Starting phenix.real_space_refine on Wed Jul 23 20:15:10 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9fh1_50436/07_2025/9fh1_50436.cif Found real_map, /net/cci-nas-00/data/ceres_data/9fh1_50436/07_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9fh1_50436/07_2025/9fh1_50436.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9fh1_50436/07_2025/9fh1_50436.map" model { file = "/net/cci-nas-00/data/ceres_data/9fh1_50436/07_2025/9fh1_50436.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9fh1_50436/07_2025/9fh1_50436.cif" } resolution = 3.2 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= 0.001 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-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 2.73, per 1000 atoms: 0.65 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: 1.08 Conformation dependent library (CDL) restraints added in 322.6 milliseconds 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: 0.46 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: 1.39 Time building geometry restraints manager: 1.33 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: 1.870 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: 0.070 Extract box with map and model: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 14.640 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.020 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:3.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.010 ------------------------------------------------------------------------------- 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 (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: -2.96 (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 HIS 0.011 0.005 HIS B 19 TYR 0.035 0.009 TYR J 16 Details of bonding type rmsd hydrogen bonds : bond 0.23989 ( 36) hydrogen bonds : angle 7.20566 ( 108) covalent geometry : bond 0.01004 ( 2070) covalent geometry : angle 2.04842 ( 2770) *********************** 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 : 0.349 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: 0.2131 time to fit residues: 21.9245 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 : 0.715 ------------------------------------------------------------------------------- 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 16 optimal weight: 2.9990 chunk 15 optimal weight: 0.8980 chunk 8 optimal weight: 0.9990 chunk 5 optimal weight: 0.8980 chunk 10 optimal weight: 0.9980 chunk 6 optimal weight: 0.9990 chunk 9 optimal weight: 0.9990 chunk 11 optimal weight: 0.9980 chunk 18 optimal weight: 1.9990 chunk 12 optimal weight: 0.9990 chunk 19 optimal weight: 0.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- 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 = 0.3764 r_free = 0.3764 target = 0.128295 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.104870 restraints weight = 7381.047| |-----------------------------------------------------------------------------| r_work (start): 0.3521 rms_B_bonded: 2.49 r_work: 0.3417 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3295 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3295 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8451 moved from start: 0.2998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 2070 Z= 0.137 Angle : 0.720 5.467 2770 Z= 0.428 Chirality : 0.067 0.184 330 Planarity : 0.002 0.009 340 Dihedral : 6.422 35.929 296 Min Nonbonded Distance : 2.661 Molprobity Statistics. All-atom Clashscore : 1.90 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 (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: -3.29 (0.32), residues: 270 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.50 (0.24), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.009 0.004 HIS H 19 TYR 0.007 0.001 TYR A 16 Details of bonding type rmsd hydrogen bonds : bond 0.08819 ( 36) hydrogen bonds : angle 7.31869 ( 108) covalent geometry : bond 0.00301 ( 2070) covalent geometry : angle 0.72017 ( 2770) *********************** 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 : 0.360 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 26 SER cc_start: 0.8904 (m) cc_final: 0.8403 (p) REVERT: B 26 SER cc_start: 0.8915 (m) cc_final: 0.8507 (p) REVERT: C 26 SER cc_start: 0.8710 (m) cc_final: 0.8300 (p) REVERT: D 26 SER cc_start: 0.8555 (m) cc_final: 0.8050 (p) REVERT: E 26 SER cc_start: 0.8656 (m) cc_final: 0.8191 (p) REVERT: F 26 SER cc_start: 0.8662 (m) cc_final: 0.8110 (p) REVERT: J 21 GLN cc_start: 0.7196 (pt0) cc_final: 0.6936 (mt0) outliers start: 0 outliers final: 0 residues processed: 52 average time/residue: 0.1982 time to fit residues: 12.8130 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 : 0.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 12 optimal weight: 5.9990 chunk 16 optimal weight: 0.8980 chunk 15 optimal weight: 0.5980 chunk 0 optimal weight: 4.9990 chunk 11 optimal weight: 0.9980 chunk 8 optimal weight: 0.7980 chunk 5 optimal weight: 3.9990 chunk 2 optimal weight: 3.9990 chunk 3 optimal weight: 2.9990 chunk 4 optimal weight: 0.9990 chunk 9 optimal weight: 0.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3889 r_free = 0.3889 target = 0.138350 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.115403 restraints weight = 7122.740| |-----------------------------------------------------------------------------| r_work (start): 0.3661 rms_B_bonded: 2.63 r_work: 0.3555 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3426 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3426 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8431 moved from start: 0.3491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.011 2070 Z= 0.099 Angle : 0.595 4.285 2770 Z= 0.355 Chirality : 0.063 0.150 330 Planarity : 0.001 0.006 340 Dihedral : 4.532 13.292 290 Min Nonbonded Distance : 2.684 Molprobity Statistics. All-atom Clashscore : 3.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 2.38 % Allowed : 6.67 % 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 (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: -2.98 (0.33), residues: 270 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.26 (0.25), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS I 19 TYR 0.007 0.001 TYR A 16 Details of bonding type rmsd hydrogen bonds : bond 0.07260 ( 36) hydrogen bonds : angle 7.14065 ( 108) covalent geometry : bond 0.00200 ( 2070) covalent geometry : angle 0.59516 ( 2770) *********************** 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: 5 poor density : 54 time to evaluate : 0.289 Fit side-chains REVERT: A 26 SER cc_start: 0.8883 (m) cc_final: 0.8532 (p) REVERT: B 26 SER cc_start: 0.8810 (m) cc_final: 0.8491 (p) REVERT: D 26 SER cc_start: 0.8566 (m) cc_final: 0.8068 (p) REVERT: E 26 SER cc_start: 0.8665 (m) cc_final: 0.8279 (p) REVERT: F 26 SER cc_start: 0.8582 (m) cc_final: 0.8079 (p) REVERT: F 34 LEU cc_start: 0.8688 (OUTLIER) cc_final: 0.8418 (tt) REVERT: G 21 GLN cc_start: 0.6836 (pt0) cc_final: 0.6453 (mt0) REVERT: I 27 ASN cc_start: 0.8844 (t0) cc_final: 0.8606 (t0) REVERT: J 21 GLN cc_start: 0.7099 (pt0) cc_final: 0.6867 (mt0) outliers start: 5 outliers final: 1 residues processed: 56 average time/residue: 0.1949 time to fit residues: 13.2981 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 : 0.314 ------------------------------------------------------------------------------- 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 12 optimal weight: 5.9990 chunk 4 optimal weight: 4.9990 chunk 8 optimal weight: 0.7980 chunk 16 optimal weight: 0.5980 chunk 18 optimal weight: 0.0970 chunk 10 optimal weight: 5.9990 chunk 14 optimal weight: 0.7980 chunk 17 optimal weight: 0.8980 chunk 1 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 2 optimal weight: 3.9990 overall best weight: 0.6378 ------------------------------------------------------------------------------- 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 = 0.3896 r_free = 0.3896 target = 0.139845 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.116934 restraints weight = 7057.313| |-----------------------------------------------------------------------------| r_work (start): 0.3543 rms_B_bonded: 2.65 r_work: 0.3437 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3310 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3310 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8422 moved from start: 0.3803 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= 0.083 Angle : 0.541 3.722 2770 Z= 0.320 Chirality : 0.062 0.150 330 Planarity : 0.001 0.004 340 Dihedral : 4.236 11.882 290 Min Nonbonded Distance : 2.686 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.74 % Favored : 99.26 % Rotamer: Outliers : 2.86 % Allowed : 8.57 % Favored : 88.57 % 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: -2.87 (0.34), residues: 270 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.18 (0.26), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.002 HIS G 19 TYR 0.005 0.001 TYR A 16 Details of bonding type rmsd hydrogen bonds : bond 0.06054 ( 36) hydrogen bonds : angle 6.73043 ( 108) covalent geometry : bond 0.00179 ( 2070) covalent geometry : angle 0.54076 ( 2770) *********************** 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 54 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 48 time to evaluate : 0.363 Fit side-chains REVERT: A 26 SER cc_start: 0.8852 (m) cc_final: 0.8589 (p) REVERT: B 26 SER cc_start: 0.8826 (m) cc_final: 0.8562 (p) REVERT: D 26 SER cc_start: 0.8574 (m) cc_final: 0.8147 (p) REVERT: E 26 SER cc_start: 0.8701 (m) cc_final: 0.8279 (p) REVERT: F 26 SER cc_start: 0.8595 (m) cc_final: 0.8133 (p) REVERT: F 34 LEU cc_start: 0.8680 (OUTLIER) cc_final: 0.8388 (tt) REVERT: G 21 GLN cc_start: 0.6866 (pt0) cc_final: 0.6499 (mt0) REVERT: G 26 SER cc_start: 0.8711 (m) cc_final: 0.8256 (p) REVERT: I 21 GLN cc_start: 0.6750 (pt0) cc_final: 0.6252 (mt0) REVERT: J 21 GLN cc_start: 0.7099 (pt0) cc_final: 0.6837 (mt0) outliers start: 6 outliers final: 2 residues processed: 52 average time/residue: 0.2407 time to fit residues: 16.5686 Evaluate side-chains 50 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 47 time to evaluate : 0.639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 17 GLU Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain F residue 34 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 15 optimal weight: 2.9990 chunk 16 optimal weight: 0.9980 chunk 5 optimal weight: 3.9990 chunk 17 optimal weight: 0.0370 chunk 10 optimal weight: 3.9990 chunk 13 optimal weight: 0.7980 chunk 1 optimal weight: 0.3980 chunk 4 optimal weight: 4.9990 chunk 12 optimal weight: 0.6980 chunk 19 optimal weight: 0.5980 chunk 7 optimal weight: 0.8980 overall best weight: 0.5058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 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 = 0.3893 r_free = 0.3893 target = 0.138600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.115942 restraints weight = 7233.146| |-----------------------------------------------------------------------------| r_work (start): 0.3624 rms_B_bonded: 2.62 r_work: 0.3513 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3388 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3388 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8438 moved from start: 0.4044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.012 2070 Z= 0.074 Angle : 0.495 3.650 2770 Z= 0.292 Chirality : 0.061 0.146 330 Planarity : 0.001 0.004 340 Dihedral : 4.017 10.603 290 Min Nonbonded Distance : 2.687 Molprobity Statistics. All-atom Clashscore : 3.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.37 % Favored : 99.63 % Rotamer: Outliers : 1.43 % Allowed : 7.62 % 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 (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: -2.93 (0.34), residues: 270 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.23 (0.26), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS I 20 TYR 0.004 0.001 TYR A 16 Details of bonding type rmsd hydrogen bonds : bond 0.05184 ( 36) hydrogen bonds : angle 6.26532 ( 108) covalent geometry : bond 0.00150 ( 2070) covalent geometry : angle 0.49480 ( 2770) *********************** 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 : 0.340 Fit side-chains REVERT: A 26 SER cc_start: 0.8774 (m) cc_final: 0.8557 (p) REVERT: B 26 SER cc_start: 0.8773 (m) cc_final: 0.8570 (p) REVERT: D 21 GLN cc_start: 0.7142 (pt0) cc_final: 0.6769 (mt0) REVERT: D 26 SER cc_start: 0.8599 (m) cc_final: 0.8215 (p) REVERT: E 26 SER cc_start: 0.8691 (m) cc_final: 0.8301 (p) REVERT: F 26 SER cc_start: 0.8630 (m) cc_final: 0.8211 (p) REVERT: F 34 LEU cc_start: 0.8695 (OUTLIER) cc_final: 0.8382 (tt) REVERT: G 21 GLN cc_start: 0.7025 (pt0) cc_final: 0.6734 (mt0) REVERT: G 26 SER cc_start: 0.8755 (m) cc_final: 0.8338 (p) outliers start: 3 outliers final: 0 residues processed: 48 average time/residue: 0.1836 time to fit residues: 11.2232 Evaluate side-chains 47 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 46 time to evaluate : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 34 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 11 optimal weight: 3.9990 chunk 8 optimal weight: 5.9990 chunk 7 optimal weight: 0.9980 chunk 17 optimal weight: 2.9990 chunk 10 optimal weight: 5.9990 chunk 9 optimal weight: 2.9990 chunk 12 optimal weight: 0.6980 chunk 15 optimal weight: 0.8980 chunk 1 optimal weight: 1.9990 chunk 13 optimal weight: 0.8980 chunk 6 optimal weight: 0.9980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 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 = 0.3888 r_free = 0.3888 target = 0.139140 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.115960 restraints weight = 7075.932| |-----------------------------------------------------------------------------| r_work (start): 0.3542 rms_B_bonded: 2.68 r_work: 0.3428 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3303 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3303 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8443 moved from start: 0.4281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 2070 Z= 0.093 Angle : 0.499 3.721 2770 Z= 0.294 Chirality : 0.061 0.149 330 Planarity : 0.001 0.004 340 Dihedral : 3.954 13.044 290 Min Nonbonded Distance : 2.686 Molprobity Statistics. All-atom Clashscore : 3.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.74 % Favored : 99.26 % Rotamer: Outliers : 0.95 % Allowed : 10.95 % 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 (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: -2.86 (0.36), residues: 270 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.17 (0.27), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.002 HIS B 19 TYR 0.008 0.001 TYR A 16 Details of bonding type rmsd hydrogen bonds : bond 0.05185 ( 36) hydrogen bonds : angle 5.96805 ( 108) covalent geometry : bond 0.00209 ( 2070) covalent geometry : angle 0.49933 ( 2770) *********************** 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 44 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 42 time to evaluate : 0.315 Fit side-chains REVERT: A 26 SER cc_start: 0.8760 (m) cc_final: 0.8545 (p) REVERT: B 26 SER cc_start: 0.8763 (m) cc_final: 0.8527 (p) REVERT: D 21 GLN cc_start: 0.7058 (pt0) cc_final: 0.6714 (mt0) REVERT: D 26 SER cc_start: 0.8596 (m) cc_final: 0.8204 (p) REVERT: E 26 SER cc_start: 0.8671 (m) cc_final: 0.8272 (p) REVERT: F 26 SER cc_start: 0.8637 (m) cc_final: 0.8207 (p) REVERT: F 34 LEU cc_start: 0.8712 (OUTLIER) cc_final: 0.8372 (tt) REVERT: G 21 GLN cc_start: 0.7009 (pt0) cc_final: 0.6766 (mt0) REVERT: G 26 SER cc_start: 0.8745 (m) cc_final: 0.8336 (p) REVERT: I 21 GLN cc_start: 0.6808 (pt0) cc_final: 0.6406 (mt0) outliers start: 2 outliers final: 1 residues processed: 44 average time/residue: 0.1701 time to fit residues: 9.6643 Evaluate side-chains 43 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 41 time to evaluate : 0.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 10 optimal weight: 5.9990 chunk 18 optimal weight: 1.9990 chunk 14 optimal weight: 0.6980 chunk 6 optimal weight: 0.4980 chunk 5 optimal weight: 3.9990 chunk 1 optimal weight: 0.7980 chunk 19 optimal weight: 0.9980 chunk 7 optimal weight: 2.9990 chunk 17 optimal weight: 0.7980 chunk 12 optimal weight: 5.9990 chunk 8 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 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 = 0.3901 r_free = 0.3901 target = 0.139685 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.116649 restraints weight = 7104.348| |-----------------------------------------------------------------------------| r_work (start): 0.3557 rms_B_bonded: 2.66 r_work: 0.3448 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3321 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3321 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8453 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 : 0.002 0.012 2070 Z= 0.079 Angle : 0.474 3.613 2770 Z= 0.278 Chirality : 0.061 0.149 330 Planarity : 0.001 0.004 340 Dihedral : 3.833 14.185 290 Min Nonbonded Distance : 2.686 Molprobity Statistics. All-atom Clashscore : 3.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.37 % Favored : 99.63 % Rotamer: Outliers : 0.95 % Allowed : 12.38 % Favored : 86.67 % 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: -2.86 (0.36), residues: 270 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.17 (0.28), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.002 HIS D 19 TYR 0.008 0.001 TYR A 16 Details of bonding type rmsd hydrogen bonds : bond 0.04734 ( 36) hydrogen bonds : angle 5.83784 ( 108) covalent geometry : bond 0.00172 ( 2070) covalent geometry : angle 0.47389 ( 2770) *********************** 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 43 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 41 time to evaluate : 0.317 Fit side-chains REVERT: B 26 SER cc_start: 0.8791 (m) cc_final: 0.8569 (p) REVERT: D 26 SER cc_start: 0.8609 (m) cc_final: 0.8236 (p) REVERT: E 26 SER cc_start: 0.8684 (m) cc_final: 0.8293 (p) REVERT: F 26 SER cc_start: 0.8647 (m) cc_final: 0.8242 (p) REVERT: F 34 LEU cc_start: 0.8723 (OUTLIER) cc_final: 0.8396 (tt) REVERT: G 26 SER cc_start: 0.8765 (m) cc_final: 0.8379 (p) REVERT: I 21 GLN cc_start: 0.6821 (pt0) cc_final: 0.6438 (mt0) REVERT: J 17 GLU cc_start: 0.8355 (pt0) cc_final: 0.7993 (tt0) REVERT: J 21 GLN cc_start: 0.8482 (mp10) cc_final: 0.8206 (mt0) outliers start: 2 outliers final: 1 residues processed: 43 average time/residue: 0.1772 time to fit residues: 9.7979 Evaluate side-chains 41 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 39 time to evaluate : 0.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 34 LEU Chi-restraints excluded: chain J residue 34 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 12 optimal weight: 0.9980 chunk 4 optimal weight: 5.9990 chunk 9 optimal weight: 3.9990 chunk 19 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 chunk 11 optimal weight: 3.9990 chunk 1 optimal weight: 0.0470 chunk 16 optimal weight: 0.9980 chunk 3 optimal weight: 2.9990 chunk 14 optimal weight: 5.9990 chunk 15 optimal weight: 0.9980 overall best weight: 1.0080 ------------------------------------------------------------------------------- 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** ** D 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 = 0.3898 r_free = 0.3898 target = 0.136756 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.115294 restraints weight = 7142.399| |-----------------------------------------------------------------------------| r_work (start): 0.3593 rms_B_bonded: 2.51 r_work: 0.3485 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3358 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3358 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8506 moved from start: 0.4462 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= 0.101 Angle : 0.487 3.689 2770 Z= 0.286 Chirality : 0.062 0.149 330 Planarity : 0.001 0.003 340 Dihedral : 3.750 12.956 290 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 3.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.37 % Favored : 99.63 % Rotamer: Outliers : 0.95 % Allowed : 13.33 % Favored : 85.71 % 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: -2.85 (0.37), residues: 270 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.16 (0.29), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.002 HIS C 19 TYR 0.008 0.001 TYR A 16 Details of bonding type rmsd hydrogen bonds : bond 0.05093 ( 36) hydrogen bonds : angle 5.86041 ( 108) covalent geometry : bond 0.00232 ( 2070) covalent geometry : angle 0.48729 ( 2770) *********************** 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 42 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 40 time to evaluate : 0.379 Fit side-chains REVERT: B 26 SER cc_start: 0.8782 (m) cc_final: 0.8546 (p) REVERT: D 26 SER cc_start: 0.8612 (m) cc_final: 0.8298 (p) REVERT: E 26 SER cc_start: 0.8733 (m) cc_final: 0.8377 (p) REVERT: F 26 SER cc_start: 0.8727 (m) cc_final: 0.8310 (p) REVERT: F 34 LEU cc_start: 0.8813 (OUTLIER) cc_final: 0.8487 (tt) REVERT: G 26 SER cc_start: 0.8811 (m) cc_final: 0.8461 (p) REVERT: H 26 SER cc_start: 0.8776 (m) cc_final: 0.8414 (p) REVERT: I 21 GLN cc_start: 0.6857 (pt0) cc_final: 0.6637 (mt0) REVERT: J 17 GLU cc_start: 0.8389 (pt0) cc_final: 0.7992 (tt0) outliers start: 2 outliers final: 1 residues processed: 42 average time/residue: 0.1690 time to fit residues: 9.2223 Evaluate side-chains 42 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 40 time to evaluate : 0.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 19 optimal weight: 0.5980 chunk 6 optimal weight: 2.9990 chunk 15 optimal weight: 0.7980 chunk 18 optimal weight: 1.9990 chunk 11 optimal weight: 0.6980 chunk 2 optimal weight: 0.5980 chunk 14 optimal weight: 0.7980 chunk 1 optimal weight: 0.3980 chunk 17 optimal weight: 0.9990 chunk 16 optimal weight: 0.5980 chunk 13 optimal weight: 0.8980 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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 = 0.3907 r_free = 0.3907 target = 0.136199 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.114748 restraints weight = 7187.738| |-----------------------------------------------------------------------------| r_work (start): 0.3598 rms_B_bonded: 2.56 r_work: 0.3494 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3365 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3365 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8496 moved from start: 0.4528 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= 0.072 Angle : 0.461 3.512 2770 Z= 0.271 Chirality : 0.061 0.148 330 Planarity : 0.001 0.003 340 Dihedral : 3.682 12.830 290 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 3.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.95 % Allowed : 13.33 % Favored : 85.71 % 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: -2.83 (0.38), residues: 270 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.15 (0.29), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS E 19 TYR 0.008 0.001 TYR A 16 Details of bonding type rmsd hydrogen bonds : bond 0.04599 ( 36) hydrogen bonds : angle 5.79978 ( 108) covalent geometry : bond 0.00160 ( 2070) covalent geometry : angle 0.46107 ( 2770) *********************** 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 41 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 39 time to evaluate : 0.353 Fit side-chains REVERT: B 26 SER cc_start: 0.8798 (m) cc_final: 0.8573 (p) REVERT: D 26 SER cc_start: 0.8620 (m) cc_final: 0.8328 (p) REVERT: E 26 SER cc_start: 0.8727 (m) cc_final: 0.8385 (p) REVERT: F 26 SER cc_start: 0.8714 (m) cc_final: 0.8313 (p) REVERT: F 34 LEU cc_start: 0.8793 (OUTLIER) cc_final: 0.8460 (tt) REVERT: G 26 SER cc_start: 0.8799 (m) cc_final: 0.8475 (p) REVERT: H 26 SER cc_start: 0.8717 (m) cc_final: 0.8375 (p) REVERT: J 17 GLU cc_start: 0.8318 (pt0) cc_final: 0.8048 (tt0) outliers start: 2 outliers final: 1 residues processed: 41 average time/residue: 0.1675 time to fit residues: 8.9625 Evaluate side-chains 41 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 39 time to evaluate : 0.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F 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 10 optimal weight: 5.9990 chunk 6 optimal weight: 2.9990 chunk 19 optimal weight: 0.6980 chunk 17 optimal weight: 0.0370 chunk 16 optimal weight: 0.0070 chunk 3 optimal weight: 0.1980 chunk 11 optimal weight: 0.8980 chunk 15 optimal weight: 0.9980 chunk 2 optimal weight: 0.7980 chunk 8 optimal weight: 3.9990 chunk 0 optimal weight: 4.9990 overall best weight: 0.3476 ------------------------------------------------------------------------------- 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 = 0.3937 r_free = 0.3937 target = 0.140115 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.118353 restraints weight = 7184.694| |-----------------------------------------------------------------------------| r_work (start): 0.3710 rms_B_bonded: 2.55 r_work: 0.3603 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3475 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3475 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8505 moved from start: 0.4630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.001 0.011 2070 Z= 0.064 Angle : 0.447 3.369 2770 Z= 0.262 Chirality : 0.060 0.145 330 Planarity : 0.001 0.003 340 Dihedral : 3.655 13.632 290 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 3.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.11 % Favored : 98.89 % Rotamer: Outliers : 0.95 % Allowed : 14.29 % 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 (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: -2.83 (0.38), residues: 270 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.15 (0.29), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS E 19 TYR 0.008 0.001 TYR A 16 Details of bonding type rmsd hydrogen bonds : bond 0.04143 ( 36) hydrogen bonds : angle 5.65803 ( 108) covalent geometry : bond 0.00142 ( 2070) covalent geometry : angle 0.44674 ( 2770) ********************** 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 42 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 40 time to evaluate : 0.354 Fit side-chains REVERT: B 26 SER cc_start: 0.8826 (m) cc_final: 0.8603 (p) REVERT: D 26 SER cc_start: 0.8623 (m) cc_final: 0.8341 (p) REVERT: E 26 SER cc_start: 0.8733 (m) cc_final: 0.8405 (p) REVERT: F 26 SER cc_start: 0.8680 (m) cc_final: 0.8297 (p) REVERT: F 34 LEU cc_start: 0.8797 (OUTLIER) cc_final: 0.8474 (tt) REVERT: G 26 SER cc_start: 0.8781 (m) cc_final: 0.8479 (p) REVERT: H 26 SER cc_start: 0.8757 (m) cc_final: 0.8432 (p) REVERT: J 17 GLU cc_start: 0.8310 (pt0) cc_final: 0.8066 (tt0) outliers start: 2 outliers final: 1 residues processed: 42 average time/residue: 0.2140 time to fit residues: 11.1950 Evaluate side-chains 40 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 38 time to evaluate : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F 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: 3.9990 chunk 19 optimal weight: 0.6980 chunk 5 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 chunk 16 optimal weight: 0.1980 chunk 1 optimal weight: 1.9990 chunk 3 optimal weight: 0.8980 chunk 12 optimal weight: 0.6980 chunk 4 optimal weight: 4.9990 chunk 13 optimal weight: 3.9990 chunk 10 optimal weight: 5.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- 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** G 21 GLN I 21 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.137648 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.115838 restraints weight = 7244.108| |-----------------------------------------------------------------------------| r_work (start): 0.3624 rms_B_bonded: 2.56 r_work: 0.3516 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3390 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3390 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8493 moved from start: 0.4658 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= 0.092 Angle : 0.476 3.485 2770 Z= 0.277 Chirality : 0.061 0.147 330 Planarity : 0.001 0.008 340 Dihedral : 3.673 17.448 290 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 2.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.74 % Favored : 99.26 % Rotamer: Outliers : 1.43 % Allowed : 16.19 % Favored : 82.38 % 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: -2.81 (0.38), residues: 270 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.13 (0.29), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.002 HIS C 19 TYR 0.008 0.001 TYR A 16 Details of bonding type rmsd hydrogen bonds : bond 0.04510 ( 36) hydrogen bonds : angle 5.62589 ( 108) covalent geometry : bond 0.00212 ( 2070) covalent geometry : angle 0.47576 ( 2770) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3698.98 seconds wall clock time: 64 minutes 39.20 seconds (3879.20 seconds total)