Starting phenix.real_space_refine on Mon Jul 28 19:34:22 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ixl_35795/07_2025/8ixl_35795.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ixl_35795/07_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8ixl_35795/07_2025/8ixl_35795.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ixl_35795/07_2025/8ixl_35795.map" model { file = "/net/cci-nas-00/data/ceres_data/8ixl_35795/07_2025/8ixl_35795.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ixl_35795/07_2025/8ixl_35795.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians 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-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 6.84, per 1000 atoms: 0.62 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: 2.89 Conformation dependent library (CDL) restraints added in 1.3 seconds 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: 0.90 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: 3.62 Time building geometry restraints manager: 3.29 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: 1.070 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: 0.010 Extract box with map and model: 0.440 Check model and map are aligned: 0.070 Set scattering table: 0.110 Process input model: 27.170 Find NCS groups from input model: 0.470 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.360 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.40 (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 TRP 0.011 0.002 TRP Q 15 PHE 0.013 0.002 PHEIA 7 TYR 0.010 0.002 TYR G 24 ARG 0.001 0.000 ARG J 18 Details of bonding type rmsd hydrogen bonds : bond 0.16681 ( 1241) hydrogen bonds : angle 5.24809 ( 3723) covalent geometry : bond 0.01229 (11185) covalent geometry : angle 1.47702 (15130) *********************** 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 : 1.326 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: 0.3088 time to fit residues: 131.5979 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 : 1.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 105 optimal weight: 0.8980 chunk 94 optimal weight: 5.9990 chunk 52 optimal weight: 0.7980 chunk 32 optimal weight: 0.9980 chunk 63 optimal weight: 1.9990 chunk 50 optimal weight: 7.9990 chunk 97 optimal weight: 0.8980 chunk 37 optimal weight: 0.8980 chunk 59 optimal weight: 0.8980 chunk 72 optimal weight: 0.7980 chunk 113 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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 AA 12 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.116265 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.099843 restraints weight = 16338.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.103736 restraints weight = 7852.423| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.106264 restraints weight = 4713.436| |-----------------------------------------------------------------------------| r_work (final): 0.3403 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8158 moved from start: 0.3046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 11185 Z= 0.153 Angle : 0.414 6.330 15130 Z= 0.248 Chirality : 0.035 0.107 1785 Planarity : 0.003 0.019 1820 Dihedral : 7.638 81.982 1535 Min Nonbonded Distance : 2.628 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 2.26 % Allowed : 10.86 % Favored : 86.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 5.20 (0.18), residues: 1385 helix: 3.45 (0.11), residues: 1345 sheet: None (None), residues: 0 loop : 0.05 (0.35), residues: 40 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRPFA 26 PHE 0.024 0.001 PHEAA 11 TYR 0.022 0.001 TYRFA 21 ARG 0.001 0.000 ARG S 33 Details of bonding type rmsd hydrogen bonds : bond 0.06118 ( 1241) hydrogen bonds : angle 3.55742 ( 3723) covalent geometry : bond 0.00280 (11185) covalent geometry : angle 0.41421 (15130) *********************** 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 350 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 325 time to evaluate : 1.158 Fit side-chains REVERT: B 44 LYS cc_start: 0.9019 (OUTLIER) cc_final: 0.8657 (ttpt) REVERT: E 24 TYR cc_start: 0.8101 (m-10) cc_final: 0.7850 (m-10) REVERT: E 28 MET cc_start: 0.7766 (ttp) cc_final: 0.7550 (ttp) REVERT: G 44 LYS cc_start: 0.8921 (ttmt) cc_final: 0.8508 (tttp) REVERT: I 20 GLU cc_start: 0.7503 (mt-10) cc_final: 0.7202 (mt-10) REVERT: K 24 TYR cc_start: 0.8092 (m-10) cc_final: 0.7845 (m-10) REVERT: R 24 TYR cc_start: 0.8226 (m-10) cc_final: 0.7992 (m-10) REVERT: S 18 SER cc_start: 0.8928 (t) cc_final: 0.8670 (m) REVERT: W 44 LYS cc_start: 0.9052 (ttmt) cc_final: 0.8807 (ttmt) REVERT: CA 40 LYS cc_start: 0.8936 (tttt) cc_final: 0.8708 (tttt) REVERT: HA 24 TYR cc_start: 0.8116 (m-10) cc_final: 0.7887 (m-10) REVERT: JA 40 LYS cc_start: 0.8974 (tttt) cc_final: 0.8660 (tttt) REVERT: JA 43 LYS cc_start: 0.8674 (mtmt) cc_final: 0.8400 (mtmt) outliers start: 25 outliers final: 10 residues processed: 341 average time/residue: 0.2437 time to fit residues: 114.3909 Evaluate side-chains 299 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 288 time to evaluate : 1.216 ------------------------------------------------------------------------------- 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 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 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 69 optimal weight: 3.9990 chunk 43 optimal weight: 0.9990 chunk 39 optimal weight: 6.9990 chunk 19 optimal weight: 3.9990 chunk 48 optimal weight: 1.9990 chunk 86 optimal weight: 0.9980 chunk 93 optimal weight: 0.9980 chunk 121 optimal weight: 7.9990 chunk 78 optimal weight: 0.9980 chunk 74 optimal weight: 0.0980 chunk 5 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 = 0.3536 r_free = 0.3536 target = 0.115503 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.098995 restraints weight = 16786.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.102720 restraints weight = 8228.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.105161 restraints weight = 5040.023| |-----------------------------------------------------------------------------| r_work (final): 0.3394 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 moved from start: 0.3592 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= 0.140 Angle : 0.374 4.660 15130 Z= 0.224 Chirality : 0.034 0.122 1785 Planarity : 0.002 0.018 1820 Dihedral : 7.209 84.658 1535 Min Nonbonded Distance : 2.625 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.14 % Favored : 99.86 % Rotamer: Outliers : 1.36 % Allowed : 16.92 % Favored : 81.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 5.79 (0.18), residues: 1385 helix: 3.79 (0.11), residues: 1350 sheet: None (None), residues: 0 loop : 1.08 (0.31), residues: 35 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRPFA 26 PHE 0.014 0.001 PHEAA 11 TYR 0.012 0.001 TYR M 24 ARG 0.001 0.000 ARG Q 26 Details of bonding type rmsd hydrogen bonds : bond 0.05704 ( 1241) hydrogen bonds : angle 3.39213 ( 3723) covalent geometry : bond 0.00251 (11185) covalent geometry : angle 0.37414 (15130) *********************** 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 317 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 302 time to evaluate : 1.360 Fit side-chains REVERT: H 30 VAL cc_start: 0.8900 (t) cc_final: 0.8665 (t) REVERT: G 44 LYS cc_start: 0.8988 (ttmt) cc_final: 0.8599 (tttp) REVERT: K 11 PHE cc_start: 0.7718 (t80) cc_final: 0.7421 (t80) REVERT: M 20 GLU cc_start: 0.7801 (tt0) cc_final: 0.7570 (tt0) REVERT: O 41 LEU cc_start: 0.9284 (mt) cc_final: 0.9054 (mt) REVERT: R 28 MET cc_start: 0.7776 (ttp) cc_final: 0.7412 (ttp) REVERT: T 40 LYS cc_start: 0.8958 (tttt) cc_final: 0.8672 (tttt) REVERT: W 44 LYS cc_start: 0.8999 (ttmt) cc_final: 0.8795 (ttpt) REVERT: W 45 PHE cc_start: 0.9072 (m-80) cc_final: 0.8726 (m-80) REVERT: CA 40 LYS cc_start: 0.8815 (tttt) cc_final: 0.8538 (tttt) REVERT: EA 45 PHE cc_start: 0.9065 (m-80) cc_final: 0.8824 (m-80) REVERT: JA 40 LYS cc_start: 0.8913 (tttt) cc_final: 0.8638 (tttt) outliers start: 15 outliers final: 9 residues processed: 308 average time/residue: 0.2497 time to fit residues: 106.5132 Evaluate side-chains 294 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 285 time to evaluate : 1.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 29 VAL Chi-restraints excluded: chain E residue 46 THR 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 CA residue 47 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 112 optimal weight: 0.8980 chunk 82 optimal weight: 2.9990 chunk 7 optimal weight: 5.9990 chunk 21 optimal weight: 8.9990 chunk 48 optimal weight: 1.9990 chunk 6 optimal weight: 0.9980 chunk 92 optimal weight: 3.9990 chunk 62 optimal weight: 2.9990 chunk 101 optimal weight: 6.9990 chunk 119 optimal weight: 1.9990 chunk 49 optimal weight: 3.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- 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 = 0.3455 r_free = 0.3455 target = 0.109314 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.092936 restraints weight = 16992.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.096428 restraints weight = 8552.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.098638 restraints weight = 5346.853| |-----------------------------------------------------------------------------| r_work (final): 0.3300 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8302 moved from start: 0.3517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 11185 Z= 0.188 Angle : 0.421 3.791 15130 Z= 0.252 Chirality : 0.035 0.112 1785 Planarity : 0.003 0.022 1820 Dihedral : 7.216 88.017 1535 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.43 % Favored : 99.57 % Rotamer: Outliers : 3.35 % Allowed : 17.01 % Favored : 79.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 5.52 (0.18), residues: 1385 helix: 3.64 (0.12), residues: 1350 sheet: None (None), residues: 0 loop : 0.33 (0.42), residues: 35 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRPFA 26 PHE 0.018 0.001 PHE E 11 TYR 0.011 0.001 TYR T 24 ARG 0.001 0.000 ARG S 33 Details of bonding type rmsd hydrogen bonds : bond 0.06492 ( 1241) hydrogen bonds : angle 3.51770 ( 3723) covalent geometry : bond 0.00409 (11185) covalent geometry : angle 0.42084 (15130) *********************** 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 327 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 290 time to evaluate : 1.170 Fit side-chains REVERT: Z 22 ILE cc_start: 0.8235 (OUTLIER) cc_final: 0.7607 (tp) REVERT: H 30 VAL cc_start: 0.9094 (t) cc_final: 0.8882 (t) REVERT: A 22 ILE cc_start: 0.8178 (OUTLIER) cc_final: 0.7900 (tp) REVERT: G 44 LYS cc_start: 0.9011 (ttmt) cc_final: 0.8648 (tttp) REVERT: I 20 GLU cc_start: 0.7709 (mt-10) cc_final: 0.7459 (mt-10) REVERT: J 28 MET cc_start: 0.7840 (OUTLIER) cc_final: 0.7584 (tpp) REVERT: K 11 PHE cc_start: 0.7871 (t80) cc_final: 0.7557 (t80) REVERT: R 11 PHE cc_start: 0.7710 (t80) cc_final: 0.7386 (t80) REVERT: S 18 SER cc_start: 0.9002 (t) cc_final: 0.8729 (m) REVERT: T 40 LYS cc_start: 0.8947 (tttt) cc_final: 0.8650 (tttt) REVERT: W 44 LYS cc_start: 0.9031 (ttmt) cc_final: 0.8687 (tttp) REVERT: CA 12 ASN cc_start: 0.8583 (m110) cc_final: 0.8366 (m110) REVERT: CA 40 LYS cc_start: 0.8904 (tttt) cc_final: 0.8627 (tttt) REVERT: DA 22 ILE cc_start: 0.8278 (OUTLIER) cc_final: 0.7838 (tp) REVERT: HA 11 PHE cc_start: 0.7871 (t80) cc_final: 0.7451 (t80) REVERT: JA 40 LYS cc_start: 0.8933 (tttt) cc_final: 0.8585 (tttt) outliers start: 37 outliers final: 28 residues processed: 312 average time/residue: 0.2288 time to fit residues: 99.4555 Evaluate side-chains 312 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 280 time to evaluate : 1.258 ------------------------------------------------------------------------------- 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 D residue 31 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 J residue 28 MET Chi-restraints excluded: chain M residue 47 SER 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 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 114 optimal weight: 2.9990 chunk 104 optimal weight: 0.9980 chunk 23 optimal weight: 0.9980 chunk 64 optimal weight: 4.9990 chunk 84 optimal weight: 5.9990 chunk 88 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 chunk 102 optimal weight: 1.9990 chunk 14 optimal weight: 0.9990 chunk 94 optimal weight: 7.9990 chunk 75 optimal weight: 3.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- 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 = 0.3504 r_free = 0.3504 target = 0.111988 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.095436 restraints weight = 16923.650| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.099012 restraints weight = 8563.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.101402 restraints weight = 5383.273| |-----------------------------------------------------------------------------| r_work (final): 0.3349 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8258 moved from start: 0.3808 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= 0.153 Angle : 0.394 5.605 15130 Z= 0.235 Chirality : 0.035 0.125 1785 Planarity : 0.003 0.024 1820 Dihedral : 6.842 88.896 1535 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.36 % Favored : 99.64 % Rotamer: Outliers : 2.53 % Allowed : 19.28 % Favored : 78.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 5.64 (0.18), residues: 1385 helix: 3.73 (0.11), residues: 1345 sheet: None (None), residues: 0 loop : 0.19 (0.48), residues: 40 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP W 26 PHE 0.019 0.001 PHE R 11 TYR 0.014 0.001 TYR K 24 ARG 0.000 0.000 ARG Q 26 Details of bonding type rmsd hydrogen bonds : bond 0.05926 ( 1241) hydrogen bonds : angle 3.43617 ( 3723) covalent geometry : bond 0.00303 (11185) covalent geometry : angle 0.39391 (15130) *********************** 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 325 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 297 time to evaluate : 1.139 Fit side-chains REVERT: D 1 MET cc_start: 0.6845 (ttt) cc_final: 0.6616 (tmm) REVERT: H 30 VAL cc_start: 0.9040 (t) cc_final: 0.8824 (t) REVERT: G 44 LYS cc_start: 0.9057 (ttmt) cc_final: 0.8691 (tttp) REVERT: I 20 GLU cc_start: 0.7671 (mt-10) cc_final: 0.7371 (mt-10) REVERT: K 11 PHE cc_start: 0.7772 (t80) cc_final: 0.7518 (t80) REVERT: N 22 ILE cc_start: 0.8349 (OUTLIER) cc_final: 0.8134 (tp) REVERT: R 28 MET cc_start: 0.7709 (ttp) cc_final: 0.7385 (ttp) REVERT: T 40 LYS cc_start: 0.8922 (tttt) cc_final: 0.8621 (tttt) REVERT: W 44 LYS cc_start: 0.9049 (ttmt) cc_final: 0.8732 (tttp) REVERT: CA 40 LYS cc_start: 0.8885 (tttt) cc_final: 0.8611 (tttt) REVERT: DA 22 ILE cc_start: 0.8278 (OUTLIER) cc_final: 0.7797 (tp) REVERT: HA 11 PHE cc_start: 0.7770 (t80) cc_final: 0.7409 (t80) REVERT: IA 18 SER cc_start: 0.8917 (t) cc_final: 0.8710 (m) REVERT: JA 40 LYS cc_start: 0.8930 (tttt) cc_final: 0.8553 (tttt) outliers start: 28 outliers final: 24 residues processed: 314 average time/residue: 0.2306 time to fit residues: 101.0289 Evaluate side-chains 308 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 282 time to evaluate : 1.248 ------------------------------------------------------------------------------- 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 31 VAL 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 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 Y residue 1 MET 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 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 48 optimal weight: 0.7980 chunk 26 optimal weight: 2.9990 chunk 67 optimal weight: 0.8980 chunk 22 optimal weight: 0.9980 chunk 40 optimal weight: 5.9990 chunk 112 optimal weight: 2.9990 chunk 53 optimal weight: 0.6980 chunk 115 optimal weight: 1.9990 chunk 19 optimal weight: 0.0050 chunk 92 optimal weight: 4.9990 chunk 88 optimal weight: 4.9990 overall best weight: 0.6794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 15 GLN CA 12 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.116419 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.099759 restraints weight = 16885.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.103414 restraints weight = 8475.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.105870 restraints weight = 5329.882| |-----------------------------------------------------------------------------| r_work (final): 0.3411 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 moved from start: 0.4117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 11185 Z= 0.132 Angle : 0.377 7.239 15130 Z= 0.220 Chirality : 0.034 0.123 1785 Planarity : 0.002 0.021 1820 Dihedral : 6.651 88.786 1535 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.43 % Favored : 99.57 % Rotamer: Outliers : 1.90 % Allowed : 21.00 % Favored : 77.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 5.88 (0.18), residues: 1385 helix: 3.86 (0.11), residues: 1345 sheet: None (None), residues: 0 loop : 0.83 (0.48), residues: 40 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP V 26 PHE 0.019 0.001 PHE E 11 TYR 0.014 0.001 TYRJA 24 ARG 0.001 0.000 ARG Y 26 Details of bonding type rmsd hydrogen bonds : bond 0.05254 ( 1241) hydrogen bonds : angle 3.34328 ( 3723) covalent geometry : bond 0.00233 (11185) covalent geometry : angle 0.37702 (15130) *********************** 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 328 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 307 time to evaluate : 1.234 Fit side-chains REVERT: H 30 VAL cc_start: 0.8919 (t) cc_final: 0.8688 (t) REVERT: H 40 LYS cc_start: 0.9116 (tttt) cc_final: 0.8912 (tttt) REVERT: A 40 LYS cc_start: 0.8123 (ttpp) cc_final: 0.7922 (ttpp) REVERT: G 44 LYS cc_start: 0.9026 (ttmt) cc_final: 0.8727 (tttp) REVERT: I 20 GLU cc_start: 0.7591 (mt-10) cc_final: 0.7263 (mt-10) REVERT: N 22 ILE cc_start: 0.8285 (OUTLIER) cc_final: 0.8060 (tp) REVERT: R 11 PHE cc_start: 0.7133 (t80) cc_final: 0.6884 (t80) REVERT: T 36 THR cc_start: 0.9091 (t) cc_final: 0.8736 (p) REVERT: T 40 LYS cc_start: 0.8901 (tttt) cc_final: 0.8640 (tttt) REVERT: W 44 LYS cc_start: 0.9025 (ttmt) cc_final: 0.8750 (tttp) REVERT: BA 18 SER cc_start: 0.8822 (t) cc_final: 0.8602 (m) REVERT: CA 40 LYS cc_start: 0.8862 (tttt) cc_final: 0.8648 (tttt) REVERT: JA 40 LYS cc_start: 0.8913 (tttt) cc_final: 0.8543 (tttt) outliers start: 21 outliers final: 17 residues processed: 319 average time/residue: 0.2264 time to fit residues: 100.9118 Evaluate side-chains 311 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 293 time to evaluate : 1.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 20 GLU Chi-restraints excluded: chain GA residue 1 MET 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 96 optimal weight: 0.2980 chunk 59 optimal weight: 5.9990 chunk 88 optimal weight: 4.9990 chunk 41 optimal weight: 3.9990 chunk 56 optimal weight: 1.9990 chunk 112 optimal weight: 6.9990 chunk 10 optimal weight: 0.9980 chunk 73 optimal weight: 0.7980 chunk 93 optimal weight: 0.9990 chunk 101 optimal weight: 0.8980 chunk 44 optimal weight: 0.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: S 32 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.114463 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.097702 restraints weight = 17546.880| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.101132 restraints weight = 9193.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.103489 restraints weight = 5904.545| |-----------------------------------------------------------------------------| r_work (final): 0.3372 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8229 moved from start: 0.4219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 11185 Z= 0.137 Angle : 0.393 6.418 15130 Z= 0.229 Chirality : 0.034 0.099 1785 Planarity : 0.002 0.020 1820 Dihedral : 6.543 88.503 1535 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.43 % Favored : 99.57 % Rotamer: Outliers : 3.08 % Allowed : 20.63 % Favored : 76.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 5.86 (0.18), residues: 1385 helix: 3.85 (0.11), residues: 1345 sheet: None (None), residues: 0 loop : 0.85 (0.48), residues: 40 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP W 26 PHE 0.018 0.001 PHE R 11 TYR 0.016 0.001 TYRCA 24 ARG 0.001 0.000 ARG Y 26 Details of bonding type rmsd hydrogen bonds : bond 0.05351 ( 1241) hydrogen bonds : angle 3.34616 ( 3723) covalent geometry : bond 0.00254 (11185) covalent geometry : angle 0.39309 (15130) *********************** 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 336 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 302 time to evaluate : 1.264 Fit side-chains REVERT: Z 22 ILE cc_start: 0.8248 (OUTLIER) cc_final: 0.7622 (tp) REVERT: C 21 TYR cc_start: 0.8697 (m-80) cc_final: 0.8291 (m-80) REVERT: F 18 SER cc_start: 0.8682 (m) cc_final: 0.8454 (t) REVERT: H 30 VAL cc_start: 0.8924 (t) cc_final: 0.8690 (t) REVERT: H 40 LYS cc_start: 0.9101 (tttt) cc_final: 0.8850 (tttt) REVERT: G 44 LYS cc_start: 0.9036 (ttmt) cc_final: 0.8720 (tttp) REVERT: I 20 GLU cc_start: 0.7637 (mt-10) cc_final: 0.7306 (mt-10) REVERT: J 1 MET cc_start: 0.6744 (OUTLIER) cc_final: 0.6469 (tmm) REVERT: N 22 ILE cc_start: 0.8285 (OUTLIER) cc_final: 0.8006 (tp) REVERT: T 36 THR cc_start: 0.9077 (t) cc_final: 0.8844 (p) REVERT: W 44 LYS cc_start: 0.9035 (ttmt) cc_final: 0.8750 (tttp) REVERT: AA 24 TYR cc_start: 0.8037 (m-10) cc_final: 0.7660 (m-10) REVERT: CA 40 LYS cc_start: 0.8839 (tttt) cc_final: 0.8624 (tttt) REVERT: DA 22 ILE cc_start: 0.8307 (OUTLIER) cc_final: 0.7810 (tp) REVERT: JA 40 LYS cc_start: 0.8895 (tttt) cc_final: 0.8542 (tttt) outliers start: 34 outliers final: 26 residues processed: 317 average time/residue: 0.2278 time to fit residues: 101.0179 Evaluate side-chains 323 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 293 time to evaluate : 1.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Z residue 22 ILE Chi-restraints excluded: chain B residue 29 VAL 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 29 VAL 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 J residue 1 MET 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 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 20 GLU 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 46 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 85 optimal weight: 1.9990 chunk 49 optimal weight: 0.6980 chunk 68 optimal weight: 0.9980 chunk 45 optimal weight: 2.9990 chunk 14 optimal weight: 3.9990 chunk 83 optimal weight: 4.9990 chunk 109 optimal weight: 5.9990 chunk 2 optimal weight: 1.9990 chunk 5 optimal weight: 4.9990 chunk 24 optimal weight: 1.9990 chunk 65 optimal weight: 6.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- 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 = 0.3463 r_free = 0.3463 target = 0.109025 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.092391 restraints weight = 17462.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.095706 restraints weight = 9236.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.097976 restraints weight = 5945.757| |-----------------------------------------------------------------------------| r_work (final): 0.3290 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8298 moved from start: 0.3975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 11185 Z= 0.174 Angle : 0.435 6.778 15130 Z= 0.254 Chirality : 0.036 0.124 1785 Planarity : 0.003 0.024 1820 Dihedral : 6.580 88.539 1535 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.58 % Favored : 99.42 % Rotamer: Outliers : 3.62 % Allowed : 20.09 % Favored : 76.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 5.55 (0.18), residues: 1385 helix: 3.66 (0.11), residues: 1350 sheet: None (None), residues: 0 loop : 0.43 (0.50), residues: 35 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP I 26 PHE 0.026 0.001 PHE R 11 TYR 0.030 0.001 TYRJA 24 ARG 0.001 0.000 ARG S 33 Details of bonding type rmsd hydrogen bonds : bond 0.06129 ( 1241) hydrogen bonds : angle 3.48273 ( 3723) covalent geometry : bond 0.00370 (11185) covalent geometry : angle 0.43468 (15130) *********************** 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 334 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 294 time to evaluate : 1.142 Fit side-chains REVERT: Z 22 ILE cc_start: 0.8306 (OUTLIER) cc_final: 0.7670 (tp) REVERT: H 30 VAL cc_start: 0.9024 (t) cc_final: 0.8813 (t) REVERT: A 22 ILE cc_start: 0.8189 (OUTLIER) cc_final: 0.7907 (tp) REVERT: G 44 LYS cc_start: 0.9045 (ttmt) cc_final: 0.8731 (tttp) REVERT: N 21 TYR cc_start: 0.9180 (t80) cc_final: 0.8893 (t80) REVERT: N 22 ILE cc_start: 0.8354 (OUTLIER) cc_final: 0.8081 (tp) REVERT: W 44 LYS cc_start: 0.8952 (ttmt) cc_final: 0.8676 (ttpt) REVERT: AA 24 TYR cc_start: 0.8081 (m-10) cc_final: 0.7717 (m-10) REVERT: BA 18 SER cc_start: 0.8878 (t) cc_final: 0.8666 (m) REVERT: CA 40 LYS cc_start: 0.8826 (tttt) cc_final: 0.8584 (tttt) REVERT: DA 22 ILE cc_start: 0.8302 (OUTLIER) cc_final: 0.7835 (tp) REVERT: JA 40 LYS cc_start: 0.8870 (tttt) cc_final: 0.8472 (tttt) outliers start: 40 outliers final: 32 residues processed: 315 average time/residue: 0.2201 time to fit residues: 98.0754 Evaluate side-chains 328 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 292 time to evaluate : 1.204 ------------------------------------------------------------------------------- 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 29 VAL 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 32 ILE Chi-restraints excluded: chain X residue 33 VAL Chi-restraints excluded: chain X residue 47 SER Chi-restraints excluded: chain Y residue 1 MET 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 16 optimal weight: 0.8980 chunk 39 optimal weight: 0.8980 chunk 1 optimal weight: 3.9990 chunk 50 optimal weight: 0.9980 chunk 59 optimal weight: 5.9990 chunk 122 optimal weight: 4.9990 chunk 98 optimal weight: 0.9990 chunk 73 optimal weight: 0.8980 chunk 5 optimal weight: 3.9990 chunk 28 optimal weight: 0.6980 chunk 86 optimal weight: 0.7980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.110839 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.094051 restraints weight = 17767.852| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.097355 restraints weight = 9432.695| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.099607 restraints weight = 6115.329| |-----------------------------------------------------------------------------| r_work (final): 0.3360 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8250 moved from start: 0.4245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 11185 Z= 0.142 Angle : 0.417 7.118 15130 Z= 0.241 Chirality : 0.035 0.131 1785 Planarity : 0.003 0.023 1820 Dihedral : 6.439 89.486 1535 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.36 % Favored : 99.64 % Rotamer: Outliers : 3.17 % Allowed : 20.72 % Favored : 76.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 5.67 (0.18), residues: 1385 helix: 3.74 (0.11), residues: 1345 sheet: None (None), residues: 0 loop : 0.50 (0.46), residues: 40 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP W 26 PHE 0.038 0.001 PHE R 11 TYR 0.022 0.001 TYRCA 24 ARG 0.001 0.000 ARG Q 26 Details of bonding type rmsd hydrogen bonds : bond 0.05536 ( 1241) hydrogen bonds : angle 3.42990 ( 3723) covalent geometry : bond 0.00269 (11185) covalent geometry : angle 0.41714 (15130) *********************** 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 335 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 300 time to evaluate : 1.181 Fit side-chains REVERT: Z 22 ILE cc_start: 0.8222 (OUTLIER) cc_final: 0.7579 (tp) REVERT: C 21 TYR cc_start: 0.8726 (m-80) cc_final: 0.8423 (m-80) REVERT: H 30 VAL cc_start: 0.8989 (t) cc_final: 0.8763 (t) REVERT: A 22 ILE cc_start: 0.8181 (OUTLIER) cc_final: 0.7852 (tp) REVERT: G 44 LYS cc_start: 0.9030 (ttmt) cc_final: 0.8819 (tttm) REVERT: I 20 GLU cc_start: 0.7649 (mt-10) cc_final: 0.7427 (mt-10) REVERT: N 22 ILE cc_start: 0.8387 (OUTLIER) cc_final: 0.8134 (tp) REVERT: W 44 LYS cc_start: 0.9001 (ttmt) cc_final: 0.8729 (ttpt) REVERT: X 21 TYR cc_start: 0.8774 (m-80) cc_final: 0.8461 (m-80) REVERT: AA 24 TYR cc_start: 0.7972 (m-10) cc_final: 0.7678 (m-10) REVERT: BA 18 SER cc_start: 0.8902 (t) cc_final: 0.8691 (m) REVERT: DA 22 ILE cc_start: 0.8271 (OUTLIER) cc_final: 0.7732 (tp) REVERT: JA 40 LYS cc_start: 0.8866 (tttt) cc_final: 0.8489 (tttt) outliers start: 35 outliers final: 27 residues processed: 319 average time/residue: 0.2220 time to fit residues: 100.3641 Evaluate side-chains 327 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 296 time to evaluate : 1.134 ------------------------------------------------------------------------------- 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 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 37 ILE 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 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 46 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 82 optimal weight: 0.7980 chunk 76 optimal weight: 0.6980 chunk 120 optimal weight: 0.8980 chunk 4 optimal weight: 5.9990 chunk 103 optimal weight: 0.6980 chunk 68 optimal weight: 0.8980 chunk 121 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 54 optimal weight: 0.6980 chunk 109 optimal weight: 0.9990 chunk 94 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.113015 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.096041 restraints weight = 17365.497| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.099411 restraints weight = 9195.087| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.101663 restraints weight = 5944.263| |-----------------------------------------------------------------------------| r_work (final): 0.3373 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.4340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 11185 Z= 0.139 Angle : 0.419 7.677 15130 Z= 0.242 Chirality : 0.035 0.137 1785 Planarity : 0.003 0.022 1820 Dihedral : 6.391 89.214 1535 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.58 % Favored : 99.42 % Rotamer: Outliers : 2.81 % Allowed : 21.00 % Favored : 76.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 5.68 (0.18), residues: 1385 helix: 3.74 (0.11), residues: 1345 sheet: None (None), residues: 0 loop : 0.68 (0.46), residues: 40 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP W 26 PHE 0.028 0.001 PHE R 11 TYR 0.022 0.001 TYRJA 24 ARG 0.001 0.000 ARG S 33 Details of bonding type rmsd hydrogen bonds : bond 0.05398 ( 1241) hydrogen bonds : angle 3.41952 ( 3723) covalent geometry : bond 0.00260 (11185) covalent geometry : angle 0.41932 (15130) ********************** 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 338 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 307 time to evaluate : 1.141 Fit side-chains REVERT: Z 22 ILE cc_start: 0.8259 (OUTLIER) cc_final: 0.7642 (tp) REVERT: C 21 TYR cc_start: 0.8744 (m-80) cc_final: 0.8449 (m-80) REVERT: H 30 VAL cc_start: 0.8930 (t) cc_final: 0.8696 (t) REVERT: A 22 ILE cc_start: 0.8103 (OUTLIER) cc_final: 0.7690 (tp) REVERT: N 21 TYR cc_start: 0.9128 (t80) cc_final: 0.8869 (t80) REVERT: N 22 ILE cc_start: 0.8258 (OUTLIER) cc_final: 0.7938 (tp) REVERT: W 44 LYS cc_start: 0.8989 (ttmt) cc_final: 0.8721 (ttpt) REVERT: X 21 TYR cc_start: 0.8772 (m-80) cc_final: 0.8429 (m-80) REVERT: BA 18 SER cc_start: 0.8897 (t) cc_final: 0.8696 (m) REVERT: CA 40 LYS cc_start: 0.8878 (tttt) cc_final: 0.8576 (tttt) REVERT: DA 22 ILE cc_start: 0.8276 (OUTLIER) cc_final: 0.7795 (tp) REVERT: JA 40 LYS cc_start: 0.8845 (tttt) cc_final: 0.8473 (tttt) outliers start: 31 outliers final: 25 residues processed: 323 average time/residue: 0.2251 time to fit residues: 102.2984 Evaluate side-chains 332 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 303 time to evaluate : 1.293 ------------------------------------------------------------------------------- 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 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 37 ILE 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 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 GA residue 1 MET 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 43 optimal weight: 3.9990 chunk 74 optimal weight: 1.9990 chunk 2 optimal weight: 0.9980 chunk 12 optimal weight: 0.6980 chunk 13 optimal weight: 0.9980 chunk 7 optimal weight: 3.9990 chunk 26 optimal weight: 0.8980 chunk 0 optimal weight: 4.9990 chunk 116 optimal weight: 2.9990 chunk 63 optimal weight: 0.9980 chunk 61 optimal weight: 0.7980 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 = 0.3496 r_free = 0.3496 target = 0.111653 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.094706 restraints weight = 17495.439| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.098033 restraints weight = 9364.411| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.100289 restraints weight = 6088.183| |-----------------------------------------------------------------------------| r_work (final): 0.3369 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8242 moved from start: 0.4382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 11185 Z= 0.144 Angle : 0.430 7.005 15130 Z= 0.249 Chirality : 0.036 0.137 1785 Planarity : 0.003 0.022 1820 Dihedral : 6.369 88.931 1535 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.58 % Favored : 99.42 % Rotamer: Outliers : 2.71 % Allowed : 21.90 % Favored : 75.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 5.63 (0.18), residues: 1385 helix: 3.71 (0.11), residues: 1345 sheet: None (None), residues: 0 loop : 0.66 (0.47), residues: 40 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP W 26 PHE 0.039 0.001 PHE R 11 TYR 0.024 0.001 TYRAA 24 ARG 0.001 0.000 ARG Q 26 Details of bonding type rmsd hydrogen bonds : bond 0.05469 ( 1241) hydrogen bonds : angle 3.44900 ( 3723) covalent geometry : bond 0.00278 (11185) covalent geometry : angle 0.43043 (15130) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3378.14 seconds wall clock time: 59 minutes 43.94 seconds (3583.94 seconds total)