Starting phenix.real_space_refine on Tue Feb 11 07:57:09 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7qv6_14168/02_2025/7qv6_14168.cif Found real_map, /net/cci-nas-00/data/ceres_data/7qv6_14168/02_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_14168/02_2025/7qv6_14168.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7qv6_14168/02_2025/7qv6_14168.map" model { file = "/net/cci-nas-00/data/ceres_data/7qv6_14168/02_2025/7qv6_14168.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7qv6_14168/02_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-5592/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: 3.13, per 1000 atoms: 0.65 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: 1.10 Conformation dependent library (CDL) restraints added in 284.5 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: 0.49 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: 1.41 Time building geometry restraints manager: 1.35 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: 1.780 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.080 Extract box with map and model: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 14.830 Find NCS groups from input model: 0.150 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:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.970 ------------------------------------------------------------------------------- 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= 0.711 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 *********************** 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 : 0.418 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: 0.7526 time to fit residues: 17.4185 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 : 0.411 ------------------------------------------------------------------------------- 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: 0.9990 chunk 10 optimal weight: 2.9990 chunk 16 optimal weight: 5.9990 chunk 11 optimal weight: 3.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- 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 = 0.3889 r_free = 0.3889 target = 0.124173 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.100011 restraints weight = 9628.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.106076 restraints weight = 4286.148| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.109853 restraints weight = 2519.031| |-----------------------------------------------------------------------------| r_work (final): 0.3739 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8424 moved from start: 0.1159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.018 2304 Z= 0.186 Angle : 0.414 2.826 3078 Z= 0.238 Chirality : 0.062 0.149 396 Planarity : 0.002 0.007 360 Dihedral : 8.245 45.384 306 Min Nonbonded Distance : 2.554 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: -0.67 (0.45), residues: 270 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.50 (0.34), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS P 12 PHE 0.005 0.001 PHE B 3 *********************** 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 : 0.391 Fit side-chains REVERT: D 8 LYS cc_start: 0.8686 (mtpt) cc_final: 0.8375 (ttmm) REVERT: J 8 LYS cc_start: 0.8638 (mtpt) cc_final: 0.8372 (mtpp) REVERT: P 8 LYS cc_start: 0.8939 (mtpt) cc_final: 0.8597 (mtpp) outliers start: 0 outliers final: 0 residues processed: 20 average time/residue: 0.5983 time to fit residues: 13.5384 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 : 0.387 ------------------------------------------------------------------------------- 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: 5.9990 chunk 9 optimal weight: 5.9990 chunk 7 optimal weight: 8.9990 chunk 16 optimal weight: 5.9990 chunk 17 optimal weight: 2.9990 chunk 4 optimal weight: 5.9990 chunk 3 optimal weight: 0.8980 chunk 11 optimal weight: 3.9990 chunk 6 optimal weight: 4.9990 chunk 13 optimal weight: 1.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- 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 = 0.3880 r_free = 0.3880 target = 0.123799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.099887 restraints weight = 9715.778| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.105797 restraints weight = 4326.472| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.109581 restraints weight = 2540.848| |-----------------------------------------------------------------------------| r_work (final): 0.3724 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8444 moved from start: 0.1713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 2304 Z= 0.262 Angle : 0.403 2.348 3078 Z= 0.228 Chirality : 0.060 0.137 396 Planarity : 0.001 0.005 360 Dihedral : 7.797 45.322 306 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 1.65 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 (0.48), residues: 270 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.06 (0.37), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS Q 12 PHE 0.008 0.001 PHE J 3 *********************** 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 : 0.401 Fit side-chains REVERT: D 7 LYS cc_start: 0.8510 (mttt) cc_final: 0.8308 (mttm) REVERT: D 8 LYS cc_start: 0.8524 (mtpt) cc_final: 0.7976 (mttm) REVERT: J 8 LYS cc_start: 0.8632 (mtpt) cc_final: 0.8331 (mtpp) REVERT: P 8 LYS cc_start: 0.8966 (mtpt) cc_final: 0.8573 (mtpp) outliers start: 0 outliers final: 0 residues processed: 22 average time/residue: 0.6773 time to fit residues: 16.5183 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 : 0.393 ------------------------------------------------------------------------------- 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: 0.0060 chunk 4 optimal weight: 5.9990 chunk 11 optimal weight: 6.9990 chunk 2 optimal weight: 4.9990 chunk 3 optimal weight: 5.9990 chunk 8 optimal weight: 0.9980 chunk 6 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 overall best weight: 2.0002 ------------------------------------------------------------------------------- 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 = 0.3933 r_free = 0.3933 target = 0.129280 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.105182 restraints weight = 9523.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.111307 restraints weight = 4260.637| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.115129 restraints weight = 2481.965| |-----------------------------------------------------------------------------| r_work (final): 0.3761 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8396 moved from start: 0.1995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.015 2304 Z= 0.167 Angle : 0.371 2.660 3078 Z= 0.208 Chirality : 0.061 0.141 396 Planarity : 0.001 0.005 360 Dihedral : 6.749 39.610 306 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 1.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: 0.20 (0.50), residues: 270 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : 0.16 (0.38), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS O 12 PHE 0.003 0.001 PHE M 3 *********************** 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 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 Fit side-chains REVERT: D 8 LYS cc_start: 0.8549 (mtpt) cc_final: 0.7990 (mttm) REVERT: P 8 LYS cc_start: 0.8947 (mtpt) cc_final: 0.8574 (mtpp) outliers start: 0 outliers final: 0 residues processed: 21 average time/residue: 0.7072 time to fit residues: 16.3482 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 : 0.380 ------------------------------------------------------------------------------- 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: 7.9990 chunk 2 optimal weight: 4.9990 chunk 15 optimal weight: 4.9990 chunk 4 optimal weight: 5.9990 chunk 16 optimal weight: 6.9990 chunk 8 optimal weight: 0.9980 chunk 13 optimal weight: 5.9990 chunk 0 optimal weight: 0.6980 chunk 10 optimal weight: 0.8980 chunk 1 optimal weight: 5.9990 overall best weight: 2.5184 ------------------------------------------------------------------------------- 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 = 0.3986 r_free = 0.3986 target = 0.133874 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.110360 restraints weight = 9202.254| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.116930 restraints weight = 3850.780| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.120854 restraints weight = 2152.345| |-----------------------------------------------------------------------------| r_work (final): 0.3837 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8450 moved from start: 0.2256 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= 0.218 Angle : 0.386 3.845 3078 Z= 0.215 Chirality : 0.061 0.137 396 Planarity : 0.001 0.004 360 Dihedral : 6.630 39.583 306 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 1.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.37 % Favored : 99.63 % Rotamer: Outliers : 0.00 % Allowed : 7.14 % Favored : 92.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.24 (0.50), residues: 270 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : 0.20 (0.39), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS Q 12 PHE 0.005 0.001 PHE O 3 *********************** 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 22 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 22 time to evaluate : 0.412 Fit side-chains REVERT: D 8 LYS cc_start: 0.8543 (mtpt) cc_final: 0.8065 (mttm) REVERT: P 8 LYS cc_start: 0.8909 (mtpt) cc_final: 0.8505 (mtpp) outliers start: 0 outliers final: 0 residues processed: 22 average time/residue: 0.6727 time to fit residues: 16.3678 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 : 0.416 ------------------------------------------------------------------------------- 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: 3.9990 chunk 8 optimal weight: 0.8980 chunk 5 optimal weight: 3.9990 chunk 15 optimal weight: 1.9990 chunk 11 optimal weight: 3.9990 chunk 16 optimal weight: 4.9990 chunk 7 optimal weight: 7.9990 chunk 10 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- 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 = 0.4004 r_free = 0.4004 target = 0.135488 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.111862 restraints weight = 9147.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.118476 restraints weight = 3842.967| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.122449 restraints weight = 2151.751| |-----------------------------------------------------------------------------| r_work (final): 0.3858 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8440 moved from start: 0.2423 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= 0.161 Angle : 0.369 3.378 3078 Z= 0.204 Chirality : 0.061 0.142 396 Planarity : 0.001 0.004 360 Dihedral : 6.002 34.623 306 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 1.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.00 % Allowed : 7.14 % Favored : 92.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.36 (0.52), residues: 270 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : 0.29 (0.39), 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 *********************** 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 : 0.419 Fit side-chains REVERT: D 8 LYS cc_start: 0.8547 (mtpt) cc_final: 0.8118 (mttm) REVERT: P 8 LYS cc_start: 0.8924 (mtpt) cc_final: 0.8500 (mtpp) outliers start: 0 outliers final: 0 residues processed: 22 average time/residue: 0.6811 time to fit residues: 16.5678 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 : 0.494 ------------------------------------------------------------------------------- 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: 3.9990 chunk 6 optimal weight: 6.9990 chunk 11 optimal weight: 4.9990 chunk 17 optimal weight: 1.9990 chunk 7 optimal weight: 6.9990 chunk 9 optimal weight: 6.9990 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: 1.8786 ------------------------------------------------------------------------------- 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 = 0.4003 r_free = 0.4003 target = 0.135716 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.112254 restraints weight = 9005.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.118843 restraints weight = 3802.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.122752 restraints weight = 2131.588| |-----------------------------------------------------------------------------| r_work (final): 0.3860 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8437 moved from start: 0.2532 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= 0.163 Angle : 0.373 3.431 3078 Z= 0.206 Chirality : 0.061 0.139 396 Planarity : 0.001 0.004 360 Dihedral : 5.748 31.132 306 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 1.65 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: 0.41 (0.52), residues: 270 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : 0.32 (0.40), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS O 12 PHE 0.004 0.001 PHE E 3 *********************** 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 : 0.461 Fit side-chains REVERT: D 8 LYS cc_start: 0.8526 (mtpt) cc_final: 0.8101 (mttm) REVERT: P 8 LYS cc_start: 0.8924 (mtpt) cc_final: 0.8481 (mtpp) outliers start: 0 outliers final: 0 residues processed: 21 average time/residue: 0.7801 time to fit residues: 18.3054 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 : 1.182 ------------------------------------------------------------------------------- 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: 7.9990 chunk 9 optimal weight: 5.9990 chunk 10 optimal weight: 7.9990 chunk 1 optimal weight: 0.6980 chunk 2 optimal weight: 3.9990 chunk 15 optimal weight: 0.9990 chunk 17 optimal weight: 0.7980 chunk 0 optimal weight: 5.9990 chunk 16 optimal weight: 2.9990 chunk 8 optimal weight: 0.9990 chunk 14 optimal weight: 0.9990 overall best weight: 0.8986 ------------------------------------------------------------------------------- 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 = 0.4029 r_free = 0.4029 target = 0.137957 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.114883 restraints weight = 9033.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.121385 restraints weight = 3892.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.125287 restraints weight = 2200.409| |-----------------------------------------------------------------------------| r_work (final): 0.3895 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8437 moved from start: 0.2666 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= 0.097 Angle : 0.354 3.426 3078 Z= 0.194 Chirality : 0.062 0.142 396 Planarity : 0.001 0.004 360 Dihedral : 4.791 21.889 306 Min Nonbonded Distance : 2.524 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: 0.57 (0.53), residues: 270 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : 0.45 (0.40), 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 *********************** 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 : 0.401 Fit side-chains REVERT: D 8 LYS cc_start: 0.8605 (mtpt) cc_final: 0.8253 (mttm) REVERT: P 8 LYS cc_start: 0.8904 (mtpt) cc_final: 0.8468 (mtpp) outliers start: 0 outliers final: 0 residues processed: 22 average time/residue: 0.6059 time to fit residues: 14.9301 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 : 0.429 ------------------------------------------------------------------------------- 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: 2.9990 chunk 14 optimal weight: 0.0670 chunk 5 optimal weight: 3.9990 chunk 17 optimal weight: 4.9990 chunk 8 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 10 optimal weight: 6.9990 chunk 16 optimal weight: 0.9990 overall best weight: 1.6126 ------------------------------------------------------------------------------- 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 = 0.4007 r_free = 0.4007 target = 0.136317 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.112718 restraints weight = 9006.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.119275 restraints weight = 3802.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.123260 restraints weight = 2146.783| |-----------------------------------------------------------------------------| r_work (final): 0.3863 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8425 moved from start: 0.2701 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= 0.141 Angle : 0.358 3.358 3078 Z= 0.197 Chirality : 0.062 0.145 396 Planarity : 0.001 0.004 360 Dihedral : 4.921 24.484 306 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 1.65 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: 0.58 (0.53), residues: 270 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : 0.45 (0.40), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS E 12 PHE 0.004 0.001 PHE Q 3 *********************** 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 : 0.438 Fit side-chains REVERT: D 8 LYS cc_start: 0.8507 (mtpt) cc_final: 0.8119 (mttm) REVERT: P 8 LYS cc_start: 0.8967 (mtpt) cc_final: 0.8515 (mtpp) outliers start: 0 outliers final: 0 residues processed: 22 average time/residue: 0.6814 time to fit residues: 16.6293 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 : 0.382 ------------------------------------------------------------------------------- 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: 0.9990 chunk 5 optimal weight: 2.9990 chunk 3 optimal weight: 5.9990 chunk 10 optimal weight: 1.9990 chunk 1 optimal weight: 5.9990 chunk 17 optimal weight: 4.9990 chunk 9 optimal weight: 2.9990 chunk 2 optimal weight: 1.9990 chunk 15 optimal weight: 0.8980 overall best weight: 1.7788 ------------------------------------------------------------------------------- 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 = 0.4006 r_free = 0.4006 target = 0.136257 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.112681 restraints weight = 9168.365| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.119220 restraints weight = 3872.047| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.123227 restraints weight = 2181.169| |-----------------------------------------------------------------------------| r_work (final): 0.3860 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8430 moved from start: 0.2762 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= 0.151 Angle : 0.362 3.299 3078 Z= 0.200 Chirality : 0.062 0.143 396 Planarity : 0.001 0.004 360 Dihedral : 5.133 29.146 306 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 1.45 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: 0.61 (0.53), residues: 270 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : 0.47 (0.41), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS O 12 PHE 0.007 0.001 PHE Q 3 ********************** 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 : 0.415 Fit side-chains REVERT: D 8 LYS cc_start: 0.8504 (mtpt) cc_final: 0.8127 (mttm) REVERT: J 7 LYS cc_start: 0.8299 (mttt) cc_final: 0.8017 (mttp) REVERT: P 8 LYS cc_start: 0.8980 (mtpt) cc_final: 0.8500 (mtpp) outliers start: 0 outliers final: 0 residues processed: 22 average time/residue: 0.6997 time to fit residues: 17.1014 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 : 0.386 ------------------------------------------------------------------------------- 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: 2.9990 chunk 9 optimal weight: 6.9990 chunk 4 optimal weight: 5.9990 chunk 13 optimal weight: 1.9990 chunk 17 optimal weight: 4.9990 chunk 11 optimal weight: 0.9980 chunk 5 optimal weight: 0.5980 chunk 14 optimal weight: 0.9980 chunk 2 optimal weight: 0.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- 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 = 0.4023 r_free = 0.4023 target = 0.137436 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.113933 restraints weight = 9035.291| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.120537 restraints weight = 3806.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.124575 restraints weight = 2136.100| |-----------------------------------------------------------------------------| r_work (final): 0.3882 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8417 moved from start: 0.2836 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= 0.110 Angle : 0.355 3.366 3078 Z= 0.194 Chirality : 0.062 0.141 396 Planarity : 0.001 0.004 360 Dihedral : 4.767 25.187 306 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 1.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.00 % Allowed : 8.33 % Favored : 91.67 % 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: 0.67 (0.53), residues: 270 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : 0.52 (0.41), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS E 12 PHE 0.004 0.000 PHE Q 3 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2208.48 seconds wall clock time: 39 minutes 37.96 seconds (2377.96 seconds total)