 5 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2373.94 seconds wall clock time: 42 minutes 57.20 seconds (2577.20 seconds total)