Starting phenix.real_space_refine on Fri Feb 14 20:44:46 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ixl_35795/02_2025/8ixl_35795.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ixl_35795/02_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_35795/02_2025/8ixl_35795.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ixl_35795/02_2025/8ixl_35795.map" model { file = "/net/cci-nas-00/data/ceres_data/8ixl_35795/02_2025/8ixl_35795.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ixl_35795/02_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-5592/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: 6.56, per 1000 atoms: 0.60 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: 2.93 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: 0.70 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: 3.43 Time building geometry restraints manager: 3.34 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: 0.760 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: 0.400 Check model and map are aligned: 0.090 Set scattering table: 0.100 Process input model: 26.100 Find NCS groups from input model: 0.430 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:2.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.930 ------------------------------------------------------------------------------- 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= 0.784 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 *********************** 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 : 1.198 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: 0.3197 time to fit residues: 136.0157 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 : 1.367 ------------------------------------------------------------------------------- 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 = 34)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.099843 restraints weight = 16338.466| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.103724 restraints weight = 7854.613| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.106164 restraints weight = 4717.659| |-----------------------------------------------------------------------------| r_work (final): 0.3401 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 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= 0.181 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 *********************** 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 : 1.178 Fit side-chains REVERT: B 44 LYS cc_start: 0.9017 (OUTLIER) cc_final: 0.8656 (ttpt) REVERT: E 24 TYR cc_start: 0.8101 (m-10) cc_final: 0.7850 (m-10) REVERT: E 28 MET cc_start: 0.7765 (ttp) cc_final: 0.7550 (ttp) REVERT: G 44 LYS cc_start: 0.8920 (ttmt) cc_final: 0.8507 (tttp) REVERT: I 20 GLU cc_start: 0.7502 (mt-10) cc_final: 0.7200 (mt-10) REVERT: K 24 TYR cc_start: 0.8094 (m-10) cc_final: 0.7843 (m-10) REVERT: R 24 TYR cc_start: 0.8227 (m-10) cc_final: 0.7992 (m-10) REVERT: S 18 SER cc_start: 0.8926 (t) cc_final: 0.8667 (m) REVERT: W 44 LYS cc_start: 0.9047 (ttmt) cc_final: 0.8803 (ttmt) REVERT: CA 40 LYS cc_start: 0.8934 (tttt) cc_final: 0.8705 (tttt) REVERT: HA 24 TYR cc_start: 0.8118 (m-10) cc_final: 0.7888 (m-10) REVERT: JA 40 LYS cc_start: 0.8975 (tttt) cc_final: 0.8658 (tttt) REVERT: JA 43 LYS cc_start: 0.8656 (mtmt) cc_final: 0.8386 (mtmt) outliers start: 25 outliers final: 10 residues processed: 341 average time/residue: 0.2469 time to fit residues: 115.8454 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 : 1.300 ------------------------------------------------------------------------------- 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: 0.8980 chunk 48 optimal weight: 1.9990 chunk 86 optimal weight: 0.8980 chunk 93 optimal weight: 0.9980 chunk 121 optimal weight: 7.9990 chunk 78 optimal weight: 0.9980 chunk 74 optimal weight: 0.3980 chunk 5 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.115531 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.098990 restraints weight = 16786.332| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.102727 restraints weight = 8255.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.105176 restraints weight = 5055.471| |-----------------------------------------------------------------------------| r_work (final): 0.3392 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 moved from start: 0.3652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 11185 Z= 0.166 Angle : 0.376 4.624 15130 Z= 0.225 Chirality : 0.034 0.120 1785 Planarity : 0.002 0.018 1820 Dihedral : 7.159 87.291 1535 Min Nonbonded Distance : 2.623 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.14 % Favored : 99.86 % Rotamer: Outliers : 1.45 % Allowed : 16.74 % Favored : 81.81 % 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: 5.78 (0.18), residues: 1385 helix: 3.78 (0.11), residues: 1350 sheet: None (None), residues: 0 loop : 1.05 (0.30), residues: 35 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRPFA 26 PHE 0.013 0.001 PHEAA 11 TYR 0.011 0.001 TYR M 24 ARG 0.001 0.000 ARG Q 26 *********************** 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 321 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 305 time to evaluate : 1.229 Fit side-chains REVERT: H 30 VAL cc_start: 0.8893 (t) cc_final: 0.8661 (t) REVERT: G 44 LYS cc_start: 0.8989 (ttmt) cc_final: 0.8600 (tttp) REVERT: J 26 ARG cc_start: 0.8607 (ttp80) cc_final: 0.8400 (ttp-170) REVERT: K 11 PHE cc_start: 0.7696 (t80) cc_final: 0.7414 (t80) REVERT: M 20 GLU cc_start: 0.7778 (tt0) cc_final: 0.7526 (tt0) REVERT: M 24 TYR cc_start: 0.8442 (m-10) cc_final: 0.8219 (m-10) REVERT: O 41 LEU cc_start: 0.9286 (mt) cc_final: 0.9060 (mt) REVERT: R 28 MET cc_start: 0.7769 (ttp) cc_final: 0.7409 (ttp) REVERT: T 40 LYS cc_start: 0.8958 (tttt) cc_final: 0.8664 (tttt) REVERT: W 44 LYS cc_start: 0.8978 (ttmt) cc_final: 0.8704 (ttpt) REVERT: W 45 PHE cc_start: 0.9049 (m-80) cc_final: 0.8706 (m-80) REVERT: BA 18 SER cc_start: 0.8778 (t) cc_final: 0.8547 (m) REVERT: CA 40 LYS cc_start: 0.8784 (tttt) cc_final: 0.8474 (tttt) REVERT: EA 45 PHE cc_start: 0.9049 (m-80) cc_final: 0.8807 (m-80) REVERT: JA 20 GLU cc_start: 0.7637 (tt0) cc_final: 0.7252 (tt0) REVERT: JA 40 LYS cc_start: 0.8916 (tttt) cc_final: 0.8632 (tttt) outliers start: 16 outliers final: 10 residues processed: 311 average time/residue: 0.2470 time to fit residues: 105.8550 Evaluate side-chains 298 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 288 time to evaluate : 1.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 A residue 48 LYS Chi-restraints excluded: chain J residue 31 SER Chi-restraints excluded: chain Q residue 1 MET 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: 0.7980 chunk 82 optimal weight: 2.9990 chunk 7 optimal weight: 5.9990 chunk 21 optimal weight: 10.0000 chunk 48 optimal weight: 0.9980 chunk 6 optimal weight: 0.9980 chunk 92 optimal weight: 0.8980 chunk 62 optimal weight: 2.9990 chunk 101 optimal weight: 6.9990 chunk 119 optimal weight: 3.9990 chunk 49 optimal weight: 0.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- 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 = 0.3530 r_free = 0.3530 target = 0.114883 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.098222 restraints weight = 16718.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.101840 restraints weight = 8373.332| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.104255 restraints weight = 5231.121| |-----------------------------------------------------------------------------| r_work (final): 0.3383 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 moved from start: 0.3790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 11185 Z= 0.174 Angle : 0.370 3.810 15130 Z= 0.221 Chirality : 0.034 0.103 1785 Planarity : 0.002 0.018 1820 Dihedral : 6.982 89.063 1535 Min Nonbonded Distance : 2.624 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.36 % Favored : 99.64 % Rotamer: Outliers : 1.81 % Allowed : 18.46 % Favored : 79.73 % 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: 5.83 (0.18), residues: 1385 helix: 3.81 (0.11), residues: 1350 sheet: None (None), residues: 0 loop : 1.20 (0.36), residues: 35 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRPFA 26 PHE 0.016 0.001 PHE R 11 TYR 0.013 0.001 TYRJA 24 ARG 0.001 0.000 ARG Y 26 *********************** 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 317 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 297 time to evaluate : 1.476 Fit side-chains REVERT: H 30 VAL cc_start: 0.8943 (t) cc_final: 0.8699 (t) REVERT: G 44 LYS cc_start: 0.8997 (ttmt) cc_final: 0.8639 (tttp) REVERT: I 20 GLU cc_start: 0.7629 (mt-10) cc_final: 0.7358 (mt-10) REVERT: J 26 ARG cc_start: 0.8609 (ttp80) cc_final: 0.8401 (ttp-170) REVERT: K 11 PHE cc_start: 0.7613 (t80) cc_final: 0.7370 (t80) REVERT: M 20 GLU cc_start: 0.7797 (tt0) cc_final: 0.7544 (tt0) REVERT: M 24 TYR cc_start: 0.8422 (m-10) cc_final: 0.8191 (m-10) REVERT: O 41 LEU cc_start: 0.9249 (mt) cc_final: 0.9042 (mt) REVERT: R 28 MET cc_start: 0.7637 (ttp) cc_final: 0.7391 (ttp) REVERT: T 40 LYS cc_start: 0.8929 (tttt) cc_final: 0.8641 (tttt) REVERT: W 44 LYS cc_start: 0.9017 (ttmt) cc_final: 0.8704 (tttp) REVERT: BA 18 SER cc_start: 0.8854 (t) cc_final: 0.8621 (m) REVERT: CA 40 LYS cc_start: 0.8824 (tttt) cc_final: 0.8580 (tttt) REVERT: DA 22 ILE cc_start: 0.8222 (OUTLIER) cc_final: 0.7758 (tp) REVERT: FA 40 LYS cc_start: 0.8577 (ttpp) cc_final: 0.8319 (tttm) REVERT: HA 11 PHE cc_start: 0.7510 (t80) cc_final: 0.7274 (t80) REVERT: JA 20 GLU cc_start: 0.7594 (tt0) cc_final: 0.7353 (tt0) REVERT: JA 40 LYS cc_start: 0.8881 (tttt) cc_final: 0.8536 (tttt) outliers start: 20 outliers final: 16 residues processed: 305 average time/residue: 0.2392 time to fit residues: 101.2533 Evaluate side-chains 302 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 285 time to evaluate : 1.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 A residue 31 VAL Chi-restraints excluded: chain A residue 48 LYS 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 28 MET 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 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 114 optimal weight: 0.6980 chunk 104 optimal weight: 1.9990 chunk 23 optimal weight: 0.9980 chunk 64 optimal weight: 2.9990 chunk 84 optimal weight: 2.9990 chunk 88 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 102 optimal weight: 5.9990 chunk 14 optimal weight: 0.8980 chunk 94 optimal weight: 1.9990 chunk 75 optimal weight: 5.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 15 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.111193 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.094641 restraints weight = 17005.166| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.098165 restraints weight = 8631.420| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.100559 restraints weight = 5454.206| |-----------------------------------------------------------------------------| r_work (final): 0.3348 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8258 moved from start: 0.3796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11185 Z= 0.214 Angle : 0.403 6.248 15130 Z= 0.237 Chirality : 0.035 0.119 1785 Planarity : 0.003 0.019 1820 Dihedral : 7.006 89.197 1535 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.43 % Favored : 99.57 % Rotamer: Outliers : 3.62 % Allowed : 17.83 % Favored : 78.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 5.73 (0.18), residues: 1385 helix: 3.76 (0.11), residues: 1350 sheet: None (None), residues: 0 loop : 0.93 (0.49), residues: 35 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRPFA 26 PHE 0.016 0.001 PHEAA 11 TYR 0.013 0.001 TYR K 24 ARG 0.001 0.000 ARG S 33 *********************** 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 329 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 289 time to evaluate : 1.199 Fit side-chains REVERT: Z 22 ILE cc_start: 0.8209 (OUTLIER) cc_final: 0.7578 (tp) REVERT: D 1 MET cc_start: 0.6842 (ttt) cc_final: 0.6549 (tmm) REVERT: H 30 VAL cc_start: 0.9019 (t) cc_final: 0.8793 (t) REVERT: H 40 LYS cc_start: 0.9153 (tttt) cc_final: 0.8885 (tttt) REVERT: A 22 ILE cc_start: 0.8152 (OUTLIER) cc_final: 0.7867 (tp) REVERT: G 44 LYS cc_start: 0.9048 (ttmt) cc_final: 0.8681 (tttp) REVERT: I 20 GLU cc_start: 0.7694 (mt-10) cc_final: 0.7402 (mt-10) REVERT: K 11 PHE cc_start: 0.7718 (t80) cc_final: 0.7485 (t80) REVERT: M 20 GLU cc_start: 0.7909 (tt0) cc_final: 0.7607 (tt0) REVERT: M 24 TYR cc_start: 0.8506 (m-10) cc_final: 0.8217 (m-10) REVERT: N 22 ILE cc_start: 0.8347 (OUTLIER) cc_final: 0.8131 (tp) REVERT: R 11 PHE cc_start: 0.7140 (t80) cc_final: 0.6850 (t80) REVERT: R 28 MET cc_start: 0.7711 (OUTLIER) cc_final: 0.7471 (ttp) REVERT: T 40 LYS cc_start: 0.8917 (tttt) cc_final: 0.8614 (tttt) REVERT: W 44 LYS cc_start: 0.9010 (ttmt) cc_final: 0.8708 (tttp) REVERT: BA 18 SER cc_start: 0.8881 (t) cc_final: 0.8584 (m) REVERT: CA 40 LYS cc_start: 0.8844 (tttt) cc_final: 0.8595 (tttt) REVERT: DA 22 ILE cc_start: 0.8285 (OUTLIER) cc_final: 0.7794 (tp) REVERT: HA 11 PHE cc_start: 0.7678 (t80) cc_final: 0.7449 (t80) REVERT: IA 18 SER cc_start: 0.8917 (t) cc_final: 0.8708 (m) REVERT: JA 40 LYS cc_start: 0.8893 (tttt) cc_final: 0.8521 (tttt) outliers start: 40 outliers final: 30 residues processed: 310 average time/residue: 0.2427 time to fit residues: 104.6484 Evaluate side-chains 322 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 287 time to evaluate : 1.132 ------------------------------------------------------------------------------- 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 A residue 48 LYS 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 28 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 28 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 48 optimal weight: 0.6980 chunk 26 optimal weight: 2.9990 chunk 67 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 40 optimal weight: 3.9990 chunk 112 optimal weight: 0.9980 chunk 53 optimal weight: 0.9990 chunk 115 optimal weight: 3.9990 chunk 19 optimal weight: 1.9990 chunk 92 optimal weight: 4.9990 chunk 88 optimal weight: 0.6980 overall best weight: 1.0784 ------------------------------------------------------------------------------- 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 = 0.3529 r_free = 0.3529 target = 0.113394 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.096512 restraints weight = 17016.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.100121 restraints weight = 8582.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.102537 restraints weight = 5403.427| |-----------------------------------------------------------------------------| r_work (final): 0.3375 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.3914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 11185 Z= 0.188 Angle : 0.394 5.738 15130 Z= 0.231 Chirality : 0.034 0.123 1785 Planarity : 0.002 0.018 1820 Dihedral : 6.976 89.969 1535 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.43 % Favored : 99.57 % Rotamer: Outliers : 3.26 % Allowed : 19.28 % 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 (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: 5.80 (0.18), residues: 1385 helix: 3.82 (0.11), residues: 1345 sheet: None (None), residues: 0 loop : 0.61 (0.50), residues: 40 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP W 26 PHE 0.025 0.001 PHE E 11 TYR 0.023 0.001 TYR T 24 ARG 0.001 0.000 ARG Y 26 *********************** 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 327 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 291 time to evaluate : 1.169 Fit side-chains REVERT: Z 22 ILE cc_start: 0.8188 (OUTLIER) cc_final: 0.7558 (tp) REVERT: D 1 MET cc_start: 0.6840 (OUTLIER) cc_final: 0.6516 (tmm) REVERT: H 30 VAL cc_start: 0.9018 (t) cc_final: 0.8799 (t) REVERT: H 40 LYS cc_start: 0.9145 (tttt) cc_final: 0.8861 (tttt) REVERT: A 22 ILE cc_start: 0.8130 (OUTLIER) cc_final: 0.7773 (tp) REVERT: G 44 LYS cc_start: 0.9029 (ttmt) cc_final: 0.8704 (tttp) REVERT: I 20 GLU cc_start: 0.7641 (mt-10) cc_final: 0.7305 (mt-10) REVERT: M 20 GLU cc_start: 0.7942 (tt0) cc_final: 0.7640 (tt0) REVERT: M 24 TYR cc_start: 0.8502 (m-10) cc_final: 0.8256 (m-10) REVERT: R 28 MET cc_start: 0.7695 (OUTLIER) cc_final: 0.7443 (ttp) REVERT: T 40 LYS cc_start: 0.8898 (tttt) cc_final: 0.8666 (tttt) REVERT: W 44 LYS cc_start: 0.9008 (ttmt) cc_final: 0.8711 (tttp) REVERT: AA 24 TYR cc_start: 0.8056 (m-10) cc_final: 0.7682 (m-10) REVERT: BA 18 SER cc_start: 0.8877 (t) cc_final: 0.8578 (m) REVERT: CA 40 LYS cc_start: 0.8832 (tttt) cc_final: 0.8589 (tttt) REVERT: DA 22 ILE cc_start: 0.8206 (OUTLIER) cc_final: 0.7745 (tp) REVERT: IA 18 SER cc_start: 0.8899 (t) cc_final: 0.8696 (m) REVERT: JA 40 LYS cc_start: 0.8906 (tttt) cc_final: 0.8540 (tttt) outliers start: 36 outliers final: 27 residues processed: 308 average time/residue: 0.2363 time to fit residues: 101.2761 Evaluate side-chains 322 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 290 time to evaluate : 1.236 ------------------------------------------------------------------------------- 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 D residue 1 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 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 28 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 X residue 47 SER Chi-restraints excluded: chain AA residue 28 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 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 96 optimal weight: 0.5980 chunk 59 optimal weight: 5.9990 chunk 88 optimal weight: 0.9990 chunk 41 optimal weight: 0.7980 chunk 56 optimal weight: 2.9990 chunk 112 optimal weight: 0.6980 chunk 10 optimal weight: 0.9990 chunk 73 optimal weight: 0.9980 chunk 93 optimal weight: 0.8980 chunk 101 optimal weight: 0.9980 chunk 44 optimal weight: 0.2980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 = 0.3567 r_free = 0.3567 target = 0.116671 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.099851 restraints weight = 17040.103| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.103562 restraints weight = 8563.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.106011 restraints weight = 5350.435| |-----------------------------------------------------------------------------| r_work (final): 0.3412 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.4206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 11185 Z= 0.151 Angle : 0.380 5.749 15130 Z= 0.222 Chirality : 0.034 0.113 1785 Planarity : 0.002 0.017 1820 Dihedral : 6.813 88.883 1535 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.43 % Favored : 99.57 % Rotamer: Outliers : 3.08 % Allowed : 19.64 % Favored : 77.29 % 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: 5.93 (0.18), residues: 1385 helix: 3.89 (0.11), residues: 1345 sheet: None (None), residues: 0 loop : 1.03 (0.50), residues: 40 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP N 26 PHE 0.018 0.001 PHE K 11 TYR 0.025 0.001 TYR T 24 ARG 0.001 0.000 ARG Y 26 *********************** 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 346 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 312 time to evaluate : 1.234 Fit side-chains REVERT: Z 22 ILE cc_start: 0.8150 (OUTLIER) cc_final: 0.7508 (tp) REVERT: C 21 TYR cc_start: 0.8638 (m-80) cc_final: 0.8310 (m-80) REVERT: D 1 MET cc_start: 0.6830 (OUTLIER) cc_final: 0.6532 (tmm) REVERT: F 18 SER cc_start: 0.8642 (m) cc_final: 0.8415 (t) REVERT: H 30 VAL cc_start: 0.8937 (t) cc_final: 0.8701 (t) REVERT: H 40 LYS cc_start: 0.9088 (tttt) cc_final: 0.8811 (tttt) REVERT: A 22 ILE cc_start: 0.8118 (OUTLIER) cc_final: 0.7787 (tp) REVERT: G 44 LYS cc_start: 0.9021 (ttmt) cc_final: 0.8730 (tttp) REVERT: I 20 GLU cc_start: 0.7583 (mt-10) cc_final: 0.7250 (mt-10) REVERT: M 20 GLU cc_start: 0.7880 (tt0) cc_final: 0.7597 (tt0) REVERT: M 21 TYR cc_start: 0.9018 (m-80) cc_final: 0.8799 (m-80) REVERT: M 24 TYR cc_start: 0.8448 (m-10) cc_final: 0.8154 (m-10) REVERT: M 36 THR cc_start: 0.9109 (t) cc_final: 0.8890 (p) REVERT: N 22 ILE cc_start: 0.8268 (OUTLIER) cc_final: 0.7999 (tp) REVERT: R 28 MET cc_start: 0.7619 (OUTLIER) cc_final: 0.7375 (ttp) REVERT: T 36 THR cc_start: 0.9135 (t) cc_final: 0.8789 (p) REVERT: T 40 LYS cc_start: 0.8899 (tttt) cc_final: 0.8673 (tttt) REVERT: W 44 LYS cc_start: 0.9044 (ttmt) cc_final: 0.8742 (tttp) REVERT: AA 24 TYR cc_start: 0.7915 (m-10) cc_final: 0.7668 (m-10) REVERT: DA 22 ILE cc_start: 0.8246 (OUTLIER) cc_final: 0.7751 (tp) REVERT: JA 40 LYS cc_start: 0.8879 (tttt) cc_final: 0.8550 (tttt) outliers start: 34 outliers final: 24 residues processed: 328 average time/residue: 0.2457 time to fit residues: 112.6191 Evaluate side-chains 321 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 291 time to evaluate : 1.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Z residue 22 ILE Chi-restraints excluded: chain Z residue 29 VAL Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain C residue 47 SER Chi-restraints excluded: chain D residue 1 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 28 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 28 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 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: 2.9990 chunk 49 optimal weight: 0.9980 chunk 68 optimal weight: 3.9990 chunk 45 optimal weight: 1.9990 chunk 14 optimal weight: 3.9990 chunk 83 optimal weight: 2.9990 chunk 109 optimal weight: 5.9990 chunk 2 optimal weight: 1.9990 chunk 5 optimal weight: 3.9990 chunk 24 optimal weight: 0.9980 chunk 65 optimal weight: 2.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- 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 = 0.3444 r_free = 0.3444 target = 0.107473 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.090939 restraints weight = 17506.406| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.094187 restraints weight = 9287.688| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.096414 restraints weight = 5997.838| |-----------------------------------------------------------------------------| r_work (final): 0.3232 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8319 moved from start: 0.3870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 11185 Z= 0.271 Angle : 0.449 6.509 15130 Z= 0.263 Chirality : 0.036 0.128 1785 Planarity : 0.003 0.022 1820 Dihedral : 6.945 89.505 1535 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.58 % Favored : 99.42 % Rotamer: Outliers : 3.98 % Allowed : 19.91 % 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: 5.55 (0.19), residues: 1385 helix: 3.66 (0.12), residues: 1350 sheet: None (None), residues: 0 loop : 0.31 (0.54), residues: 35 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP K 26 PHE 0.031 0.002 PHE E 11 TYR 0.025 0.001 TYRJA 24 ARG 0.001 0.000 ARG S 33 *********************** 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 332 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 288 time to evaluate : 1.161 Fit side-chains REVERT: H 30 VAL cc_start: 0.9089 (t) cc_final: 0.8881 (t) REVERT: A 22 ILE cc_start: 0.8293 (OUTLIER) cc_final: 0.7920 (tp) REVERT: G 44 LYS cc_start: 0.8997 (ttmt) cc_final: 0.8712 (tttm) REVERT: M 20 GLU cc_start: 0.7970 (tt0) cc_final: 0.7315 (tt0) REVERT: M 24 TYR cc_start: 0.8526 (m-10) cc_final: 0.8149 (m-80) REVERT: N 21 TYR cc_start: 0.9201 (t80) cc_final: 0.8900 (t80) REVERT: N 22 ILE cc_start: 0.8374 (OUTLIER) cc_final: 0.8106 (tp) REVERT: N 40 LYS cc_start: 0.8451 (ttmm) cc_final: 0.8248 (ttpp) REVERT: R 11 PHE cc_start: 0.7453 (t80) cc_final: 0.7151 (t80) REVERT: S 18 SER cc_start: 0.9065 (t) cc_final: 0.8749 (m) REVERT: T 36 THR cc_start: 0.9078 (t) cc_final: 0.8870 (p) REVERT: W 44 LYS cc_start: 0.9016 (ttmt) cc_final: 0.8695 (tttp) REVERT: AA 11 PHE cc_start: 0.7572 (t80) cc_final: 0.7358 (t80) REVERT: BA 18 SER cc_start: 0.8915 (t) cc_final: 0.8629 (m) REVERT: CA 40 LYS cc_start: 0.8905 (tttt) cc_final: 0.8620 (tttt) REVERT: DA 22 ILE cc_start: 0.8321 (OUTLIER) cc_final: 0.7827 (tp) REVERT: JA 40 LYS cc_start: 0.8888 (tttt) cc_final: 0.8525 (tttt) outliers start: 44 outliers final: 34 residues processed: 313 average time/residue: 0.2400 time to fit residues: 103.5850 Evaluate side-chains 320 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 283 time to evaluate : 1.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Z 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 J residue 17 LEU 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 W residue 36 THR 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 28 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 16 optimal weight: 0.7980 chunk 39 optimal weight: 0.6980 chunk 1 optimal weight: 2.9990 chunk 50 optimal weight: 0.9990 chunk 59 optimal weight: 1.9990 chunk 122 optimal weight: 5.9990 chunk 98 optimal weight: 2.9990 chunk 73 optimal weight: 0.9980 chunk 5 optimal weight: 3.9990 chunk 28 optimal weight: 0.6980 chunk 86 optimal weight: 0.0040 overall best weight: 0.6392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: AA 15 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.116173 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.099173 restraints weight = 17141.919| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.102806 restraints weight = 8685.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.105277 restraints weight = 5476.382| |-----------------------------------------------------------------------------| r_work (final): 0.3407 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 moved from start: 0.4315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.068 11185 Z= 0.165 Angle : 0.410 7.312 15130 Z= 0.238 Chirality : 0.035 0.133 1785 Planarity : 0.003 0.024 1820 Dihedral : 6.745 89.179 1535 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.36 % Favored : 99.64 % Rotamer: Outliers : 2.44 % Allowed : 21.36 % 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: 5.77 (0.18), residues: 1385 helix: 3.79 (0.11), residues: 1345 sheet: None (None), residues: 0 loop : 0.71 (0.45), residues: 40 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP N 26 PHE 0.025 0.001 PHE K 11 TYR 0.027 0.001 TYR T 24 ARG 0.001 0.000 ARG J 26 *********************** 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 331 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 304 time to evaluate : 1.199 Fit side-chains REVERT: C 21 TYR cc_start: 0.8672 (m-80) cc_final: 0.8430 (m-80) REVERT: H 30 VAL cc_start: 0.8946 (t) cc_final: 0.8710 (t) REVERT: H 40 LYS cc_start: 0.9084 (tttt) cc_final: 0.8843 (tttt) REVERT: A 22 ILE cc_start: 0.8036 (OUTLIER) cc_final: 0.7581 (tp) REVERT: G 44 LYS cc_start: 0.8962 (ttmt) cc_final: 0.8741 (tttm) REVERT: I 20 GLU cc_start: 0.7646 (mt-10) cc_final: 0.7413 (mt-10) REVERT: N 22 ILE cc_start: 0.8330 (OUTLIER) cc_final: 0.8078 (tp) REVERT: T 36 THR cc_start: 0.9053 (t) cc_final: 0.8832 (p) REVERT: W 44 LYS cc_start: 0.9048 (ttmt) cc_final: 0.8753 (tttp) REVERT: X 21 TYR cc_start: 0.8662 (m-80) cc_final: 0.8421 (m-80) REVERT: CA 40 LYS cc_start: 0.8849 (tttt) cc_final: 0.8595 (tttt) REVERT: JA 40 LYS cc_start: 0.8863 (tttt) cc_final: 0.8526 (tttt) outliers start: 27 outliers final: 20 residues processed: 319 average time/residue: 0.2283 time to fit residues: 101.7182 Evaluate side-chains 319 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 297 time to evaluate : 1.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 AA residue 28 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 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: 1.9990 chunk 76 optimal weight: 0.9990 chunk 120 optimal weight: 0.6980 chunk 4 optimal weight: 5.9990 chunk 103 optimal weight: 0.5980 chunk 68 optimal weight: 3.9990 chunk 121 optimal weight: 7.9990 chunk 38 optimal weight: 2.9990 chunk 54 optimal weight: 0.0980 chunk 109 optimal weight: 4.9990 chunk 94 optimal weight: 1.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- 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 = 0.3506 r_free = 0.3506 target = 0.112382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.095311 restraints weight = 17417.475| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.098667 restraints weight = 9310.318| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.100959 restraints weight = 6053.498| |-----------------------------------------------------------------------------| r_work (final): 0.3364 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8243 moved from start: 0.4313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 11185 Z= 0.190 Angle : 0.430 7.221 15130 Z= 0.249 Chirality : 0.035 0.175 1785 Planarity : 0.003 0.024 1820 Dihedral : 6.756 89.369 1535 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.51 % Favored : 99.49 % Rotamer: Outliers : 2.17 % Allowed : 22.26 % Favored : 75.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 5.72 (0.18), residues: 1385 helix: 3.77 (0.11), residues: 1345 sheet: None (None), residues: 0 loop : 0.73 (0.47), residues: 40 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP W 26 PHE 0.026 0.001 PHEHA 11 TYR 0.027 0.002 TYRJA 24 ARG 0.001 0.000 ARG S 33 ********************** 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 323 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 299 time to evaluate : 1.282 Fit side-chains REVERT: C 21 TYR cc_start: 0.8776 (m-80) cc_final: 0.8466 (m-80) REVERT: H 30 VAL cc_start: 0.8953 (t) cc_final: 0.8719 (t) REVERT: A 22 ILE cc_start: 0.8133 (OUTLIER) cc_final: 0.7748 (tp) REVERT: G 44 LYS cc_start: 0.8999 (ttmt) cc_final: 0.8774 (tttm) REVERT: I 20 GLU cc_start: 0.7678 (mt-10) cc_final: 0.7450 (mt-10) REVERT: N 21 TYR cc_start: 0.9140 (t80) cc_final: 0.8880 (t80) REVERT: N 22 ILE cc_start: 0.8283 (OUTLIER) cc_final: 0.7970 (tp) REVERT: W 44 LYS cc_start: 0.9057 (ttmt) cc_final: 0.8756 (tttp) REVERT: X 21 TYR cc_start: 0.8735 (m-80) cc_final: 0.8402 (m-80) REVERT: CA 40 LYS cc_start: 0.8848 (tttt) cc_final: 0.8565 (tttt) REVERT: JA 40 LYS cc_start: 0.8866 (tttt) cc_final: 0.8500 (tttt) outliers start: 24 outliers final: 22 residues processed: 312 average time/residue: 0.2283 time to fit residues: 100.0406 Evaluate side-chains 318 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 294 time to evaluate : 1.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 AA residue 28 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 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: 0.9980 chunk 2 optimal weight: 1.9990 chunk 12 optimal weight: 0.3980 chunk 13 optimal weight: 0.9980 chunk 7 optimal weight: 1.9990 chunk 26 optimal weight: 0.7980 chunk 0 optimal weight: 4.9990 chunk 116 optimal weight: 0.9980 chunk 63 optimal weight: 1.9990 chunk 61 optimal weight: 0.9990 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 = 0.3523 r_free = 0.3523 target = 0.113580 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.096500 restraints weight = 17320.782| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.099861 restraints weight = 9200.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.102101 restraints weight = 5984.451| |-----------------------------------------------------------------------------| r_work (final): 0.3372 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 0.4377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 11185 Z= 0.192 Angle : 0.434 7.085 15130 Z= 0.250 Chirality : 0.036 0.164 1785 Planarity : 0.003 0.024 1820 Dihedral : 6.735 89.667 1535 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.43 % Favored : 99.57 % Rotamer: Outliers : 2.35 % Allowed : 22.44 % Favored : 75.20 % 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: 5.66 (0.18), residues: 1385 helix: 3.72 (0.11), residues: 1345 sheet: None (None), residues: 0 loop : 0.75 (0.47), residues: 40 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP W 26 PHE 0.036 0.001 PHE R 11 TYR 0.027 0.001 TYR T 24 ARG 0.001 0.000 ARG S 33 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3036.31 seconds wall clock time: 55 minutes 44.55 seconds (3344.55 seconds total)