Starting phenix.real_space_refine on Sat Aug 23 07:41:07 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ixl_35795/08_2025/8ixl_35795.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ixl_35795/08_2025/8ixl_35795.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 { model { file = "/net/cci-nas-00/data/ceres_data/8ixl_35795/08_2025/8ixl_35795.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ixl_35795/08_2025/8ixl_35795.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8ixl_35795/08_2025/8ixl_35795.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ixl_35795/08_2025/8ixl_35795.map" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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 S 50 5.16 5 C 7220 2.51 5 N 1720 2.21 5 O 1980 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 10970 Number of models: 1 Model: "" Number of chains: 35 Chain: "Z" Number of atoms: 344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 344 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "B" Number of atoms: 344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 344 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "C" Number of atoms: 344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 344 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "D" Number of atoms: 256 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 256 Classifications: {'peptide': 32} Modifications used: {'COO': 1} Link IDs: {'TRANS': 31} Chain: "E" Number of atoms: 344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 344 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "F" Number of atoms: 218 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 218 Classifications: {'peptide': 29} Modifications used: {'COO': 1} Link IDs: {'TRANS': 28} Chain: "H" Number of atoms: 344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 344 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "A" Number of atoms: 344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 344 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "G" Number of atoms: 344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 344 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "I" Number of atoms: 344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 344 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "J" Number of atoms: 256 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 256 Classifications: {'peptide': 32} Modifications used: {'COO': 1} Link IDs: {'TRANS': 31} Chain: "K" Number of atoms: 344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 344 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "L" Number of atoms: 218 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 218 Classifications: {'peptide': 29} Modifications used: {'COO': 1} Link IDs: {'TRANS': 28} Chain: "M" Number of atoms: 344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 344 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "N" Number of atoms: 344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 344 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "O" Number of atoms: 344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 344 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "P" Number of atoms: 344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 344 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "Q" Number of atoms: 256 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 256 Classifications: {'peptide': 32} Modifications used: {'COO': 1} Link IDs: {'TRANS': 31} Chain: "R" Number of atoms: 344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 344 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "S" Number of atoms: 218 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 218 Classifications: {'peptide': 29} Modifications used: {'COO': 1} Link IDs: {'TRANS': 28} Chain: "T" Number of atoms: 344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 344 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "V" Number of atoms: 344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 344 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "W" Number of atoms: 344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 344 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "X" Number of atoms: 344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 344 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "Y" Number of atoms: 256 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 256 Classifications: {'peptide': 32} Modifications used: {'COO': 1} Link IDs: {'TRANS': 31} Chain: "AA" Number of atoms: 344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 344 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "BA" Number of atoms: 218 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 218 Classifications: {'peptide': 29} Modifications used: {'COO': 1} Link IDs: {'TRANS': 28} Chain: "CA" Number of atoms: 344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 344 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "DA" Number of atoms: 344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 344 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "EA" Number of atoms: 344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 344 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "FA" Number of atoms: 344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 344 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "GA" Number of atoms: 256 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 256 Classifications: {'peptide': 32} Modifications used: {'COO': 1} Link IDs: {'TRANS': 31} Chain: "HA" Number of atoms: 344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 344 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "IA" Number of atoms: 218 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 218 Classifications: {'peptide': 29} Modifications used: {'COO': 1} Link IDs: {'TRANS': 28} Chain: "JA" Number of atoms: 344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 344 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Time building chain proxies: 2.47, per 1000 atoms: 0.23 Number of scatterers: 10970 At special positions: 0 Unit cell: (74.69, 76.63, 155.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 50 16.00 O 1980 8.00 N 1720 7.00 C 7220 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.89 Conformation dependent library (CDL) restraints added in 383.5 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 2770 Ramachandran restraints generated. 1385 Oldfield, 0 Emsley, 1385 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2710 Finding SS restraints... Secondary structure from input PDB file: 35 helices and 0 sheets defined 96.3% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.19 Creating SS restraints... Processing helix chain 'Z' and resid 5 through 50 removed outlier: 3.954A pdb=" N VAL Z 31 " --> pdb=" O ALA Z 27 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLY Z 38 " --> pdb=" O GLY Z 34 " (cutoff:3.500A) Processing helix chain 'B' and resid 6 through 50 Processing helix chain 'C' and resid 6 through 50 Processing helix chain 'D' and resid 2 through 32 removed outlier: 3.947A pdb=" N ILE D 21 " --> pdb=" O LEU D 17 " (cutoff:3.500A) Processing helix chain 'E' and resid 7 through 49 removed outlier: 3.745A pdb=" N GLU E 20 " --> pdb=" O ALA E 16 " (cutoff:3.500A) Processing helix chain 'F' and resid 6 through 31 Processing helix chain 'H' and resid 6 through 50 Processing helix chain 'A' and resid 6 through 50 removed outlier: 3.954A pdb=" N VAL A 31 " --> pdb=" O ALA A 27 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLY A 38 " --> pdb=" O GLY A 34 " (cutoff:3.500A) Processing helix chain 'G' and resid 6 through 50 Processing helix chain 'I' and resid 6 through 50 Processing helix chain 'J' and resid 2 through 32 removed outlier: 3.947A pdb=" N ILE J 21 " --> pdb=" O LEU J 17 " (cutoff:3.500A) Processing helix chain 'K' and resid 7 through 49 removed outlier: 3.745A pdb=" N GLU K 20 " --> pdb=" O ALA K 16 " (cutoff:3.500A) Processing helix chain 'L' and resid 6 through 31 Processing helix chain 'M' and resid 6 through 50 Processing helix chain 'N' and resid 6 through 50 removed outlier: 3.954A pdb=" N VAL N 31 " --> pdb=" O ALA N 27 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLY N 38 " --> pdb=" O GLY N 34 " (cutoff:3.500A) Processing helix chain 'O' and resid 6 through 50 Processing helix chain 'P' and resid 6 through 50 Processing helix chain 'Q' and resid 2 through 32 removed outlier: 3.947A pdb=" N ILE Q 21 " --> pdb=" O LEU Q 17 " (cutoff:3.500A) Processing helix chain 'R' and resid 7 through 49 removed outlier: 3.745A pdb=" N GLU R 20 " --> pdb=" O ALA R 16 " (cutoff:3.500A) Processing helix chain 'S' and resid 6 through 31 Processing helix chain 'T' and resid 6 through 50 Processing helix chain 'V' and resid 6 through 50 removed outlier: 3.954A pdb=" N VAL V 31 " --> pdb=" O ALA V 27 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLY V 38 " --> pdb=" O GLY V 34 " (cutoff:3.500A) Processing helix chain 'W' and resid 6 through 50 Processing helix chain 'X' and resid 6 through 50 Processing helix chain 'Y' and resid 2 through 32 removed outlier: 3.947A pdb=" N ILE Y 21 " --> pdb=" O LEU Y 17 " (cutoff:3.500A) Processing helix chain 'AA' and resid 7 through 49 removed outlier: 3.745A pdb=" N GLUAA 20 " --> pdb=" O ALAAA 16 " (cutoff:3.500A) Processing helix chain 'BA' and resid 6 through 31 Processing helix chain 'CA' and resid 6 through 50 Processing helix chain 'DA' and resid 6 through 50 removed outlier: 3.954A pdb=" N VALDA 31 " --> pdb=" O ALADA 27 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLYDA 38 " --> pdb=" O GLYDA 34 " (cutoff:3.500A) Processing helix chain 'EA' and resid 6 through 50 Processing helix chain 'FA' and resid 6 through 50 Processing helix chain 'GA' and resid 2 through 32 removed outlier: 3.947A pdb=" N ILEGA 21 " --> pdb=" O LEUGA 17 " (cutoff:3.500A) Processing helix chain 'HA' and resid 7 through 49 removed outlier: 3.745A pdb=" N GLUHA 20 " --> pdb=" O ALAHA 16 " (cutoff:3.500A) Processing helix chain 'IA' and resid 6 through 31 Processing helix chain 'JA' and resid 6 through 50 1241 hydrogen bonds defined for protein. 3723 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: 1.75 Time building geometry restraints manager: 1.12 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 1998 1.33 - 1.45: 2802 1.45 - 1.57: 6295 1.57 - 1.69: 0 1.69 - 1.81: 90 Bond restraints: 11185 Sorted by residual: bond pdb=" N VALHA 31 " pdb=" CA VALHA 31 " ideal model delta sigma weight residual 1.460 1.497 -0.037 1.21e-02 6.83e+03 9.38e+00 bond pdb=" N VAL R 31 " pdb=" CA VAL R 31 " ideal model delta sigma weight residual 1.460 1.497 -0.037 1.21e-02 6.83e+03 9.35e+00 bond pdb=" N VAL A 31 " pdb=" CA VAL A 31 " ideal model delta sigma weight residual 1.461 1.497 -0.036 1.17e-02 7.31e+03 9.27e+00 bond pdb=" N VAL Z 31 " pdb=" CA VAL Z 31 " ideal model delta sigma weight residual 1.461 1.497 -0.036 1.17e-02 7.31e+03 9.27e+00 bond pdb=" N VAL V 31 " pdb=" CA VAL V 31 " ideal model delta sigma weight residual 1.461 1.497 -0.036 1.17e-02 7.31e+03 9.26e+00 ... (remaining 11180 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.37: 9981 1.37 - 2.74: 4273 2.74 - 4.12: 827 4.12 - 5.49: 18 5.49 - 6.86: 31 Bond angle restraints: 15130 Sorted by residual: angle pdb=" N ALA Z 49 " pdb=" CA ALA Z 49 " pdb=" C ALA Z 49 " ideal model delta sigma weight residual 111.28 105.79 5.49 1.09e+00 8.42e-01 2.54e+01 angle pdb=" N ALADA 49 " pdb=" CA ALADA 49 " pdb=" C ALADA 49 " ideal model delta sigma weight residual 111.28 105.80 5.48 1.09e+00 8.42e-01 2.53e+01 angle pdb=" N ALA N 49 " pdb=" CA ALA N 49 " pdb=" C ALA N 49 " ideal model delta sigma weight residual 111.28 105.80 5.48 1.09e+00 8.42e-01 2.53e+01 angle pdb=" N ALA A 49 " pdb=" CA ALA A 49 " pdb=" C ALA A 49 " ideal model delta sigma weight residual 111.28 105.81 5.47 1.09e+00 8.42e-01 2.52e+01 angle pdb=" N ALA V 49 " pdb=" CA ALA V 49 " pdb=" C ALA V 49 " ideal model delta sigma weight residual 111.28 105.82 5.46 1.09e+00 8.42e-01 2.51e+01 ... (remaining 15125 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.39: 6095 16.39 - 32.78: 305 32.78 - 49.16: 80 49.16 - 65.55: 15 65.55 - 81.94: 10 Dihedral angle restraints: 6505 sinusoidal: 2310 harmonic: 4195 Sorted by residual: dihedral pdb=" CA LEU A 14 " pdb=" CB LEU A 14 " pdb=" CG LEU A 14 " pdb=" CD1 LEU A 14 " ideal model delta sinusoidal sigma weight residual 180.00 130.13 49.87 3 1.50e+01 4.44e-03 8.83e+00 dihedral pdb=" CA LEU N 14 " pdb=" CB LEU N 14 " pdb=" CG LEU N 14 " pdb=" CD1 LEU N 14 " ideal model delta sinusoidal sigma weight residual 180.00 130.14 49.86 3 1.50e+01 4.44e-03 8.83e+00 dihedral pdb=" CA LEU V 14 " pdb=" CB LEU V 14 " pdb=" CG LEU V 14 " pdb=" CD1 LEU V 14 " ideal model delta sinusoidal sigma weight residual 180.00 130.14 49.86 3 1.50e+01 4.44e-03 8.83e+00 ... (remaining 6502 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 391 0.041 - 0.082: 488 0.082 - 0.122: 508 0.122 - 0.163: 309 0.163 - 0.204: 89 Chirality restraints: 1785 Sorted by residual: chirality pdb=" CA ILE Y 21 " pdb=" N ILE Y 21 " pdb=" C ILE Y 21 " pdb=" CB ILE Y 21 " both_signs ideal model delta sigma weight residual False 2.43 2.64 -0.20 2.00e-01 2.50e+01 1.04e+00 chirality pdb=" CA ILE Q 21 " pdb=" N ILE Q 21 " pdb=" C ILE Q 21 " pdb=" CB ILE Q 21 " both_signs ideal model delta sigma weight residual False 2.43 2.64 -0.20 2.00e-01 2.50e+01 1.04e+00 chirality pdb=" CA ILEGA 21 " pdb=" N ILEGA 21 " pdb=" C ILEGA 21 " pdb=" CB ILEGA 21 " both_signs ideal model delta sigma weight residual False 2.43 2.64 -0.20 2.00e-01 2.50e+01 1.02e+00 ... (remaining 1782 not shown) Planarity restraints: 1820 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLUCA 20 " -0.006 2.00e-02 2.50e+03 1.13e-02 1.29e+00 pdb=" C GLUCA 20 " 0.020 2.00e-02 2.50e+03 pdb=" O GLUCA 20 " -0.007 2.00e-02 2.50e+03 pdb=" N TYRCA 21 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLUJA 20 " 0.006 2.00e-02 2.50e+03 1.13e-02 1.28e+00 pdb=" C GLUJA 20 " -0.020 2.00e-02 2.50e+03 pdb=" O GLUJA 20 " 0.007 2.00e-02 2.50e+03 pdb=" N TYRJA 21 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU T 20 " -0.006 2.00e-02 2.50e+03 1.13e-02 1.27e+00 pdb=" C GLU T 20 " 0.020 2.00e-02 2.50e+03 pdb=" O GLU T 20 " -0.007 2.00e-02 2.50e+03 pdb=" N TYR T 21 " -0.007 2.00e-02 2.50e+03 ... (remaining 1817 not shown) Histogram of nonbonded interaction distances: 2.57 - 3.03: 7191 3.03 - 3.50: 12629 3.50 - 3.97: 17550 3.97 - 4.43: 19850 4.43 - 4.90: 31840 Nonbonded interactions: 89060 Sorted by model distance: nonbonded pdb=" O SER A 50 " pdb=" OG SER A 50 " model vdw 2.568 3.040 nonbonded pdb=" O SER V 50 " pdb=" OG SER V 50 " model vdw 2.569 3.040 nonbonded pdb=" O SER Z 50 " pdb=" OG SER Z 50 " model vdw 2.569 3.040 nonbonded pdb=" O SERDA 50 " pdb=" OG SERDA 50 " model vdw 2.569 3.040 nonbonded pdb=" O SER N 50 " pdb=" OG SER N 50 " model vdw 2.570 3.040 ... (remaining 89055 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 'AA' selection = chain 'B' selection = chain 'C' selection = chain 'CA' selection = chain 'DA' selection = chain 'E' selection = chain 'EA' selection = chain 'FA' selection = chain 'G' selection = chain 'H' selection = chain 'HA' selection = chain 'I' selection = chain 'JA' selection = chain 'K' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'R' selection = chain 'T' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Z' } ncs_group { reference = chain 'BA' selection = chain 'F' selection = chain 'IA' selection = chain 'L' selection = chain 'S' } ncs_group { reference = chain 'D' selection = chain 'GA' selection = chain 'J' selection = chain 'Q' selection = chain 'Y' } 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: 1.040 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 9.850 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 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 : 0.012 0.039 11185 Z= 0.948 Angle : 1.477 6.862 15130 Z= 1.242 Chirality : 0.095 0.204 1785 Planarity : 0.003 0.011 1820 Dihedral : 11.647 81.940 3795 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 2.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.36 % Favored : 99.64 % Rotamer: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.40 (0.19), residues: 1385 helix: 1.64 (0.12), residues: 1380 sheet: None (None), residues: 0 loop : -0.15 (0.01), residues: 5 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG J 18 TYR 0.010 0.002 TYR G 24 PHE 0.013 0.002 PHEIA 7 TRP 0.011 0.002 TRP Q 15 Details of bonding type rmsd covalent geometry : bond 0.01229 (11185) covalent geometry : angle 1.47702 (15130) hydrogen bonds : bond 0.16681 ( 1241) hydrogen bonds : angle 5.24809 ( 3723) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2770 Ramachandran restraints generated. 1385 Oldfield, 0 Emsley, 1385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2770 Ramachandran restraints generated. 1385 Oldfield, 0 Emsley, 1385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 328 time to evaluate : 0.391 Fit side-chains REVERT: H 43 LYS cc_start: 0.8687 (ttmt) cc_final: 0.8479 (mtmt) REVERT: M 24 TYR cc_start: 0.8055 (m-10) cc_final: 0.7593 (m-10) REVERT: Q 28 MET cc_start: 0.7656 (mmt) cc_final: 0.7366 (mmp) REVERT: R 11 PHE cc_start: 0.7761 (t80) cc_final: 0.7500 (t80) REVERT: CA 43 LYS cc_start: 0.8536 (ttmt) cc_final: 0.8207 (mtmt) REVERT: JA 24 TYR cc_start: 0.7995 (m-10) cc_final: 0.7623 (m-10) outliers start: 0 outliers final: 0 residues processed: 328 average time/residue: 0.1272 time to fit residues: 54.5709 Evaluate side-chains 246 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 246 time to evaluate : 0.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 108 optimal weight: 0.9980 chunk 49 optimal weight: 0.9990 chunk 97 optimal weight: 0.8980 chunk 113 optimal weight: 0.9980 chunk 53 optimal weight: 0.8980 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 1.9990 chunk 123 optimal weight: 2.9990 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 0.7980 chunk 51 optimal weight: 1.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 15 GLN L 32 GLN P 15 GLN R 12 ASN AA 12 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.115928 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.099473 restraints weight = 16472.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.103362 restraints weight = 7900.127| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.105828 restraints weight = 4743.233| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.107521 restraints weight = 3302.810| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.108551 restraints weight = 2499.919| |-----------------------------------------------------------------------------| r_work (final): 0.3437 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 moved from start: 0.3062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 11185 Z= 0.153 Angle : 0.415 6.261 15130 Z= 0.249 Chirality : 0.035 0.137 1785 Planarity : 0.003 0.020 1820 Dihedral : 7.633 82.185 1535 Min Nonbonded Distance : 2.622 Molprobity Statistics. All-atom Clashscore : 3.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 2.17 % Allowed : 11.04 % Favored : 86.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 5.19 (0.18), residues: 1385 helix: 3.44 (0.11), residues: 1345 sheet: None (None), residues: 0 loop : 0.02 (0.35), residues: 40 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 26 TYR 0.022 0.001 TYRFA 21 PHE 0.024 0.001 PHE K 11 TRP 0.010 0.001 TRPFA 26 Details of bonding type rmsd covalent geometry : bond 0.00288 (11185) covalent geometry : angle 0.41549 (15130) hydrogen bonds : bond 0.06151 ( 1241) hydrogen bonds : angle 3.55369 ( 3723) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2770 Ramachandran restraints generated. 1385 Oldfield, 0 Emsley, 1385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2770 Ramachandran restraints generated. 1385 Oldfield, 0 Emsley, 1385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 349 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 325 time to evaluate : 0.247 Fit side-chains REVERT: B 44 LYS cc_start: 0.9033 (OUTLIER) cc_final: 0.8685 (ttpt) REVERT: E 28 MET cc_start: 0.7751 (ttp) cc_final: 0.7539 (ttp) REVERT: G 44 LYS cc_start: 0.8940 (ttmt) cc_final: 0.8523 (tttp) REVERT: I 20 GLU cc_start: 0.7485 (mt-10) cc_final: 0.7212 (mt-10) REVERT: K 24 TYR cc_start: 0.8097 (m-10) cc_final: 0.7831 (m-10) REVERT: R 24 TYR cc_start: 0.8219 (m-10) cc_final: 0.7973 (m-10) REVERT: S 18 SER cc_start: 0.8893 (t) cc_final: 0.8638 (m) REVERT: W 44 LYS cc_start: 0.9063 (ttmt) cc_final: 0.8816 (ttpt) REVERT: AA 11 PHE cc_start: 0.7491 (t80) cc_final: 0.7252 (t80) REVERT: CA 40 LYS cc_start: 0.8927 (tttt) cc_final: 0.8697 (tttt) REVERT: HA 24 TYR cc_start: 0.8113 (m-10) cc_final: 0.7875 (m-10) REVERT: JA 40 LYS cc_start: 0.8966 (tttt) cc_final: 0.8652 (tttt) REVERT: JA 43 LYS cc_start: 0.8699 (mtmt) cc_final: 0.8416 (mtmt) outliers start: 24 outliers final: 8 residues processed: 339 average time/residue: 0.0969 time to fit residues: 45.3404 Evaluate side-chains 299 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 290 time to evaluate : 0.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 44 LYS Chi-restraints excluded: chain E residue 29 VAL Chi-restraints excluded: chain H residue 47 SER Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain N residue 31 VAL Chi-restraints excluded: chain Q residue 1 MET Chi-restraints excluded: chain V residue 31 VAL Chi-restraints excluded: chain CA residue 47 SER Chi-restraints excluded: chain DA residue 31 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 79 optimal weight: 0.9990 chunk 7 optimal weight: 4.9990 chunk 90 optimal weight: 5.9990 chunk 4 optimal weight: 0.5980 chunk 28 optimal weight: 0.9990 chunk 56 optimal weight: 1.9990 chunk 117 optimal weight: 1.9990 chunk 52 optimal weight: 3.9990 chunk 63 optimal weight: 0.9980 chunk 93 optimal weight: 0.8980 chunk 35 optimal weight: 1.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- 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 = 0.3527 r_free = 0.3527 target = 0.115031 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.098512 restraints weight = 16856.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.102238 restraints weight = 8268.675| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.104558 restraints weight = 5061.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.106148 restraints weight = 3597.969| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.107271 restraints weight = 2794.741| |-----------------------------------------------------------------------------| r_work (final): 0.3417 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 moved from start: 0.3618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 11185 Z= 0.143 Angle : 0.377 4.649 15130 Z= 0.227 Chirality : 0.034 0.123 1785 Planarity : 0.002 0.018 1820 Dihedral : 7.169 85.792 1535 Min Nonbonded Distance : 2.623 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.22 % Favored : 99.78 % Rotamer: Outliers : 1.54 % Allowed : 16.83 % Favored : 81.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 5.74 (0.18), residues: 1385 helix: 3.76 (0.11), residues: 1350 sheet: None (None), residues: 0 loop : 0.99 (0.30), residues: 35 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG Q 26 TYR 0.011 0.001 TYR M 24 PHE 0.014 0.001 PHE K 11 TRP 0.006 0.001 TRPFA 26 Details of bonding type rmsd covalent geometry : bond 0.00260 (11185) covalent geometry : angle 0.37712 (15130) hydrogen bonds : bond 0.05763 ( 1241) hydrogen bonds : angle 3.40771 ( 3723) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2770 Ramachandran restraints generated. 1385 Oldfield, 0 Emsley, 1385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2770 Ramachandran restraints generated. 1385 Oldfield, 0 Emsley, 1385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 307 time to evaluate : 0.291 Fit side-chains REVERT: H 30 VAL cc_start: 0.8925 (t) cc_final: 0.8706 (t) REVERT: G 44 LYS cc_start: 0.9006 (ttmt) cc_final: 0.8615 (tttp) REVERT: I 20 GLU cc_start: 0.7501 (mt-10) cc_final: 0.7168 (mt-10) REVERT: M 20 GLU cc_start: 0.7732 (tt0) cc_final: 0.7477 (tt0) REVERT: N 22 ILE cc_start: 0.8265 (OUTLIER) cc_final: 0.8025 (tp) REVERT: O 41 LEU cc_start: 0.9321 (mt) cc_final: 0.9118 (mt) REVERT: T 40 LYS cc_start: 0.8958 (tttt) cc_final: 0.8663 (tttt) REVERT: W 44 LYS cc_start: 0.9008 (ttmt) cc_final: 0.8733 (ttpt) REVERT: W 45 PHE cc_start: 0.9058 (m-80) cc_final: 0.8751 (m-80) REVERT: AA 11 PHE cc_start: 0.7502 (t80) cc_final: 0.7300 (t80) REVERT: CA 40 LYS cc_start: 0.8801 (tttt) cc_final: 0.8516 (tttt) REVERT: JA 20 GLU cc_start: 0.7569 (tt0) cc_final: 0.7254 (tt0) REVERT: JA 40 LYS cc_start: 0.8894 (tttt) cc_final: 0.8625 (tttt) outliers start: 17 outliers final: 13 residues processed: 315 average time/residue: 0.0893 time to fit residues: 39.6838 Evaluate side-chains 301 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 287 time to evaluate : 0.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 29 VAL Chi-restraints excluded: chain E residue 46 THR Chi-restraints excluded: chain A residue 48 LYS Chi-restraints excluded: chain M residue 47 SER Chi-restraints excluded: chain N residue 22 ILE Chi-restraints excluded: chain N residue 31 VAL Chi-restraints excluded: chain Q residue 1 MET Chi-restraints excluded: chain R residue 46 THR Chi-restraints excluded: chain T residue 47 SER Chi-restraints excluded: chain V residue 31 VAL Chi-restraints excluded: chain AA residue 46 THR Chi-restraints excluded: chain CA residue 47 SER Chi-restraints excluded: chain GA residue 31 SER Chi-restraints excluded: chain HA residue 46 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 55 optimal weight: 0.8980 chunk 50 optimal weight: 5.9990 chunk 74 optimal weight: 0.8980 chunk 102 optimal weight: 4.9990 chunk 121 optimal weight: 7.9990 chunk 41 optimal weight: 0.7980 chunk 90 optimal weight: 5.9990 chunk 35 optimal weight: 0.8980 chunk 20 optimal weight: 1.9990 chunk 37 optimal weight: 0.9990 chunk 66 optimal weight: 0.8980 overall best weight: 0.8780 ------------------------------------------------------------------------------- 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 = 0.3537 r_free = 0.3537 target = 0.115458 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.098805 restraints weight = 16928.079| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.102506 restraints weight = 8380.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.104906 restraints weight = 5168.978| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.106418 restraints weight = 3656.602| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.107502 restraints weight = 2867.457| |-----------------------------------------------------------------------------| r_work (final): 0.3429 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 moved from start: 0.3848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 11185 Z= 0.139 Angle : 0.368 4.306 15130 Z= 0.221 Chirality : 0.034 0.124 1785 Planarity : 0.002 0.019 1820 Dihedral : 6.913 89.886 1535 Min Nonbonded Distance : 2.622 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.36 % Favored : 99.64 % Rotamer: Outliers : 1.81 % Allowed : 18.64 % Favored : 79.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 5.80 (0.18), residues: 1385 helix: 3.79 (0.11), residues: 1350 sheet: None (None), residues: 0 loop : 1.24 (0.37), residues: 35 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG Y 26 TYR 0.013 0.001 TYR T 24 PHE 0.017 0.001 PHE R 11 TRP 0.005 0.001 TRP W 26 Details of bonding type rmsd covalent geometry : bond 0.00259 (11185) covalent geometry : angle 0.36826 (15130) hydrogen bonds : bond 0.05493 ( 1241) hydrogen bonds : angle 3.35510 ( 3723) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2770 Ramachandran restraints generated. 1385 Oldfield, 0 Emsley, 1385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2770 Ramachandran restraints generated. 1385 Oldfield, 0 Emsley, 1385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 323 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 303 time to evaluate : 0.429 Fit side-chains REVERT: Z 22 ILE cc_start: 0.8183 (OUTLIER) cc_final: 0.7550 (tp) REVERT: H 30 VAL cc_start: 0.8928 (t) cc_final: 0.8693 (t) REVERT: H 40 LYS cc_start: 0.9106 (tttt) cc_final: 0.8860 (tttt) REVERT: A 22 ILE cc_start: 0.8128 (OUTLIER) cc_final: 0.7771 (tp) REVERT: G 44 LYS cc_start: 0.9038 (ttmt) cc_final: 0.8671 (tttp) REVERT: M 40 LYS cc_start: 0.9016 (tttt) cc_final: 0.8767 (tttt) REVERT: O 41 LEU cc_start: 0.9256 (mt) cc_final: 0.9048 (mt) REVERT: T 20 GLU cc_start: 0.7787 (tt0) cc_final: 0.7476 (tt0) REVERT: T 40 LYS cc_start: 0.8925 (tttt) cc_final: 0.8632 (tttt) REVERT: W 44 LYS cc_start: 0.9023 (ttmt) cc_final: 0.8710 (tttp) REVERT: BA 18 SER cc_start: 0.8784 (t) cc_final: 0.8575 (m) REVERT: CA 40 LYS cc_start: 0.8842 (tttt) cc_final: 0.8575 (tttt) REVERT: EA 44 LYS cc_start: 0.8942 (ttmt) cc_final: 0.8638 (tttp) REVERT: HA 11 PHE cc_start: 0.7559 (t80) cc_final: 0.7351 (t80) REVERT: JA 40 LYS cc_start: 0.8889 (tttt) cc_final: 0.8564 (tttt) outliers start: 20 outliers final: 14 residues processed: 314 average time/residue: 0.0910 time to fit residues: 40.4696 Evaluate side-chains 305 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 289 time to evaluate : 0.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Z residue 22 ILE Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 36 THR Chi-restraints excluded: chain E residue 29 VAL Chi-restraints excluded: chain E residue 46 THR Chi-restraints excluded: chain H residue 47 SER Chi-restraints excluded: chain A residue 22 ILE Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain M residue 47 SER Chi-restraints excluded: chain N residue 31 VAL Chi-restraints excluded: chain Q residue 1 MET Chi-restraints excluded: chain T residue 47 SER Chi-restraints excluded: chain V residue 31 VAL Chi-restraints excluded: chain AA residue 46 THR Chi-restraints excluded: chain DA residue 44 LYS Chi-restraints excluded: chain HA residue 46 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 15 optimal weight: 7.9990 chunk 107 optimal weight: 0.9990 chunk 5 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 94 optimal weight: 0.8980 chunk 115 optimal weight: 0.9990 chunk 85 optimal weight: 0.9980 chunk 84 optimal weight: 2.9990 chunk 64 optimal weight: 5.9990 chunk 7 optimal weight: 5.9990 chunk 92 optimal weight: 0.8980 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 15 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.114503 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.097691 restraints weight = 16928.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.101347 restraints weight = 8539.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.103789 restraints weight = 5346.486| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.105344 restraints weight = 3811.678| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.106504 restraints weight = 2997.879| |-----------------------------------------------------------------------------| r_work (final): 0.3425 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.3948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11185 Z= 0.143 Angle : 0.388 6.592 15130 Z= 0.227 Chirality : 0.034 0.120 1785 Planarity : 0.002 0.018 1820 Dihedral : 6.918 89.874 1535 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.43 % Favored : 99.57 % Rotamer: Outliers : 2.62 % Allowed : 18.73 % Favored : 78.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 5.82 (0.18), residues: 1385 helix: 3.80 (0.11), residues: 1350 sheet: None (None), residues: 0 loop : 1.33 (0.47), residues: 35 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG S 33 TYR 0.016 0.001 TYRJA 24 PHE 0.024 0.001 PHEAA 11 TRP 0.005 0.001 TRP W 26 Details of bonding type rmsd covalent geometry : bond 0.00273 (11185) covalent geometry : angle 0.38818 (15130) hydrogen bonds : bond 0.05563 ( 1241) hydrogen bonds : angle 3.34946 ( 3723) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2770 Ramachandran restraints generated. 1385 Oldfield, 0 Emsley, 1385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2770 Ramachandran restraints generated. 1385 Oldfield, 0 Emsley, 1385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 323 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 294 time to evaluate : 0.284 Fit side-chains REVERT: Z 22 ILE cc_start: 0.8238 (OUTLIER) cc_final: 0.7602 (tp) REVERT: D 1 MET cc_start: 0.6662 (ttt) cc_final: 0.6350 (tmm) REVERT: H 30 VAL cc_start: 0.8978 (t) cc_final: 0.8758 (t) REVERT: H 36 THR cc_start: 0.8949 (t) cc_final: 0.8745 (p) REVERT: H 40 LYS cc_start: 0.9068 (tttt) cc_final: 0.8842 (tttt) REVERT: G 44 LYS cc_start: 0.9016 (ttmt) cc_final: 0.8674 (tttp) REVERT: R 11 PHE cc_start: 0.7016 (t80) cc_final: 0.6503 (t80) REVERT: T 40 LYS cc_start: 0.8895 (tttt) cc_final: 0.8611 (tttt) REVERT: W 44 LYS cc_start: 0.9031 (ttmt) cc_final: 0.8727 (tttp) REVERT: AA 24 TYR cc_start: 0.8004 (m-10) cc_final: 0.7794 (m-10) REVERT: BA 18 SER cc_start: 0.8839 (t) cc_final: 0.8596 (m) REVERT: CA 40 LYS cc_start: 0.8800 (tttt) cc_final: 0.8554 (tttt) REVERT: DA 22 ILE cc_start: 0.8254 (OUTLIER) cc_final: 0.7770 (tp) REVERT: EA 44 LYS cc_start: 0.8967 (ttmt) cc_final: 0.8664 (tttp) REVERT: JA 40 LYS cc_start: 0.8897 (tttt) cc_final: 0.8541 (tttt) outliers start: 29 outliers final: 24 residues processed: 310 average time/residue: 0.1086 time to fit residues: 47.1616 Evaluate side-chains 316 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 290 time to evaluate : 0.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Z residue 22 ILE Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 36 THR Chi-restraints excluded: chain C residue 47 SER Chi-restraints excluded: chain E residue 29 VAL Chi-restraints excluded: chain E residue 46 THR Chi-restraints excluded: chain H residue 47 SER Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 48 LYS Chi-restraints excluded: chain M residue 47 SER Chi-restraints excluded: chain N residue 31 VAL Chi-restraints excluded: chain Q residue 1 MET Chi-restraints excluded: chain R residue 46 THR Chi-restraints excluded: chain T residue 43 LYS Chi-restraints excluded: chain T residue 47 SER Chi-restraints excluded: chain V residue 22 ILE Chi-restraints excluded: chain V residue 31 VAL Chi-restraints excluded: chain X residue 33 VAL Chi-restraints excluded: chain X residue 47 SER Chi-restraints excluded: chain AA residue 36 THR Chi-restraints excluded: chain AA residue 46 THR Chi-restraints excluded: chain DA residue 22 ILE Chi-restraints excluded: chain DA residue 31 VAL Chi-restraints excluded: chain DA residue 44 LYS Chi-restraints excluded: chain HA residue 36 THR Chi-restraints excluded: chain HA residue 46 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 103 optimal weight: 0.6980 chunk 62 optimal weight: 2.9990 chunk 89 optimal weight: 0.9980 chunk 113 optimal weight: 3.9990 chunk 11 optimal weight: 2.9990 chunk 61 optimal weight: 0.8980 chunk 33 optimal weight: 4.9990 chunk 7 optimal weight: 4.9990 chunk 40 optimal weight: 2.9990 chunk 4 optimal weight: 2.9990 chunk 57 optimal weight: 0.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: CA 12 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.110295 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.093592 restraints weight = 17485.137| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.096973 restraints weight = 9206.982| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.099221 restraints weight = 5903.614| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.100795 restraints weight = 4309.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.101835 restraints weight = 3390.784| |-----------------------------------------------------------------------------| r_work (final): 0.3338 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8244 moved from start: 0.3898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 11185 Z= 0.159 Angle : 0.407 5.442 15130 Z= 0.240 Chirality : 0.035 0.122 1785 Planarity : 0.003 0.021 1820 Dihedral : 6.981 89.334 1535 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.58 % Favored : 99.42 % Rotamer: Outliers : 3.44 % Allowed : 19.10 % Favored : 77.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 5.71 (0.18), residues: 1385 helix: 3.77 (0.11), residues: 1345 sheet: None (None), residues: 0 loop : 0.46 (0.49), residues: 40 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG Y 26 TYR 0.014 0.001 TYR K 24 PHE 0.029 0.001 PHE E 11 TRP 0.005 0.001 TRPFA 26 Details of bonding type rmsd covalent geometry : bond 0.00326 (11185) covalent geometry : angle 0.40704 (15130) hydrogen bonds : bond 0.05924 ( 1241) hydrogen bonds : angle 3.41588 ( 3723) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2770 Ramachandran restraints generated. 1385 Oldfield, 0 Emsley, 1385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2770 Ramachandran restraints generated. 1385 Oldfield, 0 Emsley, 1385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 298 time to evaluate : 0.426 Fit side-chains REVERT: Z 22 ILE cc_start: 0.8295 (OUTLIER) cc_final: 0.7675 (tp) REVERT: H 30 VAL cc_start: 0.9018 (t) cc_final: 0.8810 (t) REVERT: H 36 THR cc_start: 0.8963 (t) cc_final: 0.8759 (p) REVERT: H 40 LYS cc_start: 0.9039 (tttt) cc_final: 0.8742 (tttt) REVERT: A 22 ILE cc_start: 0.8226 (OUTLIER) cc_final: 0.7875 (tp) REVERT: G 44 LYS cc_start: 0.9022 (ttmt) cc_final: 0.8692 (tttp) REVERT: N 22 ILE cc_start: 0.8336 (OUTLIER) cc_final: 0.8058 (tp) REVERT: T 40 LYS cc_start: 0.8900 (tttt) cc_final: 0.8609 (tttt) REVERT: W 44 LYS cc_start: 0.9015 (ttmt) cc_final: 0.8717 (tttp) REVERT: BA 18 SER cc_start: 0.8886 (t) cc_final: 0.8660 (m) REVERT: CA 40 LYS cc_start: 0.8832 (tttt) cc_final: 0.8578 (tttt) REVERT: DA 22 ILE cc_start: 0.8275 (OUTLIER) cc_final: 0.7779 (tp) REVERT: JA 40 LYS cc_start: 0.8893 (tttt) cc_final: 0.8533 (tttt) outliers start: 38 outliers final: 28 residues processed: 317 average time/residue: 0.1105 time to fit residues: 49.1516 Evaluate side-chains 325 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 293 time to evaluate : 0.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Z residue 22 ILE Chi-restraints excluded: chain B residue 36 THR Chi-restraints excluded: chain C residue 47 SER Chi-restraints excluded: chain E residue 29 VAL Chi-restraints excluded: chain E residue 46 THR Chi-restraints excluded: chain H residue 47 SER Chi-restraints excluded: chain A residue 22 ILE Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain G residue 36 THR Chi-restraints excluded: chain I residue 47 SER Chi-restraints excluded: chain M residue 47 SER Chi-restraints excluded: chain N residue 22 ILE Chi-restraints excluded: chain N residue 31 VAL Chi-restraints excluded: chain P residue 47 SER Chi-restraints excluded: chain Q residue 1 MET Chi-restraints excluded: chain R residue 46 THR Chi-restraints excluded: chain T residue 43 LYS Chi-restraints excluded: chain T residue 47 SER Chi-restraints excluded: chain V residue 22 ILE Chi-restraints excluded: chain V residue 31 VAL Chi-restraints excluded: chain X residue 33 VAL Chi-restraints excluded: chain X residue 47 SER Chi-restraints excluded: chain AA residue 36 THR Chi-restraints excluded: chain AA residue 46 THR Chi-restraints excluded: chain CA residue 47 SER Chi-restraints excluded: chain DA residue 22 ILE Chi-restraints excluded: chain DA residue 31 VAL Chi-restraints excluded: chain DA residue 44 LYS Chi-restraints excluded: chain GA residue 1 MET Chi-restraints excluded: chain GA residue 31 SER Chi-restraints excluded: chain HA residue 36 THR Chi-restraints excluded: chain HA residue 46 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 36 optimal weight: 0.9990 chunk 9 optimal weight: 0.6980 chunk 103 optimal weight: 0.8980 chunk 64 optimal weight: 4.9990 chunk 45 optimal weight: 0.9980 chunk 56 optimal weight: 0.9990 chunk 90 optimal weight: 3.9990 chunk 11 optimal weight: 1.9990 chunk 123 optimal weight: 4.9990 chunk 95 optimal weight: 2.9990 chunk 99 optimal weight: 0.9980 overall best weight: 0.9182 ------------------------------------------------------------------------------- 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 = 0.3515 r_free = 0.3515 target = 0.112872 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.096260 restraints weight = 17269.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.099676 restraints weight = 9073.236| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.101904 restraints weight = 5806.038| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.103572 restraints weight = 4236.143| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.104420 restraints weight = 3293.766| |-----------------------------------------------------------------------------| r_work (final): 0.3395 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.4070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 11185 Z= 0.142 Angle : 0.393 5.441 15130 Z= 0.230 Chirality : 0.034 0.117 1785 Planarity : 0.002 0.019 1820 Dihedral : 6.882 88.925 1535 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.43 % Favored : 99.57 % Rotamer: Outliers : 2.90 % Allowed : 19.91 % Favored : 77.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 5.78 (0.18), residues: 1385 helix: 3.80 (0.11), residues: 1345 sheet: None (None), residues: 0 loop : 0.82 (0.50), residues: 40 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG Y 26 TYR 0.024 0.001 TYRJA 24 PHE 0.022 0.001 PHE K 11 TRP 0.005 0.001 TRP W 26 Details of bonding type rmsd covalent geometry : bond 0.00267 (11185) covalent geometry : angle 0.39286 (15130) hydrogen bonds : bond 0.05544 ( 1241) hydrogen bonds : angle 3.37974 ( 3723) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2770 Ramachandran restraints generated. 1385 Oldfield, 0 Emsley, 1385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2770 Ramachandran restraints generated. 1385 Oldfield, 0 Emsley, 1385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 301 time to evaluate : 0.380 Fit side-chains REVERT: Z 22 ILE cc_start: 0.8266 (OUTLIER) cc_final: 0.7612 (tp) REVERT: C 21 TYR cc_start: 0.8716 (m-80) cc_final: 0.8383 (m-80) REVERT: H 30 VAL cc_start: 0.8999 (t) cc_final: 0.8785 (t) REVERT: H 40 LYS cc_start: 0.8996 (tttt) cc_final: 0.8690 (tttt) REVERT: A 22 ILE cc_start: 0.8202 (OUTLIER) cc_final: 0.7886 (tp) REVERT: G 44 LYS cc_start: 0.9045 (ttmt) cc_final: 0.8729 (tttp) REVERT: K 11 PHE cc_start: 0.7552 (t80) cc_final: 0.7282 (t80) REVERT: N 22 ILE cc_start: 0.8352 (OUTLIER) cc_final: 0.8103 (tp) REVERT: T 40 LYS cc_start: 0.8883 (tttt) cc_final: 0.8652 (tttt) REVERT: W 44 LYS cc_start: 0.9063 (ttmt) cc_final: 0.8756 (tttp) REVERT: BA 18 SER cc_start: 0.8853 (t) cc_final: 0.8599 (m) REVERT: CA 40 LYS cc_start: 0.8802 (tttt) cc_final: 0.8543 (tttt) REVERT: DA 22 ILE cc_start: 0.8312 (OUTLIER) cc_final: 0.7804 (tp) REVERT: EA 44 LYS cc_start: 0.9048 (ttmt) cc_final: 0.8653 (tttp) REVERT: HA 11 PHE cc_start: 0.7629 (t80) cc_final: 0.7425 (t80) REVERT: JA 40 LYS cc_start: 0.8900 (tttt) cc_final: 0.8553 (tttt) outliers start: 32 outliers final: 25 residues processed: 319 average time/residue: 0.1096 time to fit residues: 49.5381 Evaluate side-chains 324 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 295 time to evaluate : 0.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Z residue 22 ILE Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 36 THR Chi-restraints excluded: chain C residue 47 SER Chi-restraints excluded: chain E residue 29 VAL Chi-restraints excluded: chain E residue 46 THR Chi-restraints excluded: chain H residue 47 SER Chi-restraints excluded: chain A residue 22 ILE Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain G residue 36 THR Chi-restraints excluded: chain I residue 47 SER Chi-restraints excluded: chain M residue 47 SER Chi-restraints excluded: chain N residue 22 ILE Chi-restraints excluded: chain N residue 31 VAL Chi-restraints excluded: chain P residue 47 SER Chi-restraints excluded: chain Q residue 1 MET Chi-restraints excluded: chain R residue 46 THR Chi-restraints excluded: chain T residue 47 SER Chi-restraints excluded: chain V residue 31 VAL Chi-restraints excluded: chain X residue 33 VAL Chi-restraints excluded: chain AA residue 36 THR Chi-restraints excluded: chain AA residue 46 THR Chi-restraints excluded: chain CA residue 20 GLU Chi-restraints excluded: chain CA residue 47 SER Chi-restraints excluded: chain DA residue 22 ILE Chi-restraints excluded: chain DA residue 31 VAL Chi-restraints excluded: chain DA residue 44 LYS Chi-restraints excluded: chain HA residue 36 THR Chi-restraints excluded: chain HA residue 46 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 68 optimal weight: 0.6980 chunk 14 optimal weight: 3.9990 chunk 87 optimal weight: 0.7980 chunk 35 optimal weight: 0.8980 chunk 104 optimal weight: 0.7980 chunk 59 optimal weight: 5.9990 chunk 38 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 chunk 25 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 70 optimal weight: 0.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 15 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.113869 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.097054 restraints weight = 17288.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.100462 restraints weight = 9106.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.102802 restraints weight = 5858.503| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.104322 restraints weight = 4242.264| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.105354 restraints weight = 3369.426| |-----------------------------------------------------------------------------| r_work (final): 0.3405 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 moved from start: 0.4157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 11185 Z= 0.140 Angle : 0.403 7.331 15130 Z= 0.234 Chirality : 0.035 0.123 1785 Planarity : 0.003 0.018 1820 Dihedral : 6.811 88.619 1535 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.58 % Favored : 99.42 % Rotamer: Outliers : 3.17 % Allowed : 20.18 % Favored : 76.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 5.78 (0.18), residues: 1385 helix: 3.80 (0.11), residues: 1345 sheet: None (None), residues: 0 loop : 0.93 (0.49), residues: 40 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG S 33 TYR 0.026 0.001 TYR T 24 PHE 0.037 0.001 PHE R 11 TRP 0.004 0.001 TRP W 26 Details of bonding type rmsd covalent geometry : bond 0.00265 (11185) covalent geometry : angle 0.40338 (15130) hydrogen bonds : bond 0.05434 ( 1241) hydrogen bonds : angle 3.39465 ( 3723) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2770 Ramachandran restraints generated. 1385 Oldfield, 0 Emsley, 1385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2770 Ramachandran restraints generated. 1385 Oldfield, 0 Emsley, 1385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 301 time to evaluate : 0.356 Fit side-chains REVERT: Z 22 ILE cc_start: 0.8293 (OUTLIER) cc_final: 0.7650 (tp) REVERT: C 21 TYR cc_start: 0.8749 (m-80) cc_final: 0.8344 (m-80) REVERT: H 30 VAL cc_start: 0.8966 (t) cc_final: 0.8734 (t) REVERT: H 40 LYS cc_start: 0.8953 (tttt) cc_final: 0.8679 (tttt) REVERT: A 22 ILE cc_start: 0.8130 (OUTLIER) cc_final: 0.7718 (tp) REVERT: G 44 LYS cc_start: 0.9033 (ttmt) cc_final: 0.8735 (tttp) REVERT: K 11 PHE cc_start: 0.7579 (t80) cc_final: 0.7325 (t80) REVERT: N 22 ILE cc_start: 0.8364 (OUTLIER) cc_final: 0.8110 (tp) REVERT: R 28 MET cc_start: 0.7808 (ttp) cc_final: 0.7578 (ttp) REVERT: W 44 LYS cc_start: 0.9070 (ttmt) cc_final: 0.8760 (tttp) REVERT: CA 40 LYS cc_start: 0.8782 (tttt) cc_final: 0.8550 (tttt) REVERT: DA 22 ILE cc_start: 0.8292 (OUTLIER) cc_final: 0.7797 (tp) REVERT: EA 44 LYS cc_start: 0.9032 (ttmt) cc_final: 0.8668 (tttp) REVERT: HA 11 PHE cc_start: 0.7590 (t80) cc_final: 0.7385 (t80) REVERT: IA 18 SER cc_start: 0.8689 (m) cc_final: 0.8415 (t) REVERT: JA 40 LYS cc_start: 0.8887 (tttt) cc_final: 0.8534 (tttt) outliers start: 35 outliers final: 27 residues processed: 320 average time/residue: 0.0986 time to fit residues: 45.0194 Evaluate side-chains 329 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 298 time to evaluate : 0.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Z residue 22 ILE Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 36 THR Chi-restraints excluded: chain C residue 47 SER Chi-restraints excluded: chain E residue 28 MET Chi-restraints excluded: chain E residue 29 VAL Chi-restraints excluded: chain E residue 46 THR Chi-restraints excluded: chain H residue 47 SER Chi-restraints excluded: chain A residue 22 ILE Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain G residue 36 THR Chi-restraints excluded: chain I residue 47 SER Chi-restraints excluded: chain M residue 47 SER Chi-restraints excluded: chain N residue 22 ILE Chi-restraints excluded: chain N residue 31 VAL Chi-restraints excluded: chain Q residue 1 MET Chi-restraints excluded: chain R residue 46 THR Chi-restraints excluded: chain S residue 15 ILE Chi-restraints excluded: chain T residue 47 SER Chi-restraints excluded: chain V residue 22 ILE Chi-restraints excluded: chain V residue 31 VAL Chi-restraints excluded: chain X residue 33 VAL Chi-restraints excluded: chain X residue 47 SER Chi-restraints excluded: chain AA residue 36 THR Chi-restraints excluded: chain AA residue 46 THR Chi-restraints excluded: chain CA residue 47 SER Chi-restraints excluded: chain DA residue 22 ILE Chi-restraints excluded: chain DA residue 44 LYS Chi-restraints excluded: chain GA residue 1 MET Chi-restraints excluded: chain HA residue 36 THR Chi-restraints excluded: chain HA residue 46 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 101 optimal weight: 0.9980 chunk 84 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 115 optimal weight: 2.9990 chunk 80 optimal weight: 4.9990 chunk 110 optimal weight: 4.9990 chunk 58 optimal weight: 2.9990 chunk 17 optimal weight: 4.9990 chunk 34 optimal weight: 1.9990 chunk 117 optimal weight: 0.9990 chunk 2 optimal weight: 1.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 15 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.107255 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.090829 restraints weight = 17408.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.094053 restraints weight = 9151.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.096248 restraints weight = 5900.627| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.097773 restraints weight = 4302.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.098767 restraints weight = 3392.764| |-----------------------------------------------------------------------------| r_work (final): 0.3316 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8294 moved from start: 0.3906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 11185 Z= 0.190 Angle : 0.463 6.389 15130 Z= 0.269 Chirality : 0.037 0.167 1785 Planarity : 0.003 0.022 1820 Dihedral : 6.941 89.659 1535 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.58 % Favored : 99.42 % Rotamer: Outliers : 3.44 % Allowed : 19.73 % Favored : 76.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 5.40 (0.19), residues: 1385 helix: 3.56 (0.12), residues: 1350 sheet: None (None), residues: 0 loop : 0.22 (0.52), residues: 35 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG S 33 TYR 0.028 0.002 TYRJA 24 PHE 0.026 0.002 PHEAA 11 TRP 0.006 0.001 TRP K 26 Details of bonding type rmsd covalent geometry : bond 0.00419 (11185) covalent geometry : angle 0.46282 (15130) hydrogen bonds : bond 0.06484 ( 1241) hydrogen bonds : angle 3.57897 ( 3723) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2770 Ramachandran restraints generated. 1385 Oldfield, 0 Emsley, 1385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2770 Ramachandran restraints generated. 1385 Oldfield, 0 Emsley, 1385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 291 time to evaluate : 0.282 Fit side-chains REVERT: H 30 VAL cc_start: 0.9087 (t) cc_final: 0.8873 (t) REVERT: H 40 LYS cc_start: 0.8999 (tttt) cc_final: 0.8722 (tttt) REVERT: A 22 ILE cc_start: 0.8286 (OUTLIER) cc_final: 0.7944 (tp) REVERT: G 44 LYS cc_start: 0.8999 (ttmt) cc_final: 0.8761 (tttm) REVERT: K 11 PHE cc_start: 0.7965 (t80) cc_final: 0.7580 (t80) REVERT: N 22 ILE cc_start: 0.8384 (OUTLIER) cc_final: 0.8134 (tp) REVERT: S 18 SER cc_start: 0.9015 (t) cc_final: 0.8753 (m) REVERT: W 44 LYS cc_start: 0.9019 (ttmt) cc_final: 0.8708 (tttp) REVERT: AA 11 PHE cc_start: 0.7158 (t80) cc_final: 0.6709 (t80) REVERT: CA 40 LYS cc_start: 0.8845 (tttt) cc_final: 0.8592 (tttt) REVERT: DA 21 TYR cc_start: 0.9137 (t80) cc_final: 0.8786 (t80) REVERT: DA 22 ILE cc_start: 0.8374 (OUTLIER) cc_final: 0.7869 (tp) REVERT: HA 11 PHE cc_start: 0.7894 (t80) cc_final: 0.7647 (t80) REVERT: JA 40 LYS cc_start: 0.8888 (tttt) cc_final: 0.8500 (tttt) outliers start: 38 outliers final: 30 residues processed: 311 average time/residue: 0.1060 time to fit residues: 46.4262 Evaluate side-chains 319 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 286 time to evaluate : 0.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 36 THR Chi-restraints excluded: chain C residue 47 SER Chi-restraints excluded: chain E residue 29 VAL Chi-restraints excluded: chain E residue 46 THR Chi-restraints excluded: chain H residue 47 SER Chi-restraints excluded: chain A residue 22 ILE Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain G residue 36 THR Chi-restraints excluded: chain I residue 47 SER Chi-restraints excluded: chain M residue 47 SER Chi-restraints excluded: chain N residue 22 ILE Chi-restraints excluded: chain N residue 31 VAL Chi-restraints excluded: chain P residue 47 SER Chi-restraints excluded: chain Q residue 1 MET Chi-restraints excluded: chain R residue 46 THR Chi-restraints excluded: chain S residue 15 ILE Chi-restraints excluded: chain T residue 43 LYS Chi-restraints excluded: chain T residue 47 SER Chi-restraints excluded: chain V residue 22 ILE Chi-restraints excluded: chain V residue 30 VAL Chi-restraints excluded: chain V residue 31 VAL Chi-restraints excluded: chain X residue 33 VAL Chi-restraints excluded: chain X residue 47 SER Chi-restraints excluded: chain AA residue 36 THR Chi-restraints excluded: chain AA residue 46 THR Chi-restraints excluded: chain CA residue 20 GLU Chi-restraints excluded: chain CA residue 47 SER Chi-restraints excluded: chain DA residue 22 ILE Chi-restraints excluded: chain DA residue 31 VAL Chi-restraints excluded: chain DA residue 44 LYS Chi-restraints excluded: chain GA residue 1 MET Chi-restraints excluded: chain HA residue 36 THR Chi-restraints excluded: chain HA residue 46 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 101 optimal weight: 4.9990 chunk 38 optimal weight: 0.9990 chunk 59 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 94 optimal weight: 0.8980 chunk 31 optimal weight: 0.9990 chunk 115 optimal weight: 0.8980 chunk 99 optimal weight: 0.9990 chunk 41 optimal weight: 2.9990 chunk 112 optimal weight: 1.9990 chunk 93 optimal weight: 1.9990 overall best weight: 0.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AA 15 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.113562 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.096672 restraints weight = 17110.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.100226 restraints weight = 8689.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.102669 restraints weight = 5500.113| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.104241 restraints weight = 3934.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.105303 restraints weight = 3102.335| |-----------------------------------------------------------------------------| r_work (final): 0.3411 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.4149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 11185 Z= 0.149 Angle : 0.432 7.058 15130 Z= 0.250 Chirality : 0.036 0.131 1785 Planarity : 0.003 0.026 1820 Dihedral : 6.814 87.448 1535 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.36 % Favored : 99.64 % Rotamer: Outliers : 2.99 % Allowed : 20.54 % Favored : 76.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 5.56 (0.18), residues: 1385 helix: 3.67 (0.12), residues: 1345 sheet: None (None), residues: 0 loop : 0.43 (0.46), residues: 40 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG S 33 TYR 0.027 0.002 TYR T 24 PHE 0.039 0.001 PHE R 11 TRP 0.004 0.001 TRP W 26 Details of bonding type rmsd covalent geometry : bond 0.00290 (11185) covalent geometry : angle 0.43150 (15130) hydrogen bonds : bond 0.05745 ( 1241) hydrogen bonds : angle 3.49875 ( 3723) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2770 Ramachandran restraints generated. 1385 Oldfield, 0 Emsley, 1385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2770 Ramachandran restraints generated. 1385 Oldfield, 0 Emsley, 1385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 304 time to evaluate : 0.435 Fit side-chains REVERT: C 21 TYR cc_start: 0.8758 (m-80) cc_final: 0.8502 (m-80) REVERT: H 30 VAL cc_start: 0.9020 (t) cc_final: 0.8797 (t) REVERT: A 22 ILE cc_start: 0.8086 (OUTLIER) cc_final: 0.7688 (tp) REVERT: G 44 LYS cc_start: 0.8999 (ttmt) cc_final: 0.8783 (tttm) REVERT: K 11 PHE cc_start: 0.7854 (t80) cc_final: 0.7583 (t80) REVERT: M 45 PHE cc_start: 0.9008 (m-80) cc_final: 0.8735 (m-80) REVERT: N 22 ILE cc_start: 0.8337 (OUTLIER) cc_final: 0.8084 (tp) REVERT: W 44 LYS cc_start: 0.9036 (ttmt) cc_final: 0.8736 (tttp) REVERT: X 21 TYR cc_start: 0.8760 (m-80) cc_final: 0.8491 (m-80) REVERT: AA 24 TYR cc_start: 0.8244 (m-10) cc_final: 0.7941 (m-10) REVERT: CA 24 TYR cc_start: 0.8514 (m-80) cc_final: 0.8257 (m-80) REVERT: CA 40 LYS cc_start: 0.8817 (tttt) cc_final: 0.8578 (tttt) REVERT: DA 22 ILE cc_start: 0.8265 (OUTLIER) cc_final: 0.7755 (tp) REVERT: EA 44 LYS cc_start: 0.9044 (ttmt) cc_final: 0.8622 (tttp) REVERT: HA 11 PHE cc_start: 0.7788 (t80) cc_final: 0.7563 (t80) REVERT: JA 40 LYS cc_start: 0.8832 (tttt) cc_final: 0.8444 (tttt) outliers start: 33 outliers final: 26 residues processed: 320 average time/residue: 0.1053 time to fit residues: 47.8400 Evaluate side-chains 331 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 302 time to evaluate : 0.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 36 THR Chi-restraints excluded: chain C residue 47 SER Chi-restraints excluded: chain E residue 29 VAL Chi-restraints excluded: chain E residue 46 THR Chi-restraints excluded: chain H residue 47 SER Chi-restraints excluded: chain A residue 22 ILE Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain G residue 36 THR Chi-restraints excluded: chain I residue 47 SER Chi-restraints excluded: chain M residue 47 SER Chi-restraints excluded: chain N residue 22 ILE Chi-restraints excluded: chain N residue 31 VAL Chi-restraints excluded: chain P residue 47 SER Chi-restraints excluded: chain Q residue 1 MET Chi-restraints excluded: chain R residue 46 THR Chi-restraints excluded: chain S residue 15 ILE Chi-restraints excluded: chain T residue 47 SER Chi-restraints excluded: chain V residue 22 ILE Chi-restraints excluded: chain V residue 30 VAL Chi-restraints excluded: chain V residue 31 VAL Chi-restraints excluded: chain X residue 47 SER Chi-restraints excluded: chain AA residue 36 THR Chi-restraints excluded: chain AA residue 46 THR Chi-restraints excluded: chain CA residue 47 SER Chi-restraints excluded: chain DA residue 22 ILE Chi-restraints excluded: chain DA residue 44 LYS Chi-restraints excluded: chain GA residue 1 MET Chi-restraints excluded: chain HA residue 36 THR Chi-restraints excluded: chain HA residue 46 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 9 optimal weight: 2.9990 chunk 63 optimal weight: 0.9980 chunk 38 optimal weight: 0.9990 chunk 82 optimal weight: 2.9990 chunk 80 optimal weight: 1.9990 chunk 124 optimal weight: 0.0060 chunk 73 optimal weight: 0.9980 chunk 98 optimal weight: 0.9990 chunk 3 optimal weight: 2.9990 chunk 49 optimal weight: 3.9990 chunk 121 optimal weight: 2.9990 overall best weight: 0.8000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 15 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.115555 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.098652 restraints weight = 16936.374| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.102231 restraints weight = 8588.912| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.104657 restraints weight = 5424.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.106021 restraints weight = 3897.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.107281 restraints weight = 3136.904| |-----------------------------------------------------------------------------| r_work (final): 0.3432 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.4293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.079 11185 Z= 0.143 Angle : 0.423 6.975 15130 Z= 0.244 Chirality : 0.035 0.165 1785 Planarity : 0.003 0.023 1820 Dihedral : 6.764 87.291 1535 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.51 % Favored : 99.49 % Rotamer: Outliers : 2.62 % Allowed : 20.63 % Favored : 76.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 5.67 (0.18), residues: 1385 helix: 3.73 (0.11), residues: 1345 sheet: None (None), residues: 0 loop : 0.77 (0.47), residues: 40 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG S 33 TYR 0.027 0.001 TYRJA 24 PHE 0.035 0.001 PHEAA 11 TRP 0.004 0.001 TRP A 26 Details of bonding type rmsd covalent geometry : bond 0.00273 (11185) covalent geometry : angle 0.42286 (15130) hydrogen bonds : bond 0.05444 ( 1241) hydrogen bonds : angle 3.46765 ( 3723) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1553.26 seconds wall clock time: 27 minutes 51.09 seconds (1671.09 seconds total)