Starting phenix.real_space_refine on Thu Jun 5 01:28:02 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7qv6_14168/06_2025/7qv6_14168.cif Found real_map, /net/cci-nas-00/data/ceres_data/7qv6_14168/06_2025/7qv6_14168.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7qv6_14168/06_2025/7qv6_14168.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7qv6_14168/06_2025/7qv6_14168.map" model { file = "/net/cci-nas-00/data/ceres_data/7qv6_14168/06_2025/7qv6_14168.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7qv6_14168/06_2025/7qv6_14168.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians C 1512 2.51 5 N 378 2.21 5 O 396 1.98 5 H 2556 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 4842 Number of models: 1 Model: "" Number of chains: 18 Chain: "B" Number of atoms: 269 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 269 Classifications: {'peptide': 17} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'TRANS': 16} Chain: "A" Number of atoms: 269 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 269 Classifications: {'peptide': 17} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'TRANS': 16} Chain: "E" Number of atoms: 269 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 269 Classifications: {'peptide': 17} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'TRANS': 16} Chain: "D" Number of atoms: 269 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 269 Classifications: {'peptide': 17} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'TRANS': 16} Chain: "C" Number of atoms: 269 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 269 Classifications: {'peptide': 17} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'TRANS': 16} Chain: "F" Number of atoms: 269 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 269 Classifications: {'peptide': 17} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'TRANS': 16} Chain: "H" Number of atoms: 269 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 269 Classifications: {'peptide': 17} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'TRANS': 16} Chain: "G" Number of atoms: 269 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 269 Classifications: {'peptide': 17} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'TRANS': 16} Chain: "K" Number of atoms: 269 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 269 Classifications: {'peptide': 17} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'TRANS': 16} Chain: "J" Number of atoms: 269 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 269 Classifications: {'peptide': 17} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'TRANS': 16} Chain: "I" Number of atoms: 269 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 269 Classifications: {'peptide': 17} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'TRANS': 16} Chain: "L" Number of atoms: 269 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 269 Classifications: {'peptide': 17} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'TRANS': 16} Chain: "N" Number of atoms: 269 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 269 Classifications: {'peptide': 17} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'TRANS': 16} Chain: "M" Number of atoms: 269 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 269 Classifications: {'peptide': 17} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'TRANS': 16} Chain: "Q" Number of atoms: 269 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 269 Classifications: {'peptide': 17} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'TRANS': 16} Chain: "P" Number of atoms: 269 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 269 Classifications: {'peptide': 17} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'TRANS': 16} Chain: "O" Number of atoms: 269 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 269 Classifications: {'peptide': 17} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'TRANS': 16} Chain: "R" Number of atoms: 269 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 269 Classifications: {'peptide': 17} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'TRANS': 16} Time building chain proxies: 3.38, per 1000 atoms: 0.70 Number of scatterers: 4842 At special positions: 0 Unit cell: (94.35, 78.2, 33.15, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) O 396 8.00 N 378 7.00 C 1512 6.00 H 2556 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: 1.19 Conformation dependent library (CDL) restraints added in 308.9 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: 540 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 9 sheets defined 0.0% alpha, 58.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.44 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'B' and resid 2 through 10 Processing sheet with id=AA2, first strand: chain 'B' and resid 13 through 16 removed outlier: 6.582A pdb=" N ILE B 13 " --> pdb=" O VAL H 14 " (cutoff:3.500A) removed outlier: 8.258A pdb=" N SER H 16 " --> pdb=" O ILE B 13 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N SER B 15 " --> pdb=" O SER H 16 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N ILE H 13 " --> pdb=" O VAL N 14 " (cutoff:3.500A) removed outlier: 8.257A pdb=" N SER N 16 " --> pdb=" O ILE H 13 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N SER H 15 " --> pdb=" O SER N 16 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 2 through 8 removed outlier: 6.293A pdb=" N PHE A 3 " --> pdb=" O ASP G 4 " (cutoff:3.500A) removed outlier: 7.602A pdb=" N VAL G 6 " --> pdb=" O PHE A 3 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N ILE A 5 " --> pdb=" O VAL G 6 " (cutoff:3.500A) removed outlier: 7.859A pdb=" N LYS G 8 " --> pdb=" O ILE A 5 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N LYS A 7 " --> pdb=" O LYS G 8 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N PHE G 3 " --> pdb=" O ASP M 4 " (cutoff:3.500A) removed outlier: 7.602A pdb=" N VAL M 6 " --> pdb=" O PHE G 3 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N ILE G 5 " --> pdb=" O VAL M 6 " (cutoff:3.500A) removed outlier: 7.859A pdb=" N LYS M 8 " --> pdb=" O ILE G 5 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N LYS G 7 " --> pdb=" O LYS M 8 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 13 through 14 Processing sheet with id=AA5, first strand: chain 'E' and resid 5 through 7 Processing sheet with id=AA6, first strand: chain 'E' and resid 10 through 12 removed outlier: 6.322A pdb=" N ALA E 10 " --> pdb=" O GLY K 11 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N ALA K 10 " --> pdb=" O GLY Q 11 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'D' and resid 2 through 16 removed outlier: 9.319A pdb=" N PHE D 3 " --> pdb=" O ASP J 4 " (cutoff:3.500A) removed outlier: 10.367A pdb=" N VAL J 6 " --> pdb=" O PHE D 3 " (cutoff:3.500A) removed outlier: 9.033A pdb=" N ILE D 5 " --> pdb=" O VAL J 6 " (cutoff:3.500A) removed outlier: 10.271A pdb=" N LYS J 8 " --> pdb=" O ILE D 5 " (cutoff:3.500A) removed outlier: 9.063A pdb=" N LYS D 7 " --> pdb=" O LYS J 8 " (cutoff:3.500A) removed outlier: 10.437A pdb=" N ALA J 10 " --> pdb=" O LYS D 7 " (cutoff:3.500A) removed outlier: 9.064A pdb=" N ILE D 9 " --> pdb=" O ALA J 10 " (cutoff:3.500A) removed outlier: 10.262A pdb=" N HIS J 12 " --> pdb=" O ILE D 9 " (cutoff:3.500A) removed outlier: 5.652A pdb=" N GLY D 11 " --> pdb=" O HIS J 12 " (cutoff:3.500A) removed outlier: 7.330A pdb=" N VAL J 14 " --> pdb=" O GLY D 11 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N ILE D 13 " --> pdb=" O VAL J 14 " (cutoff:3.500A) removed outlier: 8.159A pdb=" N SER J 16 " --> pdb=" O ILE D 13 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N SER D 15 " --> pdb=" O SER J 16 " (cutoff:3.500A) removed outlier: 9.319A pdb=" N PHE J 3 " --> pdb=" O ASP P 4 " (cutoff:3.500A) removed outlier: 10.367A pdb=" N VAL P 6 " --> pdb=" O PHE J 3 " (cutoff:3.500A) removed outlier: 9.033A pdb=" N ILE J 5 " --> pdb=" O VAL P 6 " (cutoff:3.500A) removed outlier: 10.271A pdb=" N LYS P 8 " --> pdb=" O ILE J 5 " (cutoff:3.500A) removed outlier: 9.064A pdb=" N LYS J 7 " --> pdb=" O LYS P 8 " (cutoff:3.500A) removed outlier: 10.437A pdb=" N ALA P 10 " --> pdb=" O LYS J 7 " (cutoff:3.500A) removed outlier: 9.064A pdb=" N ILE J 9 " --> pdb=" O ALA P 10 " (cutoff:3.500A) removed outlier: 10.262A pdb=" N HIS P 12 " --> pdb=" O ILE J 9 " (cutoff:3.500A) removed outlier: 5.652A pdb=" N GLY J 11 " --> pdb=" O HIS P 12 " (cutoff:3.500A) removed outlier: 7.330A pdb=" N VAL P 14 " --> pdb=" O GLY J 11 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N ILE J 13 " --> pdb=" O VAL P 14 " (cutoff:3.500A) removed outlier: 8.158A pdb=" N SER P 16 " --> pdb=" O ILE J 13 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N SER J 15 " --> pdb=" O SER P 16 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'C' and resid 3 through 15 removed outlier: 5.970A pdb=" N PHE C 3 " --> pdb=" O ASP I 4 " (cutoff:3.500A) removed outlier: 7.149A pdb=" N VAL I 6 " --> pdb=" O PHE C 3 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N ILE C 5 " --> pdb=" O VAL I 6 " (cutoff:3.500A) removed outlier: 8.171A pdb=" N LYS I 8 " --> pdb=" O ILE C 5 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N LYS C 7 " --> pdb=" O LYS I 8 " (cutoff:3.500A) removed outlier: 8.384A pdb=" N ALA I 10 " --> pdb=" O LYS C 7 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N ILE C 9 " --> pdb=" O ALA I 10 " (cutoff:3.500A) removed outlier: 8.940A pdb=" N HIS I 12 " --> pdb=" O ILE C 9 " (cutoff:3.500A) removed outlier: 9.379A pdb=" N GLY C 11 " --> pdb=" O HIS I 12 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N VAL I 14 " --> pdb=" O GLY C 11 " (cutoff:3.500A) removed outlier: 9.049A pdb=" N ILE C 13 " --> pdb=" O VAL I 14 " (cutoff:3.500A) removed outlier: 5.970A pdb=" N PHE I 3 " --> pdb=" O ASP O 4 " (cutoff:3.500A) removed outlier: 7.150A pdb=" N VAL O 6 " --> pdb=" O PHE I 3 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N ILE I 5 " --> pdb=" O VAL O 6 " (cutoff:3.500A) removed outlier: 8.170A pdb=" N LYS O 8 " --> pdb=" O ILE I 5 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N LYS I 7 " --> pdb=" O LYS O 8 " (cutoff:3.500A) removed outlier: 8.384A pdb=" N ALA O 10 " --> pdb=" O LYS I 7 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N ILE I 9 " --> pdb=" O ALA O 10 " (cutoff:3.500A) removed outlier: 8.940A pdb=" N HIS O 12 " --> pdb=" O ILE I 9 " (cutoff:3.500A) removed outlier: 9.378A pdb=" N GLY I 11 " --> pdb=" O HIS O 12 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N VAL O 14 " --> pdb=" O GLY I 11 " (cutoff:3.500A) removed outlier: 9.048A pdb=" N ILE I 13 " --> pdb=" O VAL O 14 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'F' and resid 3 through 15 46 hydrogen bonds defined for protein. 138 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.32 Time building geometry restraints manager: 1.45 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 0.98: 2556 0.98 - 1.12: 0 1.12 - 1.26: 360 1.26 - 1.40: 486 1.40 - 1.54: 1458 Bond restraints: 4860 Sorted by residual: bond pdb=" CB VAL C 14 " pdb=" CG2 VAL C 14 " ideal model delta sigma weight residual 1.521 1.474 0.047 3.30e-02 9.18e+02 2.01e+00 bond pdb=" CB VAL I 14 " pdb=" CG2 VAL I 14 " ideal model delta sigma weight residual 1.521 1.474 0.047 3.30e-02 9.18e+02 1.99e+00 bond pdb=" CB VAL O 14 " pdb=" CG2 VAL O 14 " ideal model delta sigma weight residual 1.521 1.475 0.046 3.30e-02 9.18e+02 1.93e+00 bond pdb=" CG1 ILE F 13 " pdb=" CD1 ILE F 13 " ideal model delta sigma weight residual 1.513 1.461 0.052 3.90e-02 6.57e+02 1.77e+00 bond pdb=" CG1 ILE L 13 " pdb=" CD1 ILE L 13 " ideal model delta sigma weight residual 1.513 1.462 0.051 3.90e-02 6.57e+02 1.74e+00 ... (remaining 4855 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.90: 8229 0.90 - 1.80: 615 1.80 - 2.70: 50 2.70 - 3.59: 7 3.59 - 4.49: 9 Bond angle restraints: 8910 Sorted by residual: angle pdb=" N GLY Q 11 " pdb=" CA GLY Q 11 " pdb=" C GLY Q 11 " ideal model delta sigma weight residual 110.45 114.94 -4.49 1.30e+00 5.92e-01 1.19e+01 angle pdb=" N GLY K 11 " pdb=" CA GLY K 11 " pdb=" C GLY K 11 " ideal model delta sigma weight residual 110.45 114.93 -4.48 1.30e+00 5.92e-01 1.19e+01 angle pdb=" N GLY E 11 " pdb=" CA GLY E 11 " pdb=" C GLY E 11 " ideal model delta sigma weight residual 110.45 114.93 -4.48 1.30e+00 5.92e-01 1.19e+01 angle pdb=" N GLY R 11 " pdb=" CA GLY R 11 " pdb=" C GLY R 11 " ideal model delta sigma weight residual 110.29 114.31 -4.02 1.28e+00 6.10e-01 9.84e+00 angle pdb=" N GLY F 11 " pdb=" CA GLY F 11 " pdb=" C GLY F 11 " ideal model delta sigma weight residual 110.29 114.31 -4.02 1.28e+00 6.10e-01 9.84e+00 ... (remaining 8905 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 12.69: 1896 12.69 - 25.37: 119 25.37 - 38.06: 61 38.06 - 50.74: 54 50.74 - 63.43: 30 Dihedral angle restraints: 2160 sinusoidal: 1188 harmonic: 972 Sorted by residual: dihedral pdb=" CA ASP L 4 " pdb=" C ASP L 4 " pdb=" N ILE L 5 " pdb=" CA ILE L 5 " ideal model delta harmonic sigma weight residual 180.00 165.32 14.68 0 5.00e+00 4.00e-02 8.62e+00 dihedral pdb=" CA ASP F 4 " pdb=" C ASP F 4 " pdb=" N ILE F 5 " pdb=" CA ILE F 5 " ideal model delta harmonic sigma weight residual 180.00 165.33 14.67 0 5.00e+00 4.00e-02 8.60e+00 dihedral pdb=" CA ASP R 4 " pdb=" C ASP R 4 " pdb=" N ILE R 5 " pdb=" CA ILE R 5 " ideal model delta harmonic sigma weight residual 180.00 165.35 14.65 0 5.00e+00 4.00e-02 8.59e+00 ... (remaining 2157 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.024: 141 0.024 - 0.047: 87 0.047 - 0.071: 66 0.071 - 0.094: 75 0.094 - 0.118: 27 Chirality restraints: 396 Sorted by residual: chirality pdb=" CA ILE Q 5 " pdb=" N ILE Q 5 " pdb=" C ILE Q 5 " pdb=" CB ILE Q 5 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.48e-01 chirality pdb=" CA ILE F 9 " pdb=" N ILE F 9 " pdb=" C ILE F 9 " pdb=" CB ILE F 9 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.47e-01 chirality pdb=" CA ILE L 9 " pdb=" N ILE L 9 " pdb=" C ILE L 9 " pdb=" CB ILE L 9 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.47e-01 ... (remaining 393 not shown) Planarity restraints: 648 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB HIS J 12 " 0.007 2.00e-02 2.50e+03 4.46e-03 4.48e-01 pdb=" CG HIS J 12 " -0.011 2.00e-02 2.50e+03 pdb=" ND1 HIS J 12 " 0.001 2.00e-02 2.50e+03 pdb=" CD2 HIS J 12 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 HIS J 12 " 0.000 2.00e-02 2.50e+03 pdb=" NE2 HIS J 12 " -0.000 2.00e-02 2.50e+03 pdb=" HD2 HIS J 12 " -0.000 2.00e-02 2.50e+03 pdb=" HE1 HIS J 12 " 0.001 2.00e-02 2.50e+03 pdb=" HE2 HIS J 12 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS P 12 " 0.007 2.00e-02 2.50e+03 4.38e-03 4.31e-01 pdb=" CG HIS P 12 " -0.011 2.00e-02 2.50e+03 pdb=" ND1 HIS P 12 " 0.001 2.00e-02 2.50e+03 pdb=" CD2 HIS P 12 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 HIS P 12 " -0.000 2.00e-02 2.50e+03 pdb=" NE2 HIS P 12 " 0.000 2.00e-02 2.50e+03 pdb=" HD2 HIS P 12 " 0.000 2.00e-02 2.50e+03 pdb=" HE1 HIS P 12 " 0.001 2.00e-02 2.50e+03 pdb=" HE2 HIS P 12 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS D 12 " 0.006 2.00e-02 2.50e+03 4.35e-03 4.26e-01 pdb=" CG HIS D 12 " -0.011 2.00e-02 2.50e+03 pdb=" ND1 HIS D 12 " 0.001 2.00e-02 2.50e+03 pdb=" CD2 HIS D 12 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 HIS D 12 " 0.000 2.00e-02 2.50e+03 pdb=" NE2 HIS D 12 " -0.000 2.00e-02 2.50e+03 pdb=" HD2 HIS D 12 " -0.000 2.00e-02 2.50e+03 pdb=" HE1 HIS D 12 " 0.001 2.00e-02 2.50e+03 pdb=" HE2 HIS D 12 " 0.002 2.00e-02 2.50e+03 ... (remaining 645 not shown) Histogram of nonbonded interaction distances: 1.94 - 2.45: 3232 2.45 - 2.97: 10383 2.97 - 3.48: 9111 3.48 - 3.99: 13759 3.99 - 4.50: 18178 Nonbonded interactions: 54663 Sorted by model distance: nonbonded pdb=" O GLY F 1 " pdb=" H2 GLY L 1 " model vdw 1.943 2.450 nonbonded pdb=" O GLY L 1 " pdb=" H2 GLY R 1 " model vdw 1.943 2.450 nonbonded pdb="HD23 LEU J 2 " pdb="HD13 LEU P 2 " model vdw 1.954 2.440 nonbonded pdb="HD23 LEU D 2 " pdb="HD13 LEU J 2 " model vdw 1.954 2.440 nonbonded pdb=" O PHE C 3 " pdb=" H ASP I 4 " model vdw 2.008 2.450 ... (remaining 54658 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' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' } 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 group one per residue 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: 2.620 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: 0.090 Extract box with map and model: 0.190 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 15.270 Find NCS groups from input model: 0.140 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:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8405 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 : 0.011 0.052 2304 Z= 0.435 Angle : 0.587 4.492 3078 Z= 0.355 Chirality : 0.054 0.118 396 Planarity : 0.001 0.005 360 Dihedral : 11.565 54.871 810 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 1.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.11 % Favored : 98.89 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.85 (0.39), residues: 270 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.40 (0.30), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS J 12 PHE 0.008 0.002 PHE M 3 Details of bonding type rmsd hydrogen bonds : bond 0.22231 ( 46) hydrogen bonds : angle 7.62708 ( 138) covalent geometry : bond 0.01063 ( 2304) covalent geometry : angle 0.58679 ( 3078) *********************** 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 21 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 21 time to evaluate : 0.411 Fit side-chains REVERT: D 8 LYS cc_start: 0.8600 (mtpt) cc_final: 0.8347 (ttmm) REVERT: J 8 LYS cc_start: 0.8534 (mtpt) cc_final: 0.8292 (mtpp) REVERT: P 8 LYS cc_start: 0.8923 (mtpt) cc_final: 0.8594 (mtpp) outliers start: 0 outliers final: 0 residues processed: 21 average time/residue: 0.7540 time to fit residues: 17.4121 Evaluate side-chains 20 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 20 time to evaluate : 0.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 15 optimal weight: 3.9990 chunk 13 optimal weight: 3.9990 chunk 7 optimal weight: 0.9990 chunk 4 optimal weight: 4.9990 chunk 9 optimal weight: 2.9990 chunk 14 optimal weight: 3.9990 chunk 5 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 16 optimal weight: 5.9990 chunk 11 optimal weight: 3.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 12 HIS Q 12 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.124145 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.099983 restraints weight = 9543.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.106204 restraints weight = 4202.839| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.109973 restraints weight = 2452.671| |-----------------------------------------------------------------------------| r_work (final): 0.3736 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8426 moved from start: 0.1146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 2304 Z= 0.152 Angle : 0.423 2.849 3078 Z= 0.243 Chirality : 0.061 0.146 396 Planarity : 0.002 0.007 360 Dihedral : 8.378 45.830 306 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 1.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % 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: -0.72 (0.45), residues: 270 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.54 (0.34), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS A 12 PHE 0.005 0.001 PHE B 3 Details of bonding type rmsd hydrogen bonds : bond 0.03290 ( 46) hydrogen bonds : angle 4.75607 ( 138) covalent geometry : bond 0.00308 ( 2304) covalent geometry : angle 0.42290 ( 3078) *********************** 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 20 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 20 time to evaluate : 0.449 Fit side-chains REVERT: D 8 LYS cc_start: 0.8683 (mtpt) cc_final: 0.8374 (ttmm) REVERT: J 8 LYS cc_start: 0.8638 (mtpt) cc_final: 0.8376 (mtpp) REVERT: P 8 LYS cc_start: 0.8949 (mtpt) cc_final: 0.8610 (mtpp) outliers start: 0 outliers final: 0 residues processed: 20 average time/residue: 0.6068 time to fit residues: 13.9127 Evaluate side-chains 18 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 18 time to evaluate : 0.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 12 optimal weight: 5.9990 chunk 14 optimal weight: 4.9990 chunk 9 optimal weight: 5.9990 chunk 7 optimal weight: 8.9990 chunk 16 optimal weight: 0.0470 chunk 17 optimal weight: 2.9990 chunk 4 optimal weight: 5.9990 chunk 3 optimal weight: 0.6980 chunk 11 optimal weight: 0.8980 chunk 6 optimal weight: 3.9990 chunk 13 optimal weight: 2.9990 overall best weight: 1.5282 ------------------------------------------------------------------------------- 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 = 0.3927 r_free = 0.3927 target = 0.127199 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.102703 restraints weight = 9565.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.108925 restraints weight = 4208.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.112747 restraints weight = 2454.562| |-----------------------------------------------------------------------------| r_work (final): 0.3776 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8406 moved from start: 0.1677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.017 2304 Z= 0.107 Angle : 0.365 2.160 3078 Z= 0.206 Chirality : 0.061 0.141 396 Planarity : 0.001 0.006 360 Dihedral : 6.409 33.192 306 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 1.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.00 % Allowed : 5.95 % Favored : 94.05 % 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: 0.09 (0.49), residues: 270 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : 0.08 (0.37), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS E 12 PHE 0.007 0.001 PHE J 3 Details of bonding type rmsd hydrogen bonds : bond 0.02606 ( 46) hydrogen bonds : angle 4.42633 ( 138) covalent geometry : bond 0.00212 ( 2304) covalent geometry : angle 0.36507 ( 3078) *********************** 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 22 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 22 time to evaluate : 0.429 Fit side-chains REVERT: D 8 LYS cc_start: 0.8608 (mtpt) cc_final: 0.8033 (mttm) REVERT: J 8 LYS cc_start: 0.8620 (mtpt) cc_final: 0.8349 (mtpp) REVERT: P 8 LYS cc_start: 0.8982 (mtpt) cc_final: 0.8601 (mtpp) outliers start: 0 outliers final: 0 residues processed: 22 average time/residue: 0.5570 time to fit residues: 13.8837 Evaluate side-chains 18 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 18 time to evaluate : 0.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 14 optimal weight: 5.9990 chunk 12 optimal weight: 5.9990 chunk 0 optimal weight: 5.9990 chunk 15 optimal weight: 5.9990 chunk 4 optimal weight: 5.9990 chunk 11 optimal weight: 6.9990 chunk 2 optimal weight: 2.9990 chunk 3 optimal weight: 5.9990 chunk 8 optimal weight: 0.9980 chunk 6 optimal weight: 0.8980 chunk 10 optimal weight: 0.9980 overall best weight: 2.3784 ------------------------------------------------------------------------------- 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 = 0.3896 r_free = 0.3896 target = 0.124910 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.100559 restraints weight = 9691.700| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.106610 restraints weight = 4296.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.110412 restraints weight = 2509.254| |-----------------------------------------------------------------------------| r_work (final): 0.3737 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8422 moved from start: 0.1973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 2304 Z= 0.149 Angle : 0.380 3.033 3078 Z= 0.212 Chirality : 0.061 0.142 396 Planarity : 0.001 0.006 360 Dihedral : 6.424 35.267 306 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 1.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.37 % Favored : 99.63 % Rotamer: Outliers : 0.00 % Allowed : 6.35 % Favored : 93.65 % 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: 0.24 (0.50), residues: 270 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : 0.20 (0.38), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS Q 12 PHE 0.005 0.001 PHE A 3 Details of bonding type rmsd hydrogen bonds : bond 0.02354 ( 46) hydrogen bonds : angle 4.41764 ( 138) covalent geometry : bond 0.00312 ( 2304) covalent geometry : angle 0.38007 ( 3078) *********************** 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 20 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 20 time to evaluate : 0.448 Fit side-chains REVERT: D 8 LYS cc_start: 0.8564 (mtpt) cc_final: 0.8009 (mttm) REVERT: J 8 LYS cc_start: 0.8684 (mtpt) cc_final: 0.8400 (mtpp) REVERT: P 8 LYS cc_start: 0.8964 (mtpt) cc_final: 0.8588 (mtpp) outliers start: 0 outliers final: 0 residues processed: 20 average time/residue: 0.7272 time to fit residues: 16.0827 Evaluate side-chains 20 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 20 time to evaluate : 0.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 14 optimal weight: 5.9990 chunk 6 optimal weight: 6.9990 chunk 2 optimal weight: 4.9990 chunk 15 optimal weight: 2.9990 chunk 4 optimal weight: 5.9990 chunk 16 optimal weight: 6.9990 chunk 8 optimal weight: 1.9990 chunk 13 optimal weight: 6.9990 chunk 0 optimal weight: 0.6980 chunk 10 optimal weight: 2.9990 chunk 1 optimal weight: 5.9990 overall best weight: 2.7388 ------------------------------------------------------------------------------- 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 = 0.3979 r_free = 0.3979 target = 0.133492 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.109948 restraints weight = 9230.975| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.116531 restraints weight = 3860.939| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.120454 restraints weight = 2162.168| |-----------------------------------------------------------------------------| r_work (final): 0.3831 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8447 moved from start: 0.2257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 2304 Z= 0.163 Angle : 0.376 2.822 3078 Z= 0.212 Chirality : 0.060 0.142 396 Planarity : 0.001 0.005 360 Dihedral : 6.618 39.264 306 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 1.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.37 % Favored : 99.63 % Rotamer: Outliers : 0.00 % Allowed : 6.35 % Favored : 93.65 % 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: 0.29 (0.50), residues: 270 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : 0.23 (0.38), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS Q 12 PHE 0.004 0.001 PHE B 3 Details of bonding type rmsd hydrogen bonds : bond 0.02442 ( 46) hydrogen bonds : angle 4.32542 ( 138) covalent geometry : bond 0.00338 ( 2304) covalent geometry : angle 0.37629 ( 3078) *********************** 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 21 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 21 time to evaluate : 0.373 Fit side-chains REVERT: D 8 LYS cc_start: 0.8538 (mtpt) cc_final: 0.8068 (mttm) REVERT: P 8 LYS cc_start: 0.8923 (mtpt) cc_final: 0.8501 (mtpp) outliers start: 0 outliers final: 0 residues processed: 21 average time/residue: 0.6668 time to fit residues: 15.4093 Evaluate side-chains 19 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 19 time to evaluate : 0.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 0 optimal weight: 5.9990 chunk 14 optimal weight: 5.9990 chunk 8 optimal weight: 0.9980 chunk 5 optimal weight: 3.9990 chunk 15 optimal weight: 2.9990 chunk 11 optimal weight: 3.9990 chunk 16 optimal weight: 4.9990 chunk 7 optimal weight: 7.9990 chunk 10 optimal weight: 3.9990 chunk 13 optimal weight: 0.9980 chunk 9 optimal weight: 2.9990 overall best weight: 2.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.134450 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.110951 restraints weight = 9177.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.117446 restraints weight = 3858.522| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.121408 restraints weight = 2175.131| |-----------------------------------------------------------------------------| r_work (final): 0.3845 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8445 moved from start: 0.2428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 2304 Z= 0.145 Angle : 0.381 3.858 3078 Z= 0.212 Chirality : 0.061 0.143 396 Planarity : 0.001 0.004 360 Dihedral : 6.325 37.775 306 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 1.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.37 % Favored : 99.63 % Rotamer: Outliers : 0.00 % Allowed : 6.75 % Favored : 93.25 % 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: 0.31 (0.51), residues: 270 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : 0.25 (0.39), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS Q 12 PHE 0.004 0.001 PHE O 3 Details of bonding type rmsd hydrogen bonds : bond 0.02115 ( 46) hydrogen bonds : angle 4.19620 ( 138) covalent geometry : bond 0.00299 ( 2304) covalent geometry : angle 0.38112 ( 3078) *********************** 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 22 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 22 time to evaluate : 0.379 Fit side-chains REVERT: D 8 LYS cc_start: 0.8547 (mtpt) cc_final: 0.8099 (mttm) REVERT: P 8 LYS cc_start: 0.8927 (mtpt) cc_final: 0.8495 (mtpp) outliers start: 0 outliers final: 0 residues processed: 22 average time/residue: 0.6648 time to fit residues: 16.1188 Evaluate side-chains 20 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 20 time to evaluate : 0.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 16 optimal weight: 4.9990 chunk 6 optimal weight: 6.9990 chunk 11 optimal weight: 3.9990 chunk 17 optimal weight: 0.9990 chunk 7 optimal weight: 6.9990 chunk 9 optimal weight: 5.9990 chunk 1 optimal weight: 0.6980 chunk 4 optimal weight: 5.9990 chunk 13 optimal weight: 2.9990 chunk 2 optimal weight: 2.9990 chunk 0 optimal weight: 0.6980 overall best weight: 1.6786 ------------------------------------------------------------------------------- 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 = 0.4008 r_free = 0.4008 target = 0.136167 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.112743 restraints weight = 8995.810| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.119309 restraints weight = 3808.055| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.123269 restraints weight = 2138.152| |-----------------------------------------------------------------------------| r_work (final): 0.3862 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8430 moved from start: 0.2606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.017 2304 Z= 0.104 Angle : 0.361 3.176 3078 Z= 0.200 Chirality : 0.062 0.144 396 Planarity : 0.001 0.004 360 Dihedral : 5.585 30.324 306 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 1.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.37 % Favored : 99.63 % Rotamer: Outliers : 0.00 % Allowed : 7.54 % Favored : 92.46 % 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: 0.46 (0.52), residues: 270 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : 0.36 (0.40), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS O 12 PHE 0.003 0.001 PHE O 3 Details of bonding type rmsd hydrogen bonds : bond 0.01791 ( 46) hydrogen bonds : angle 4.04128 ( 138) covalent geometry : bond 0.00212 ( 2304) covalent geometry : angle 0.36085 ( 3078) *********************** 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 21 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 21 time to evaluate : 0.376 Fit side-chains REVERT: D 8 LYS cc_start: 0.8514 (mtpt) cc_final: 0.8106 (mttm) REVERT: P 8 LYS cc_start: 0.8940 (mtpt) cc_final: 0.8489 (mtpp) outliers start: 0 outliers final: 0 residues processed: 21 average time/residue: 0.6790 time to fit residues: 15.6818 Evaluate side-chains 20 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 20 time to evaluate : 0.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 7 optimal weight: 6.9990 chunk 9 optimal weight: 6.9990 chunk 10 optimal weight: 6.9990 chunk 1 optimal weight: 0.7980 chunk 2 optimal weight: 4.9990 chunk 15 optimal weight: 0.8980 chunk 17 optimal weight: 4.9990 chunk 0 optimal weight: 5.9990 chunk 16 optimal weight: 0.8980 chunk 8 optimal weight: 2.9990 chunk 14 optimal weight: 1.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- 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 = 0.4010 r_free = 0.4010 target = 0.136255 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.112663 restraints weight = 9128.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.119305 restraints weight = 3849.134| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.123341 restraints weight = 2156.741| |-----------------------------------------------------------------------------| r_work (final): 0.3867 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8424 moved from start: 0.2663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 2304 Z= 0.098 Angle : 0.361 3.390 3078 Z= 0.199 Chirality : 0.062 0.143 396 Planarity : 0.001 0.004 360 Dihedral : 5.331 28.283 306 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 1.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.37 % Favored : 99.63 % Rotamer: Outliers : 0.00 % Allowed : 7.94 % Favored : 92.06 % 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: 0.51 (0.52), residues: 270 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : 0.40 (0.40), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS E 12 PHE 0.003 0.001 PHE E 3 Details of bonding type rmsd hydrogen bonds : bond 0.01733 ( 46) hydrogen bonds : angle 4.00226 ( 138) covalent geometry : bond 0.00198 ( 2304) covalent geometry : angle 0.36118 ( 3078) *********************** 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 22 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 22 time to evaluate : 0.389 Fit side-chains REVERT: D 8 LYS cc_start: 0.8512 (mtpt) cc_final: 0.8118 (mttm) REVERT: P 8 LYS cc_start: 0.8958 (mtpt) cc_final: 0.8520 (mtpp) outliers start: 0 outliers final: 0 residues processed: 22 average time/residue: 0.6609 time to fit residues: 16.0513 Evaluate side-chains 21 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 21 time to evaluate : 0.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 1 optimal weight: 6.9990 chunk 3 optimal weight: 5.9990 chunk 6 optimal weight: 6.9990 chunk 12 optimal weight: 0.7980 chunk 14 optimal weight: 0.7980 chunk 5 optimal weight: 0.7980 chunk 17 optimal weight: 4.9990 chunk 8 optimal weight: 0.7980 chunk 9 optimal weight: 3.9990 chunk 10 optimal weight: 6.9990 chunk 16 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 = 0.4027 r_free = 0.4027 target = 0.137933 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.115052 restraints weight = 8931.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.121461 restraints weight = 3861.683| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.125282 restraints weight = 2190.813| |-----------------------------------------------------------------------------| r_work (final): 0.3896 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8438 moved from start: 0.2771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.001 0.019 2304 Z= 0.069 Angle : 0.354 3.395 3078 Z= 0.194 Chirality : 0.063 0.143 396 Planarity : 0.001 0.005 360 Dihedral : 4.752 22.487 306 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 1.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.00 % Allowed : 7.94 % Favored : 92.06 % 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: 0.63 (0.53), residues: 270 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : 0.49 (0.41), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS E 12 PHE 0.002 0.000 PHE E 3 Details of bonding type rmsd hydrogen bonds : bond 0.01425 ( 46) hydrogen bonds : angle 3.88519 ( 138) covalent geometry : bond 0.00145 ( 2304) covalent geometry : angle 0.35412 ( 3078) *********************** 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 22 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 22 time to evaluate : 0.380 Fit side-chains REVERT: D 8 LYS cc_start: 0.8567 (mtpt) cc_final: 0.8216 (mttm) REVERT: P 8 LYS cc_start: 0.8945 (mtpt) cc_final: 0.8497 (mtpp) outliers start: 0 outliers final: 0 residues processed: 22 average time/residue: 0.6259 time to fit residues: 15.3946 Evaluate side-chains 21 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 21 time to evaluate : 0.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 6 optimal weight: 6.9990 chunk 4 optimal weight: 5.9990 chunk 16 optimal weight: 0.3980 chunk 5 optimal weight: 0.7980 chunk 3 optimal weight: 5.9990 chunk 10 optimal weight: 0.7980 chunk 1 optimal weight: 5.9990 chunk 17 optimal weight: 3.9990 chunk 9 optimal weight: 3.9990 chunk 2 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- 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 = 0.4015 r_free = 0.4015 target = 0.137038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.113841 restraints weight = 9127.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.120307 restraints weight = 3943.093| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.124211 restraints weight = 2238.168| |-----------------------------------------------------------------------------| r_work (final): 0.3874 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8444 moved from start: 0.2791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 2304 Z= 0.093 Angle : 0.357 3.346 3078 Z= 0.196 Chirality : 0.062 0.142 396 Planarity : 0.001 0.005 360 Dihedral : 4.761 23.353 306 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 1.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.00 % Allowed : 7.54 % Favored : 92.46 % 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: 0.65 (0.53), residues: 270 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : 0.51 (0.40), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS E 12 PHE 0.005 0.001 PHE Q 3 Details of bonding type rmsd hydrogen bonds : bond 0.01682 ( 46) hydrogen bonds : angle 3.92755 ( 138) covalent geometry : bond 0.00190 ( 2304) covalent geometry : angle 0.35714 ( 3078) ********************** 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 22 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 22 time to evaluate : 0.372 Fit side-chains REVERT: D 8 LYS cc_start: 0.8535 (mtpt) cc_final: 0.8186 (mttm) REVERT: P 8 LYS cc_start: 0.8949 (mtpt) cc_final: 0.8491 (mtpp) outliers start: 0 outliers final: 0 residues processed: 22 average time/residue: 0.6451 time to fit residues: 15.7034 Evaluate side-chains 22 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 22 time to evaluate : 0.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 8 optimal weight: 6.9990 chunk 1 optimal weight: 5.9990 chunk 7 optimal weight: 1.9990 chunk 9 optimal weight: 4.9990 chunk 4 optimal weight: 5.9990 chunk 13 optimal weight: 0.9980 chunk 17 optimal weight: 3.9990 chunk 11 optimal weight: 4.9990 chunk 5 optimal weight: 0.9990 chunk 14 optimal weight: 1.9990 chunk 2 optimal weight: 0.9980 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.137654 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.114704 restraints weight = 9054.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.121030 restraints weight = 3960.836| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.124963 restraints weight = 2260.833| |-----------------------------------------------------------------------------| r_work (final): 0.3883 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8445 moved from start: 0.2871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 2304 Z= 0.089 Angle : 0.354 3.333 3078 Z= 0.195 Chirality : 0.062 0.142 396 Planarity : 0.001 0.005 360 Dihedral : 4.712 24.197 306 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 1.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.00 % Allowed : 7.54 % Favored : 92.46 % 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: 0.71 (0.53), residues: 270 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : 0.55 (0.41), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS E 12 PHE 0.005 0.001 PHE Q 3 Details of bonding type rmsd hydrogen bonds : bond 0.01621 ( 46) hydrogen bonds : angle 3.91638 ( 138) covalent geometry : bond 0.00181 ( 2304) covalent geometry : angle 0.35450 ( 3078) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2517.58 seconds wall clock time: 44 minutes 14.39 seconds (2654.39 seconds total)