Starting phenix.real_space_refine on Wed Sep 17 04:32:11 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9fh1_50436/09_2025/9fh1_50436.cif Found real_map, /net/cci-nas-00/data/ceres_data/9fh1_50436/09_2025/9fh1_50436.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9fh1_50436/09_2025/9fh1_50436.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9fh1_50436/09_2025/9fh1_50436.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9fh1_50436/09_2025/9fh1_50436.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9fh1_50436/09_2025/9fh1_50436.map" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.010 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: 5 Type Number sf(0) Gaussians S 10 5.16 5 C 1310 2.51 5 N 370 2.21 5 O 360 1.98 5 H 2160 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 4210 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 421 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 421 Classifications: {'peptide': 29} Link IDs: {'TRANS': 28} Chain: "B" Number of atoms: 421 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 421 Classifications: {'peptide': 29} Link IDs: {'TRANS': 28} Chain: "C" Number of atoms: 421 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 421 Classifications: {'peptide': 29} Link IDs: {'TRANS': 28} Chain: "D" Number of atoms: 421 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 421 Classifications: {'peptide': 29} Link IDs: {'TRANS': 28} Chain: "E" Number of atoms: 421 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 421 Classifications: {'peptide': 29} Link IDs: {'TRANS': 28} Chain: "F" Number of atoms: 421 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 421 Classifications: {'peptide': 29} Link IDs: {'TRANS': 28} Chain: "G" Number of atoms: 421 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 421 Classifications: {'peptide': 29} Link IDs: {'TRANS': 28} Chain: "H" Number of atoms: 421 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 421 Classifications: {'peptide': 29} Link IDs: {'TRANS': 28} Chain: "I" Number of atoms: 421 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 421 Classifications: {'peptide': 29} Link IDs: {'TRANS': 28} Chain: "J" Number of atoms: 421 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 421 Classifications: {'peptide': 29} Link IDs: {'TRANS': 28} Time building chain proxies: 0.97, per 1000 atoms: 0.23 Number of scatterers: 4210 At special positions: 0 Unit cell: (53.328, 88.072, 46.056, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 10 16.00 O 360 8.00 N 370 7.00 C 1310 6.00 H 2160 1.00 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: 0.33 Conformation dependent library (CDL) restraints added in 96.1 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 540 Ramachandran restraints generated. 270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 460 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 8 sheets defined 0.0% alpha, 51.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.08 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 16 through 19 Processing sheet with id=AA2, first strand: chain 'A' and resid 22 through 27 removed outlier: 6.423A pdb=" N LYS A 22 " --> pdb=" O LEU C 23 " (cutoff:3.500A) removed outlier: 8.144A pdb=" N GLY C 25 " --> pdb=" O LYS A 22 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N VAL A 24 " --> pdb=" O GLY C 25 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N ASN C 27 " --> pdb=" O VAL A 24 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N SER A 26 " --> pdb=" O ASN C 27 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N LYS C 22 " --> pdb=" O LEU E 23 " (cutoff:3.500A) removed outlier: 8.089A pdb=" N GLY E 25 " --> pdb=" O LYS C 22 " (cutoff:3.500A) removed outlier: 6.012A pdb=" N VAL C 24 " --> pdb=" O GLY E 25 " (cutoff:3.500A) removed outlier: 7.155A pdb=" N ASN E 27 " --> pdb=" O VAL C 24 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N SER C 26 " --> pdb=" O ASN E 27 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N LYS E 22 " --> pdb=" O LEU G 23 " (cutoff:3.500A) removed outlier: 8.152A pdb=" N GLY G 25 " --> pdb=" O LYS E 22 " (cutoff:3.500A) removed outlier: 6.032A pdb=" N VAL E 24 " --> pdb=" O GLY G 25 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N ASN G 27 " --> pdb=" O VAL E 24 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N SER E 26 " --> pdb=" O ASN G 27 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N LYS G 22 " --> pdb=" O LEU I 23 " (cutoff:3.500A) removed outlier: 8.133A pdb=" N GLY I 25 " --> pdb=" O LYS G 22 " (cutoff:3.500A) removed outlier: 6.037A pdb=" N VAL G 24 " --> pdb=" O GLY I 25 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N ASN I 27 " --> pdb=" O VAL G 24 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N SER G 26 " --> pdb=" O ASN I 27 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 30 through 35 removed outlier: 6.402A pdb=" N ALA A 30 " --> pdb=" O ILE C 31 " (cutoff:3.500A) removed outlier: 8.078A pdb=" N GLY C 33 " --> pdb=" O ALA A 30 " (cutoff:3.500A) removed outlier: 8.822A pdb=" N ILE A 32 " --> pdb=" O GLY C 33 " (cutoff:3.500A) removed outlier: 7.295A pdb=" N MET C 35 " --> pdb=" O ILE A 32 " (cutoff:3.500A) removed outlier: 9.140A pdb=" N LEU A 34 " --> pdb=" O MET C 35 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N ALA C 30 " --> pdb=" O ILE E 31 " (cutoff:3.500A) removed outlier: 8.036A pdb=" N GLY E 33 " --> pdb=" O ALA C 30 " (cutoff:3.500A) removed outlier: 8.769A pdb=" N ILE C 32 " --> pdb=" O GLY E 33 " (cutoff:3.500A) removed outlier: 7.258A pdb=" N MET E 35 " --> pdb=" O ILE C 32 " (cutoff:3.500A) removed outlier: 9.144A pdb=" N LEU C 34 " --> pdb=" O MET E 35 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N ALA E 30 " --> pdb=" O ILE G 31 " (cutoff:3.500A) removed outlier: 8.016A pdb=" N GLY G 33 " --> pdb=" O ALA E 30 " (cutoff:3.500A) removed outlier: 8.756A pdb=" N ILE E 32 " --> pdb=" O GLY G 33 " (cutoff:3.500A) removed outlier: 7.237A pdb=" N MET G 35 " --> pdb=" O ILE E 32 " (cutoff:3.500A) removed outlier: 9.194A pdb=" N LEU E 34 " --> pdb=" O MET G 35 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N ALA G 30 " --> pdb=" O ILE I 31 " (cutoff:3.500A) removed outlier: 7.996A pdb=" N GLY I 33 " --> pdb=" O ALA G 30 " (cutoff:3.500A) removed outlier: 8.759A pdb=" N ILE G 32 " --> pdb=" O GLY I 33 " (cutoff:3.500A) removed outlier: 7.231A pdb=" N MET I 35 " --> pdb=" O ILE G 32 " (cutoff:3.500A) removed outlier: 9.182A pdb=" N LEU G 34 " --> pdb=" O MET I 35 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 39 through 41 removed outlier: 6.614A pdb=" N VAL A 40 " --> pdb=" O ILE C 41 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N VAL C 40 " --> pdb=" O ILE E 41 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 16 through 19 Processing sheet with id=AA6, first strand: chain 'B' and resid 22 through 27 removed outlier: 6.476A pdb=" N LYS B 22 " --> pdb=" O LEU D 23 " (cutoff:3.500A) removed outlier: 8.187A pdb=" N GLY D 25 " --> pdb=" O LYS B 22 " (cutoff:3.500A) removed outlier: 6.074A pdb=" N VAL B 24 " --> pdb=" O GLY D 25 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N ASN D 27 " --> pdb=" O VAL B 24 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N SER B 26 " --> pdb=" O ASN D 27 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N LYS D 22 " --> pdb=" O LEU F 23 " (cutoff:3.500A) removed outlier: 8.140A pdb=" N GLY F 25 " --> pdb=" O LYS D 22 " (cutoff:3.500A) removed outlier: 6.050A pdb=" N VAL D 24 " --> pdb=" O GLY F 25 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N ASN F 27 " --> pdb=" O VAL D 24 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N SER D 26 " --> pdb=" O ASN F 27 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N LYS F 22 " --> pdb=" O LEU H 23 " (cutoff:3.500A) removed outlier: 8.121A pdb=" N GLY H 25 " --> pdb=" O LYS F 22 " (cutoff:3.500A) removed outlier: 6.026A pdb=" N VAL F 24 " --> pdb=" O GLY H 25 " (cutoff:3.500A) removed outlier: 7.024A pdb=" N ASN H 27 " --> pdb=" O VAL F 24 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N SER F 26 " --> pdb=" O ASN H 27 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N LYS H 22 " --> pdb=" O LEU J 23 " (cutoff:3.500A) removed outlier: 8.132A pdb=" N GLY J 25 " --> pdb=" O LYS H 22 " (cutoff:3.500A) removed outlier: 6.030A pdb=" N VAL H 24 " --> pdb=" O GLY J 25 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N ASN J 27 " --> pdb=" O VAL H 24 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N SER H 26 " --> pdb=" O ASN J 27 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'B' and resid 30 through 35 removed outlier: 6.404A pdb=" N ALA B 30 " --> pdb=" O ILE D 31 " (cutoff:3.500A) removed outlier: 8.055A pdb=" N GLY D 33 " --> pdb=" O ALA B 30 " (cutoff:3.500A) removed outlier: 8.821A pdb=" N ILE B 32 " --> pdb=" O GLY D 33 " (cutoff:3.500A) removed outlier: 7.252A pdb=" N MET D 35 " --> pdb=" O ILE B 32 " (cutoff:3.500A) removed outlier: 9.127A pdb=" N LEU B 34 " --> pdb=" O MET D 35 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N ALA D 30 " --> pdb=" O ILE F 31 " (cutoff:3.500A) removed outlier: 8.027A pdb=" N GLY F 33 " --> pdb=" O ALA D 30 " (cutoff:3.500A) removed outlier: 8.759A pdb=" N ILE D 32 " --> pdb=" O GLY F 33 " (cutoff:3.500A) removed outlier: 7.238A pdb=" N MET F 35 " --> pdb=" O ILE D 32 " (cutoff:3.500A) removed outlier: 9.157A pdb=" N LEU D 34 " --> pdb=" O MET F 35 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N ALA F 30 " --> pdb=" O ILE H 31 " (cutoff:3.500A) removed outlier: 8.020A pdb=" N GLY H 33 " --> pdb=" O ALA F 30 " (cutoff:3.500A) removed outlier: 8.753A pdb=" N ILE F 32 " --> pdb=" O GLY H 33 " (cutoff:3.500A) removed outlier: 7.238A pdb=" N MET H 35 " --> pdb=" O ILE F 32 " (cutoff:3.500A) removed outlier: 9.184A pdb=" N LEU F 34 " --> pdb=" O MET H 35 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N ALA H 30 " --> pdb=" O ILE J 31 " (cutoff:3.500A) removed outlier: 7.987A pdb=" N GLY J 33 " --> pdb=" O ALA H 30 " (cutoff:3.500A) removed outlier: 8.749A pdb=" N ILE H 32 " --> pdb=" O GLY J 33 " (cutoff:3.500A) removed outlier: 7.254A pdb=" N MET J 35 " --> pdb=" O ILE H 32 " (cutoff:3.500A) removed outlier: 9.189A pdb=" N LEU H 34 " --> pdb=" O MET J 35 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'B' and resid 39 through 41 36 hydrogen bonds defined for protein. 108 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: 0.55 Time building geometry restraints manager: 0.46 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.96 - 1.13: 2160 1.13 - 1.30: 330 1.30 - 1.47: 654 1.47 - 1.64: 1066 1.64 - 1.81: 20 Bond restraints: 4230 Sorted by residual: bond pdb=" N GLY I 38 " pdb=" H GLY I 38 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.70e+01 bond pdb=" N VAL G 18 " pdb=" H VAL G 18 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.70e+01 bond pdb=" N VAL I 39 " pdb=" H VAL I 39 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.69e+01 bond pdb=" N ILE A 32 " pdb=" H ILE A 32 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.69e+01 bond pdb=" CD1 TYR A 16 " pdb=" HD1 TYR A 16 " ideal model delta sigma weight residual 0.930 1.081 -0.151 2.00e-02 2.50e+03 5.68e+01 ... (remaining 4225 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.61: 5060 1.61 - 3.22: 1688 3.22 - 4.83: 533 4.83 - 6.44: 308 6.44 - 8.04: 81 Bond angle restraints: 7670 Sorted by residual: angle pdb=" N HIS C 19 " pdb=" CA HIS C 19 " pdb=" C HIS C 19 " ideal model delta sigma weight residual 109.07 116.90 -7.83 1.52e+00 4.33e-01 2.65e+01 angle pdb=" CB HIS B 20 " pdb=" CG HIS B 20 " pdb=" CD2 HIS B 20 " ideal model delta sigma weight residual 131.20 124.79 6.41 1.30e+00 5.92e-01 2.43e+01 angle pdb=" N HIS F 19 " pdb=" CA HIS F 19 " pdb=" C HIS F 19 " ideal model delta sigma weight residual 109.07 116.47 -7.40 1.52e+00 4.33e-01 2.37e+01 angle pdb=" CB HIS A 20 " pdb=" CG HIS A 20 " pdb=" CD2 HIS A 20 " ideal model delta sigma weight residual 131.20 124.91 6.29 1.30e+00 5.92e-01 2.34e+01 angle pdb=" N HIS H 19 " pdb=" CA HIS H 19 " pdb=" C HIS H 19 " ideal model delta sigma weight residual 109.07 116.35 -7.28 1.52e+00 4.33e-01 2.29e+01 ... (remaining 7665 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.98: 1665 13.98 - 27.97: 63 27.97 - 41.95: 39 41.95 - 55.93: 66 55.93 - 69.92: 87 Dihedral angle restraints: 1920 sinusoidal: 1070 harmonic: 850 Sorted by residual: dihedral pdb=" C HIS A 20 " pdb=" N HIS A 20 " pdb=" CA HIS A 20 " pdb=" CB HIS A 20 " ideal model delta harmonic sigma weight residual -122.60 -132.36 9.76 0 2.50e+00 1.60e-01 1.52e+01 dihedral pdb=" C HIS H 20 " pdb=" N HIS H 20 " pdb=" CA HIS H 20 " pdb=" CB HIS H 20 " ideal model delta harmonic sigma weight residual -122.60 -132.29 9.69 0 2.50e+00 1.60e-01 1.50e+01 dihedral pdb=" C HIS F 20 " pdb=" N HIS F 20 " pdb=" CA HIS F 20 " pdb=" CB HIS F 20 " ideal model delta harmonic sigma weight residual -122.60 -132.15 9.55 0 2.50e+00 1.60e-01 1.46e+01 ... (remaining 1917 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.079: 177 0.079 - 0.158: 90 0.158 - 0.237: 50 0.237 - 0.316: 3 0.316 - 0.395: 10 Chirality restraints: 330 Sorted by residual: chirality pdb=" CA HIS H 20 " pdb=" N HIS H 20 " pdb=" C HIS H 20 " pdb=" CB HIS H 20 " both_signs ideal model delta sigma weight residual False 2.51 2.11 0.40 2.00e-01 2.50e+01 3.91e+00 chirality pdb=" CA HIS A 20 " pdb=" N HIS A 20 " pdb=" C HIS A 20 " pdb=" CB HIS A 20 " both_signs ideal model delta sigma weight residual False 2.51 2.12 0.39 2.00e-01 2.50e+01 3.90e+00 chirality pdb=" CA HIS F 20 " pdb=" N HIS F 20 " pdb=" C HIS F 20 " pdb=" CB HIS F 20 " both_signs ideal model delta sigma weight residual False 2.51 2.12 0.39 2.00e-01 2.50e+01 3.78e+00 ... (remaining 327 not shown) Planarity restraints: 620 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB HIS E 19 " -0.019 2.00e-02 2.50e+03 5.59e-02 7.03e+01 pdb=" CG HIS E 19 " 0.087 2.00e-02 2.50e+03 pdb=" ND1 HIS E 19 " 0.077 2.00e-02 2.50e+03 pdb=" CD2 HIS E 19 " 0.009 2.00e-02 2.50e+03 pdb=" CE1 HIS E 19 " 0.034 2.00e-02 2.50e+03 pdb=" NE2 HIS E 19 " -0.019 2.00e-02 2.50e+03 pdb=" HD1 HIS E 19 " -0.098 2.00e-02 2.50e+03 pdb=" HD2 HIS E 19 " -0.054 2.00e-02 2.50e+03 pdb=" HE1 HIS E 19 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS F 19 " 0.026 2.00e-02 2.50e+03 5.51e-02 6.84e+01 pdb=" CG HIS F 19 " -0.087 2.00e-02 2.50e+03 pdb=" ND1 HIS F 19 " -0.078 2.00e-02 2.50e+03 pdb=" CD2 HIS F 19 " -0.011 2.00e-02 2.50e+03 pdb=" CE1 HIS F 19 " -0.033 2.00e-02 2.50e+03 pdb=" NE2 HIS F 19 " 0.020 2.00e-02 2.50e+03 pdb=" HD1 HIS F 19 " 0.092 2.00e-02 2.50e+03 pdb=" HD2 HIS F 19 " 0.051 2.00e-02 2.50e+03 pdb=" HE1 HIS F 19 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS H 19 " 0.032 2.00e-02 2.50e+03 5.48e-02 6.77e+01 pdb=" CG HIS H 19 " -0.088 2.00e-02 2.50e+03 pdb=" ND1 HIS H 19 " -0.080 2.00e-02 2.50e+03 pdb=" CD2 HIS H 19 " -0.013 2.00e-02 2.50e+03 pdb=" CE1 HIS H 19 " -0.031 2.00e-02 2.50e+03 pdb=" NE2 HIS H 19 " 0.020 2.00e-02 2.50e+03 pdb=" HD1 HIS H 19 " 0.086 2.00e-02 2.50e+03 pdb=" HD2 HIS H 19 " 0.048 2.00e-02 2.50e+03 pdb=" HE1 HIS H 19 " 0.025 2.00e-02 2.50e+03 ... (remaining 617 not shown) Histogram of nonbonded interaction distances: 1.79 - 2.35: 889 2.35 - 2.91: 9250 2.91 - 3.47: 10979 3.47 - 4.04: 15005 4.04 - 4.60: 20599 Nonbonded interactions: 56722 Sorted by model distance: nonbonded pdb=" O MET C 35 " pdb=" H VAL E 36 " model vdw 1.786 2.450 nonbonded pdb=" O MET D 35 " pdb=" H VAL F 36 " model vdw 1.795 2.450 nonbonded pdb=" OD1 ASN E 27 " pdb="HD21 ASN G 27 " model vdw 1.796 2.450 nonbonded pdb=" O SER D 26 " pdb=" H ASN F 27 " model vdw 1.797 2.450 nonbonded pdb=" OD1 ASN F 27 " pdb="HD21 ASN H 27 " model vdw 1.799 2.450 ... (remaining 56717 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.780 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: 0.030 Extract box with map and model: 0.060 Check model and map are aligned: 0.010 Set scattering table: 0.000 Process input model: 5.490 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.000 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:1.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 8.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7435 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 : 0.010 0.031 2070 Z= 0.702 Angle : 2.048 7.857 2770 Z= 1.391 Chirality : 0.122 0.395 330 Planarity : 0.009 0.038 340 Dihedral : 13.806 69.916 710 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 0.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.37 % Favored : 99.63 % Rotamer: Outliers : 4.76 % Allowed : 4.29 % Favored : 90.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.96 (0.37), residues: 270 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.25 (0.28), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.035 0.009 TYR J 16 HIS 0.011 0.005 HIS B 19 Details of bonding type rmsd covalent geometry : bond 0.01004 ( 2070) covalent geometry : angle 2.04842 ( 2770) hydrogen bonds : bond 0.23989 ( 36) hydrogen bonds : angle 7.20566 ( 108) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 540 Ramachandran restraints generated. 270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 540 Ramachandran restraints generated. 270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 75 time to evaluate : 0.103 Fit side-chains REVERT: A 17 GLU cc_start: 0.7972 (pt0) cc_final: 0.7407 (pt0) REVERT: A 26 SER cc_start: 0.7971 (m) cc_final: 0.7080 (p) REVERT: B 17 GLU cc_start: 0.8004 (pt0) cc_final: 0.7609 (pt0) REVERT: B 26 SER cc_start: 0.7969 (m) cc_final: 0.7158 (p) REVERT: C 17 GLU cc_start: 0.7605 (pt0) cc_final: 0.7069 (pt0) REVERT: C 26 SER cc_start: 0.7658 (m) cc_final: 0.7249 (t) REVERT: D 17 GLU cc_start: 0.7659 (pt0) cc_final: 0.7158 (pt0) REVERT: D 26 SER cc_start: 0.7632 (m) cc_final: 0.6738 (p) REVERT: E 17 GLU cc_start: 0.7732 (pt0) cc_final: 0.6880 (pt0) REVERT: E 26 SER cc_start: 0.7618 (m) cc_final: 0.6706 (p) REVERT: F 17 GLU cc_start: 0.7540 (pt0) cc_final: 0.6856 (pt0) REVERT: F 26 SER cc_start: 0.7706 (m) cc_final: 0.6914 (t) REVERT: F 34 LEU cc_start: 0.7918 (OUTLIER) cc_final: 0.7548 (tt) REVERT: G 17 GLU cc_start: 0.7438 (pt0) cc_final: 0.6798 (pt0) REVERT: G 26 SER cc_start: 0.7749 (m) cc_final: 0.7004 (t) REVERT: G 34 LEU cc_start: 0.7960 (OUTLIER) cc_final: 0.7727 (tt) REVERT: H 17 GLU cc_start: 0.7580 (pt0) cc_final: 0.6953 (pt0) REVERT: H 26 SER cc_start: 0.7703 (m) cc_final: 0.7066 (t) REVERT: I 17 GLU cc_start: 0.8151 (pt0) cc_final: 0.7676 (pt0) REVERT: J 17 GLU cc_start: 0.8091 (pt0) cc_final: 0.7693 (pt0) REVERT: J 34 LEU cc_start: 0.7948 (OUTLIER) cc_final: 0.7532 (tt) outliers start: 10 outliers final: 0 residues processed: 85 average time/residue: 0.0864 time to fit residues: 8.9577 Evaluate side-chains 62 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 59 time to evaluate : 0.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 34 LEU Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain J residue 34 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 12 optimal weight: 2.9990 chunk 13 optimal weight: 0.9990 chunk 1 optimal weight: 0.7980 chunk 8 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 15 optimal weight: 0.9990 chunk 9 optimal weight: 0.9980 chunk 11 optimal weight: 0.9980 chunk 18 optimal weight: 0.9990 chunk 6 optimal weight: 3.9990 chunk 4 optimal weight: 2.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- 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 = 0.3763 r_free = 0.3763 target = 0.128101 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.104468 restraints weight = 7398.188| |-----------------------------------------------------------------------------| r_work (start): 0.3517 rms_B_bonded: 2.53 r_work: 0.3409 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3286 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3286 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8474 moved from start: 0.2922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 2070 Z= 0.146 Angle : 0.741 5.320 2770 Z= 0.444 Chirality : 0.068 0.178 330 Planarity : 0.002 0.008 340 Dihedral : 6.358 35.835 296 Min Nonbonded Distance : 2.667 Molprobity Statistics. All-atom Clashscore : 2.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.37 % Favored : 99.63 % Rotamer: Outliers : 0.00 % Allowed : 5.71 % Favored : 94.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.22 (0.32), residues: 270 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.45 (0.25), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.007 0.001 TYR A 16 HIS 0.008 0.004 HIS H 19 Details of bonding type rmsd covalent geometry : bond 0.00306 ( 2070) covalent geometry : angle 0.74070 ( 2770) hydrogen bonds : bond 0.09100 ( 36) hydrogen bonds : angle 7.25362 ( 108) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 540 Ramachandran restraints generated. 270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 540 Ramachandran restraints generated. 270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 52 time to evaluate : 0.118 Fit side-chains REVERT: A 26 SER cc_start: 0.8902 (m) cc_final: 0.8389 (p) REVERT: B 26 SER cc_start: 0.8937 (m) cc_final: 0.8505 (p) REVERT: C 26 SER cc_start: 0.8712 (m) cc_final: 0.8302 (p) REVERT: D 26 SER cc_start: 0.8573 (m) cc_final: 0.8054 (p) REVERT: E 26 SER cc_start: 0.8658 (m) cc_final: 0.8186 (p) REVERT: F 26 SER cc_start: 0.8659 (m) cc_final: 0.8116 (p) REVERT: I 27 ASN cc_start: 0.8912 (t0) cc_final: 0.8648 (t0) REVERT: J 21 GLN cc_start: 0.7193 (pt0) cc_final: 0.6937 (mt0) outliers start: 0 outliers final: 0 residues processed: 52 average time/residue: 0.0804 time to fit residues: 5.3125 Evaluate side-chains 52 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 52 time to evaluate : 0.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 16 optimal weight: 0.0970 chunk 5 optimal weight: 3.9990 chunk 17 optimal weight: 1.9990 chunk 3 optimal weight: 2.9990 chunk 4 optimal weight: 2.9990 chunk 11 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 chunk 2 optimal weight: 3.9990 chunk 1 optimal weight: 0.7980 chunk 7 optimal weight: 0.6980 chunk 12 optimal weight: 2.9990 overall best weight: 1.3182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.135980 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.112633 restraints weight = 7208.230| |-----------------------------------------------------------------------------| r_work (start): 0.3515 rms_B_bonded: 2.66 r_work: 0.3409 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3282 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3282 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8478 moved from start: 0.3402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.018 2070 Z= 0.127 Angle : 0.628 4.620 2770 Z= 0.372 Chirality : 0.065 0.154 330 Planarity : 0.002 0.006 340 Dihedral : 4.599 12.861 290 Min Nonbonded Distance : 2.679 Molprobity Statistics. All-atom Clashscore : 2.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.37 % Favored : 99.63 % Rotamer: Outliers : 2.86 % Allowed : 6.19 % Favored : 90.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.93 (0.33), residues: 270 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.23 (0.25), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.007 0.001 TYR A 16 HIS 0.006 0.003 HIS H 19 Details of bonding type rmsd covalent geometry : bond 0.00269 ( 2070) covalent geometry : angle 0.62758 ( 2770) hydrogen bonds : bond 0.07563 ( 36) hydrogen bonds : angle 7.09286 ( 108) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 540 Ramachandran restraints generated. 270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 540 Ramachandran restraints generated. 270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 53 time to evaluate : 0.131 Fit side-chains REVERT: A 26 SER cc_start: 0.8907 (m) cc_final: 0.8550 (p) REVERT: B 26 SER cc_start: 0.8910 (m) cc_final: 0.8598 (p) REVERT: D 26 SER cc_start: 0.8537 (m) cc_final: 0.8134 (p) REVERT: E 26 SER cc_start: 0.8697 (m) cc_final: 0.8324 (p) REVERT: F 26 SER cc_start: 0.8664 (m) cc_final: 0.8186 (p) REVERT: F 34 LEU cc_start: 0.8762 (OUTLIER) cc_final: 0.8502 (tt) REVERT: G 21 GLN cc_start: 0.6882 (pt0) cc_final: 0.6477 (mt0) REVERT: I 27 ASN cc_start: 0.8916 (t0) cc_final: 0.8673 (t0) REVERT: J 21 GLN cc_start: 0.7134 (pt0) cc_final: 0.6909 (mt0) outliers start: 6 outliers final: 1 residues processed: 56 average time/residue: 0.0862 time to fit residues: 5.9357 Evaluate side-chains 51 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 49 time to evaluate : 0.066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain F residue 34 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 16 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 17 optimal weight: 2.9990 chunk 6 optimal weight: 0.8980 chunk 4 optimal weight: 6.9990 chunk 19 optimal weight: 3.9990 chunk 14 optimal weight: 0.7980 chunk 12 optimal weight: 3.9990 chunk 2 optimal weight: 2.9990 chunk 8 optimal weight: 0.6980 chunk 9 optimal weight: 2.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.135133 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.112040 restraints weight = 7141.238| |-----------------------------------------------------------------------------| r_work (start): 0.3558 rms_B_bonded: 2.64 r_work: 0.3449 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3325 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3325 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8487 moved from start: 0.3729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 2070 Z= 0.132 Angle : 0.597 4.066 2770 Z= 0.348 Chirality : 0.064 0.154 330 Planarity : 0.002 0.005 340 Dihedral : 4.256 10.109 290 Min Nonbonded Distance : 2.684 Molprobity Statistics. All-atom Clashscore : 2.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.74 % Favored : 99.26 % Rotamer: Outliers : 1.90 % Allowed : 10.00 % Favored : 88.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.84 (0.35), residues: 270 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.16 (0.27), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.005 0.001 TYR A 16 HIS 0.005 0.002 HIS F 19 Details of bonding type rmsd covalent geometry : bond 0.00300 ( 2070) covalent geometry : angle 0.59723 ( 2770) hydrogen bonds : bond 0.06710 ( 36) hydrogen bonds : angle 6.63949 ( 108) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 540 Ramachandran restraints generated. 270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 540 Ramachandran restraints generated. 270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 45 time to evaluate : 0.094 Fit side-chains REVERT: A 26 SER cc_start: 0.8832 (m) cc_final: 0.8543 (p) REVERT: B 26 SER cc_start: 0.8848 (m) cc_final: 0.8556 (p) REVERT: D 26 SER cc_start: 0.8623 (m) cc_final: 0.8185 (p) REVERT: E 26 SER cc_start: 0.8678 (m) cc_final: 0.8243 (p) REVERT: F 26 SER cc_start: 0.8674 (m) cc_final: 0.8195 (p) REVERT: G 21 GLN cc_start: 0.7003 (pt0) cc_final: 0.6678 (mt0) REVERT: G 26 SER cc_start: 0.8764 (m) cc_final: 0.8313 (p) outliers start: 4 outliers final: 1 residues processed: 48 average time/residue: 0.0573 time to fit residues: 3.7500 Evaluate side-chains 46 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 45 time to evaluate : 0.100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 34 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 17 optimal weight: 3.9990 chunk 1 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 8 optimal weight: 6.9990 chunk 4 optimal weight: 2.9990 chunk 18 optimal weight: 2.9990 chunk 2 optimal weight: 3.9990 chunk 16 optimal weight: 2.9990 chunk 12 optimal weight: 0.8980 chunk 14 optimal weight: 0.9990 chunk 19 optimal weight: 2.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.132198 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.108607 restraints weight = 7245.327| |-----------------------------------------------------------------------------| r_work (start): 0.3461 rms_B_bonded: 2.70 r_work: 0.3347 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3221 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3221 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8548 moved from start: 0.3951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 2070 Z= 0.170 Angle : 0.595 4.221 2770 Z= 0.345 Chirality : 0.064 0.156 330 Planarity : 0.002 0.005 340 Dihedral : 4.326 11.379 290 Min Nonbonded Distance : 2.680 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.74 % Favored : 99.26 % Rotamer: Outliers : 1.43 % Allowed : 10.48 % Favored : 88.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.95 (0.37), residues: 270 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.24 (0.28), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.005 0.001 TYR A 16 HIS 0.006 0.003 HIS C 19 Details of bonding type rmsd covalent geometry : bond 0.00395 ( 2070) covalent geometry : angle 0.59511 ( 2770) hydrogen bonds : bond 0.06518 ( 36) hydrogen bonds : angle 6.30932 ( 108) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 540 Ramachandran restraints generated. 270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 540 Ramachandran restraints generated. 270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 46 time to evaluate : 0.139 Fit side-chains REVERT: A 26 SER cc_start: 0.8890 (m) cc_final: 0.8580 (p) REVERT: B 26 SER cc_start: 0.8839 (m) cc_final: 0.8515 (p) REVERT: D 26 SER cc_start: 0.8674 (m) cc_final: 0.8311 (p) REVERT: E 26 SER cc_start: 0.8704 (m) cc_final: 0.8287 (p) REVERT: F 26 SER cc_start: 0.8701 (m) cc_final: 0.8237 (p) REVERT: F 34 LEU cc_start: 0.8872 (OUTLIER) cc_final: 0.8610 (tt) REVERT: G 21 GLN cc_start: 0.7245 (pt0) cc_final: 0.6930 (mt0) REVERT: G 26 SER cc_start: 0.8855 (m) cc_final: 0.8434 (p) REVERT: H 26 SER cc_start: 0.8815 (m) cc_final: 0.8376 (p) outliers start: 3 outliers final: 2 residues processed: 49 average time/residue: 0.0605 time to fit residues: 4.0525 Evaluate side-chains 48 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 45 time to evaluate : 0.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain F residue 34 LEU Chi-restraints excluded: chain J residue 34 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 7 optimal weight: 4.9990 chunk 13 optimal weight: 3.9990 chunk 14 optimal weight: 5.9990 chunk 16 optimal weight: 0.0470 chunk 1 optimal weight: 0.7980 chunk 19 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 18 optimal weight: 0.8980 chunk 12 optimal weight: 0.9980 chunk 2 optimal weight: 3.9990 chunk 8 optimal weight: 3.9990 overall best weight: 0.9480 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.132094 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.110239 restraints weight = 7382.673| |-----------------------------------------------------------------------------| r_work (start): 0.3544 rms_B_bonded: 2.52 r_work: 0.3438 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3313 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3313 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8530 moved from start: 0.4127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.016 2070 Z= 0.098 Angle : 0.519 3.755 2770 Z= 0.303 Chirality : 0.062 0.154 330 Planarity : 0.001 0.005 340 Dihedral : 4.205 11.275 290 Min Nonbonded Distance : 2.687 Molprobity Statistics. All-atom Clashscore : 3.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.11 % Favored : 98.89 % Rotamer: Outliers : 1.43 % Allowed : 12.38 % Favored : 86.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.03 (0.37), residues: 270 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.30 (0.28), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.005 0.001 TYR A 16 HIS 0.003 0.001 HIS F 19 Details of bonding type rmsd covalent geometry : bond 0.00218 ( 2070) covalent geometry : angle 0.51932 ( 2770) hydrogen bonds : bond 0.05530 ( 36) hydrogen bonds : angle 6.15774 ( 108) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 540 Ramachandran restraints generated. 270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 540 Ramachandran restraints generated. 270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 45 time to evaluate : 0.119 Fit side-chains REVERT: A 26 SER cc_start: 0.8860 (m) cc_final: 0.8578 (p) REVERT: B 26 SER cc_start: 0.8846 (m) cc_final: 0.8550 (p) REVERT: D 26 SER cc_start: 0.8641 (m) cc_final: 0.8294 (p) REVERT: E 26 SER cc_start: 0.8735 (m) cc_final: 0.8328 (p) REVERT: F 26 SER cc_start: 0.8749 (m) cc_final: 0.8307 (p) REVERT: F 34 LEU cc_start: 0.8848 (OUTLIER) cc_final: 0.8571 (tt) REVERT: G 21 GLN cc_start: 0.7223 (pt0) cc_final: 0.6944 (mt0) REVERT: G 26 SER cc_start: 0.8870 (m) cc_final: 0.8486 (p) REVERT: H 26 SER cc_start: 0.8814 (m) cc_final: 0.8399 (p) REVERT: I 21 GLN cc_start: 0.7013 (pt0) cc_final: 0.6715 (mt0) outliers start: 3 outliers final: 2 residues processed: 48 average time/residue: 0.0579 time to fit residues: 3.8424 Evaluate side-chains 49 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 46 time to evaluate : 0.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain F residue 34 LEU Chi-restraints excluded: chain J residue 34 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 12 optimal weight: 5.9990 chunk 16 optimal weight: 0.9990 chunk 8 optimal weight: 0.8980 chunk 18 optimal weight: 0.0070 chunk 14 optimal weight: 1.9990 chunk 19 optimal weight: 0.6980 chunk 10 optimal weight: 3.9990 chunk 3 optimal weight: 0.0870 chunk 6 optimal weight: 0.6980 chunk 15 optimal weight: 0.9990 chunk 9 optimal weight: 2.9990 overall best weight: 0.4776 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.134762 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.113046 restraints weight = 7286.695| |-----------------------------------------------------------------------------| r_work (start): 0.3595 rms_B_bonded: 2.50 r_work: 0.3490 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3363 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3363 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8508 moved from start: 0.4252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.013 2070 Z= 0.074 Angle : 0.482 3.592 2770 Z= 0.282 Chirality : 0.061 0.148 330 Planarity : 0.001 0.004 340 Dihedral : 4.105 15.558 290 Min Nonbonded Distance : 2.687 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.74 % Favored : 99.26 % Rotamer: Outliers : 1.90 % Allowed : 13.33 % Favored : 84.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.10 (0.37), residues: 270 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.36 (0.28), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.004 0.001 TYR A 16 HIS 0.003 0.001 HIS C 19 Details of bonding type rmsd covalent geometry : bond 0.00157 ( 2070) covalent geometry : angle 0.48154 ( 2770) hydrogen bonds : bond 0.04801 ( 36) hydrogen bonds : angle 5.94448 ( 108) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 540 Ramachandran restraints generated. 270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 540 Ramachandran restraints generated. 270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 46 time to evaluate : 0.092 Fit side-chains REVERT: A 26 SER cc_start: 0.8849 (m) cc_final: 0.8615 (p) REVERT: B 26 SER cc_start: 0.8841 (m) cc_final: 0.8559 (p) REVERT: D 26 SER cc_start: 0.8639 (m) cc_final: 0.8310 (p) REVERT: E 26 SER cc_start: 0.8756 (m) cc_final: 0.8371 (p) REVERT: F 26 SER cc_start: 0.8758 (m) cc_final: 0.8329 (p) REVERT: F 34 LEU cc_start: 0.8822 (OUTLIER) cc_final: 0.8531 (tt) REVERT: G 21 GLN cc_start: 0.7215 (pt0) cc_final: 0.6972 (mt0) REVERT: G 26 SER cc_start: 0.8850 (m) cc_final: 0.8488 (p) REVERT: H 26 SER cc_start: 0.8804 (m) cc_final: 0.8410 (p) REVERT: I 21 GLN cc_start: 0.7066 (pt0) cc_final: 0.6784 (mt0) REVERT: J 17 GLU cc_start: 0.8345 (pt0) cc_final: 0.8031 (tt0) outliers start: 4 outliers final: 3 residues processed: 49 average time/residue: 0.0581 time to fit residues: 3.9423 Evaluate side-chains 49 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 45 time to evaluate : 0.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain F residue 34 LEU Chi-restraints excluded: chain J residue 34 LEU Chi-restraints excluded: chain J residue 35 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 7 optimal weight: 4.9990 chunk 14 optimal weight: 4.9990 chunk 3 optimal weight: 0.9980 chunk 17 optimal weight: 2.9990 chunk 19 optimal weight: 0.9990 chunk 6 optimal weight: 5.9990 chunk 11 optimal weight: 0.7980 chunk 4 optimal weight: 5.9990 chunk 13 optimal weight: 0.9990 chunk 18 optimal weight: 0.6980 chunk 8 optimal weight: 0.8980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.134533 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.112607 restraints weight = 7226.033| |-----------------------------------------------------------------------------| r_work (start): 0.3638 rms_B_bonded: 2.54 r_work: 0.3527 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3401 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3401 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8544 moved from start: 0.4318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.015 2070 Z= 0.094 Angle : 0.490 3.648 2770 Z= 0.286 Chirality : 0.061 0.149 330 Planarity : 0.001 0.004 340 Dihedral : 3.968 14.943 290 Min Nonbonded Distance : 2.686 Molprobity Statistics. All-atom Clashscore : 2.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.11 % Favored : 98.89 % Rotamer: Outliers : 1.90 % Allowed : 13.33 % Favored : 84.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.09 (0.38), residues: 270 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.35 (0.29), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.003 0.001 TYR B 16 HIS 0.003 0.002 HIS E 19 Details of bonding type rmsd covalent geometry : bond 0.00216 ( 2070) covalent geometry : angle 0.48960 ( 2770) hydrogen bonds : bond 0.05034 ( 36) hydrogen bonds : angle 5.87045 ( 108) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 540 Ramachandran restraints generated. 270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 540 Ramachandran restraints generated. 270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 41 time to evaluate : 0.114 Fit side-chains REVERT: A 26 SER cc_start: 0.8854 (m) cc_final: 0.8624 (p) REVERT: B 26 SER cc_start: 0.8843 (m) cc_final: 0.8563 (p) REVERT: D 26 SER cc_start: 0.8685 (m) cc_final: 0.8374 (p) REVERT: E 26 SER cc_start: 0.8749 (m) cc_final: 0.8368 (p) REVERT: F 26 SER cc_start: 0.8755 (m) cc_final: 0.8342 (p) REVERT: F 34 LEU cc_start: 0.8875 (OUTLIER) cc_final: 0.8579 (tt) REVERT: G 26 SER cc_start: 0.8866 (m) cc_final: 0.8519 (p) REVERT: H 26 SER cc_start: 0.8816 (m) cc_final: 0.8435 (p) REVERT: J 17 GLU cc_start: 0.8388 (pt0) cc_final: 0.8097 (tt0) outliers start: 4 outliers final: 2 residues processed: 45 average time/residue: 0.0582 time to fit residues: 3.6705 Evaluate side-chains 44 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 41 time to evaluate : 0.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain F residue 34 LEU Chi-restraints excluded: chain J residue 34 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 7 optimal weight: 3.9990 chunk 1 optimal weight: 3.9990 chunk 14 optimal weight: 4.9990 chunk 8 optimal weight: 5.9990 chunk 6 optimal weight: 5.9990 chunk 3 optimal weight: 0.7980 chunk 13 optimal weight: 3.9990 chunk 16 optimal weight: 0.3980 chunk 10 optimal weight: 0.8980 chunk 5 optimal weight: 0.9990 chunk 12 optimal weight: 1.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.133770 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.111948 restraints weight = 7309.034| |-----------------------------------------------------------------------------| r_work (start): 0.3610 rms_B_bonded: 2.52 r_work: 0.3504 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3377 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3377 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8537 moved from start: 0.4378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.017 2070 Z= 0.099 Angle : 0.493 3.634 2770 Z= 0.288 Chirality : 0.061 0.150 330 Planarity : 0.001 0.004 340 Dihedral : 3.950 14.394 290 Min Nonbonded Distance : 2.686 Molprobity Statistics. All-atom Clashscore : 2.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.11 % Favored : 98.89 % Rotamer: Outliers : 1.90 % Allowed : 14.29 % Favored : 83.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.08 (0.39), residues: 270 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.34 (0.29), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.004 0.001 TYR B 16 HIS 0.005 0.002 HIS E 19 Details of bonding type rmsd covalent geometry : bond 0.00226 ( 2070) covalent geometry : angle 0.49323 ( 2770) hydrogen bonds : bond 0.04973 ( 36) hydrogen bonds : angle 5.83441 ( 108) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 540 Ramachandran restraints generated. 270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 540 Ramachandran restraints generated. 270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 41 time to evaluate : 0.153 Fit side-chains REVERT: A 26 SER cc_start: 0.8852 (m) cc_final: 0.8618 (p) REVERT: B 26 SER cc_start: 0.8844 (m) cc_final: 0.8547 (p) REVERT: D 26 SER cc_start: 0.8736 (m) cc_final: 0.8411 (p) REVERT: E 26 SER cc_start: 0.8773 (m) cc_final: 0.8402 (p) REVERT: F 26 SER cc_start: 0.8742 (m) cc_final: 0.8319 (p) REVERT: F 34 LEU cc_start: 0.8858 (OUTLIER) cc_final: 0.8567 (tt) REVERT: G 26 SER cc_start: 0.8878 (m) cc_final: 0.8517 (p) REVERT: H 26 SER cc_start: 0.8825 (m) cc_final: 0.8432 (p) REVERT: I 21 GLN cc_start: 0.7902 (mt0) cc_final: 0.7638 (mp10) REVERT: J 17 GLU cc_start: 0.8412 (pt0) cc_final: 0.8144 (tt0) outliers start: 4 outliers final: 3 residues processed: 45 average time/residue: 0.0547 time to fit residues: 3.4668 Evaluate side-chains 45 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 41 time to evaluate : 0.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain F residue 34 LEU Chi-restraints excluded: chain I residue 34 LEU Chi-restraints excluded: chain J residue 34 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 7 optimal weight: 2.9990 chunk 1 optimal weight: 2.9990 chunk 16 optimal weight: 0.9980 chunk 4 optimal weight: 5.9990 chunk 3 optimal weight: 1.9990 chunk 11 optimal weight: 0.1980 chunk 5 optimal weight: 0.6980 chunk 19 optimal weight: 2.9990 chunk 10 optimal weight: 0.9980 chunk 12 optimal weight: 3.9990 chunk 2 optimal weight: 3.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.133409 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.111749 restraints weight = 7279.451| |-----------------------------------------------------------------------------| r_work (start): 0.3582 rms_B_bonded: 2.52 r_work: 0.3472 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3342 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3342 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8518 moved from start: 0.4435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.016 2070 Z= 0.097 Angle : 0.489 3.589 2770 Z= 0.285 Chirality : 0.061 0.150 330 Planarity : 0.001 0.005 340 Dihedral : 3.873 14.064 290 Min Nonbonded Distance : 2.685 Molprobity Statistics. All-atom Clashscore : 3.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 2.38 % Allowed : 13.81 % Favored : 83.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.11 (0.39), residues: 270 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.36 (0.30), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.004 0.001 TYR B 16 HIS 0.005 0.002 HIS E 19 Details of bonding type rmsd covalent geometry : bond 0.00218 ( 2070) covalent geometry : angle 0.48869 ( 2770) hydrogen bonds : bond 0.05007 ( 36) hydrogen bonds : angle 5.82624 ( 108) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 540 Ramachandran restraints generated. 270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 540 Ramachandran restraints generated. 270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 41 time to evaluate : 0.120 Fit side-chains REVERT: A 26 SER cc_start: 0.8860 (m) cc_final: 0.8603 (p) REVERT: B 26 SER cc_start: 0.8828 (m) cc_final: 0.8507 (p) REVERT: D 26 SER cc_start: 0.8712 (m) cc_final: 0.8366 (p) REVERT: E 26 SER cc_start: 0.8771 (m) cc_final: 0.8390 (p) REVERT: F 26 SER cc_start: 0.8727 (m) cc_final: 0.8305 (p) REVERT: F 34 LEU cc_start: 0.8825 (OUTLIER) cc_final: 0.8507 (tt) REVERT: G 26 SER cc_start: 0.8883 (m) cc_final: 0.8503 (p) REVERT: H 26 SER cc_start: 0.8800 (m) cc_final: 0.8390 (p) REVERT: J 17 GLU cc_start: 0.8409 (pt0) cc_final: 0.8137 (tt0) outliers start: 5 outliers final: 3 residues processed: 45 average time/residue: 0.0531 time to fit residues: 3.3627 Evaluate side-chains 45 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 41 time to evaluate : 0.110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain F residue 34 LEU Chi-restraints excluded: chain I residue 34 LEU Chi-restraints excluded: chain J residue 34 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 14 optimal weight: 4.9990 chunk 18 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 chunk 6 optimal weight: 4.9990 chunk 5 optimal weight: 3.9990 chunk 2 optimal weight: 0.5980 chunk 13 optimal weight: 0.9990 chunk 10 optimal weight: 0.9980 chunk 0 optimal weight: 3.9990 chunk 15 optimal weight: 0.6980 chunk 1 optimal weight: 0.7980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.134569 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.112715 restraints weight = 7256.593| |-----------------------------------------------------------------------------| r_work (start): 0.3534 rms_B_bonded: 2.56 r_work: 0.3423 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3293 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3293 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8496 moved from start: 0.4496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.014 2070 Z= 0.085 Angle : 0.477 3.494 2770 Z= 0.279 Chirality : 0.061 0.147 330 Planarity : 0.001 0.004 340 Dihedral : 3.859 13.939 290 Min Nonbonded Distance : 2.685 Molprobity Statistics. All-atom Clashscore : 3.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 1.90 % Allowed : 14.29 % Favored : 83.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.11 (0.39), residues: 270 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.36 (0.30), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.004 0.001 TYR B 16 HIS 0.005 0.002 HIS E 19 Details of bonding type rmsd covalent geometry : bond 0.00190 ( 2070) covalent geometry : angle 0.47720 ( 2770) hydrogen bonds : bond 0.04793 ( 36) hydrogen bonds : angle 5.76776 ( 108) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1685.63 seconds wall clock time: 29 minutes 14.99 seconds (1754.99 seconds total)