Starting phenix.real_space_refine on Wed Mar 4 19:46:47 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6xmx_22265/03_2026/6xmx_22265_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/6xmx_22265/03_2026/6xmx_22265.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6xmx_22265/03_2026/6xmx_22265.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6xmx_22265/03_2026/6xmx_22265.map" model { file = "/net/cci-nas-00/data/ceres_data/6xmx_22265/03_2026/6xmx_22265_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6xmx_22265/03_2026/6xmx_22265_trim.cif" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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: 6 Type Number sf(0) Gaussians S 88 5.16 5 Cl 8 4.86 5 C 5136 2.51 5 N 1408 2.21 5 O 1432 1.98 5 H 7942 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 16014 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 1967 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 1967 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 2, 'TRANS': 119} Chain: "B" Number of atoms: 1968 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 1968 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 2, 'TRANS': 119} Chain: "C" Number of atoms: 1968 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 1968 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 2, 'TRANS': 119} Chain: "D" Number of atoms: 1968 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 1968 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 2, 'TRANS': 119} Chain: "E" Number of atoms: 1968 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 1968 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 2, 'TRANS': 119} Chain: "F" Number of atoms: 1967 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 1967 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 2, 'TRANS': 119} Chain: "G" Number of atoms: 1968 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 1968 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 2, 'TRANS': 119} Chain: "H" Number of atoms: 1968 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 1968 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 2, 'TRANS': 119} Chain: "A" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 34 Unusual residues: {'U52': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 34 Unusual residues: {'U52': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 34 Unusual residues: {'U52': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 34 Unusual residues: {'U52': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 34 Unusual residues: {'U52': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 34 Unusual residues: {'U52': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 34 Unusual residues: {'U52': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 34 Unusual residues: {'U52': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.09, per 1000 atoms: 0.19 Number of scatterers: 16014 At special positions: 0 Unit cell: (137.775, 77.55, 113.025, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Cl 8 17.00 S 88 16.00 O 1432 8.00 N 1408 7.00 C 5136 6.00 H 7942 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.11 Conformation dependent library (CDL) restraints added in 375.4 milliseconds 1920 Ramachandran restraints generated. 960 Oldfield, 0 Emsley, 960 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1904 Finding SS restraints... Secondary structure from input PDB file: 56 helices and 15 sheets defined 68.9% alpha, 9.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.35 Creating SS restraints... Processing helix chain 'A' and resid 13 through 28 Processing helix chain 'A' and resid 46 through 54 Processing helix chain 'A' and resid 54 through 63 removed outlier: 3.671A pdb=" N ASP A 63 " --> pdb=" O SER A 59 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 68 removed outlier: 4.784A pdb=" N ASN A 68 " --> pdb=" O GLN A 64 " (cutoff:3.500A) Processing helix chain 'A' and resid 79 through 93 Processing helix chain 'A' and resid 101 through 113 Processing helix chain 'A' and resid 114 through 128 Processing helix chain 'B' and resid 13 through 28 Processing helix chain 'B' and resid 46 through 54 Processing helix chain 'B' and resid 54 through 63 removed outlier: 3.670A pdb=" N ASP B 63 " --> pdb=" O SER B 59 " (cutoff:3.500A) Processing helix chain 'B' and resid 63 through 68 removed outlier: 4.784A pdb=" N ASN B 68 " --> pdb=" O GLN B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 79 through 93 Processing helix chain 'B' and resid 101 through 113 Processing helix chain 'B' and resid 114 through 128 Processing helix chain 'C' and resid 13 through 28 Processing helix chain 'C' and resid 46 through 54 Processing helix chain 'C' and resid 54 through 63 removed outlier: 3.670A pdb=" N ASP C 63 " --> pdb=" O SER C 59 " (cutoff:3.500A) Processing helix chain 'C' and resid 63 through 68 removed outlier: 4.784A pdb=" N ASN C 68 " --> pdb=" O GLN C 64 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 93 Processing helix chain 'C' and resid 101 through 113 Processing helix chain 'C' and resid 114 through 128 Processing helix chain 'D' and resid 13 through 28 Processing helix chain 'D' and resid 46 through 54 Processing helix chain 'D' and resid 54 through 63 removed outlier: 3.671A pdb=" N ASP D 63 " --> pdb=" O SER D 59 " (cutoff:3.500A) Processing helix chain 'D' and resid 63 through 68 removed outlier: 4.784A pdb=" N ASN D 68 " --> pdb=" O GLN D 64 " (cutoff:3.500A) Processing helix chain 'D' and resid 79 through 93 Processing helix chain 'D' and resid 101 through 113 Processing helix chain 'D' and resid 114 through 128 Processing helix chain 'E' and resid 13 through 28 Processing helix chain 'E' and resid 46 through 54 Processing helix chain 'E' and resid 54 through 63 removed outlier: 3.671A pdb=" N ASP E 63 " --> pdb=" O SER E 59 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 68 removed outlier: 4.784A pdb=" N ASN E 68 " --> pdb=" O GLN E 64 " (cutoff:3.500A) Processing helix chain 'E' and resid 79 through 93 Processing helix chain 'E' and resid 101 through 113 Processing helix chain 'E' and resid 114 through 128 Processing helix chain 'F' and resid 13 through 28 Processing helix chain 'F' and resid 46 through 54 Processing helix chain 'F' and resid 54 through 63 removed outlier: 3.670A pdb=" N ASP F 63 " --> pdb=" O SER F 59 " (cutoff:3.500A) Processing helix chain 'F' and resid 63 through 68 removed outlier: 4.784A pdb=" N ASN F 68 " --> pdb=" O GLN F 64 " (cutoff:3.500A) Processing helix chain 'F' and resid 79 through 93 Processing helix chain 'F' and resid 101 through 113 Processing helix chain 'F' and resid 114 through 128 Processing helix chain 'G' and resid 13 through 28 Processing helix chain 'G' and resid 46 through 54 Processing helix chain 'G' and resid 54 through 63 removed outlier: 3.671A pdb=" N ASP G 63 " --> pdb=" O SER G 59 " (cutoff:3.500A) Processing helix chain 'G' and resid 63 through 68 removed outlier: 4.785A pdb=" N ASN G 68 " --> pdb=" O GLN G 64 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 93 Processing helix chain 'G' and resid 101 through 113 Processing helix chain 'G' and resid 114 through 128 Processing helix chain 'H' and resid 13 through 28 Processing helix chain 'H' and resid 46 through 54 Processing helix chain 'H' and resid 54 through 63 removed outlier: 3.671A pdb=" N ASP H 63 " --> pdb=" O SER H 59 " (cutoff:3.500A) Processing helix chain 'H' and resid 63 through 68 removed outlier: 4.784A pdb=" N ASN H 68 " --> pdb=" O GLN H 64 " (cutoff:3.500A) Processing helix chain 'H' and resid 79 through 93 Processing helix chain 'H' and resid 101 through 113 Processing helix chain 'H' and resid 114 through 128 Processing sheet with id=AA1, first strand: chain 'A' and resid 9 through 10 removed outlier: 3.675A pdb=" N ILE A 9 " --> pdb=" O LEU B 95 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LEU B 95 " --> pdb=" O ILE A 9 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 41 through 45 Processing sheet with id=AA3, first strand: chain 'A' and resid 94 through 95 removed outlier: 4.289A pdb=" N LEU A 95 " --> pdb=" O ILE B 9 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N ILE B 9 " --> pdb=" O LEU A 95 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'B' and resid 41 through 45 Processing sheet with id=AA5, first strand: chain 'C' and resid 9 through 10 removed outlier: 4.280A pdb=" N ILE C 9 " --> pdb=" O LEU D 95 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N LEU D 95 " --> pdb=" O ILE C 9 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'C' and resid 41 through 45 Processing sheet with id=AA7, first strand: chain 'D' and resid 41 through 45 Processing sheet with id=AA8, first strand: chain 'E' and resid 9 through 10 removed outlier: 4.430A pdb=" N ILE E 9 " --> pdb=" O LEU F 95 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N LEU F 95 " --> pdb=" O ILE E 9 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'E' and resid 41 through 45 Processing sheet with id=AB1, first strand: chain 'E' and resid 94 through 95 removed outlier: 3.505A pdb=" N ILE F 9 " --> pdb=" O LEU E 95 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 41 through 45 Processing sheet with id=AB3, first strand: chain 'G' and resid 9 through 10 removed outlier: 4.572A pdb=" N ILE G 9 " --> pdb=" O LEU H 95 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N LEU H 95 " --> pdb=" O ILE G 9 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'G' and resid 41 through 45 Processing sheet with id=AB5, first strand: chain 'G' and resid 94 through 95 removed outlier: 4.179A pdb=" N LEU G 95 " --> pdb=" O ILE H 9 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N ILE H 9 " --> pdb=" O LEU G 95 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'H' and resid 41 through 45 497 hydrogen bonds defined for protein. 1443 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: 3.34 Time building geometry restraints manager: 1.59 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.82 - 1.02: 7903 1.02 - 1.21: 39 1.21 - 1.41: 3312 1.41 - 1.61: 4752 1.61 - 1.80: 144 Bond restraints: 16150 Sorted by residual: bond pdb=" C24 U52 A 401 " pdb=" N20 U52 A 401 " ideal model delta sigma weight residual 1.352 1.425 -0.073 2.00e-02 2.50e+03 1.33e+01 bond pdb=" C24 U52 D 401 " pdb=" N20 U52 D 401 " ideal model delta sigma weight residual 1.352 1.425 -0.073 2.00e-02 2.50e+03 1.33e+01 bond pdb=" C24 U52 G 401 " pdb=" N20 U52 G 401 " ideal model delta sigma weight residual 1.352 1.425 -0.073 2.00e-02 2.50e+03 1.33e+01 bond pdb=" C24 U52 C 401 " pdb=" N20 U52 C 401 " ideal model delta sigma weight residual 1.352 1.425 -0.073 2.00e-02 2.50e+03 1.32e+01 bond pdb=" C24 U52 B 401 " pdb=" N20 U52 B 401 " ideal model delta sigma weight residual 1.352 1.424 -0.072 2.00e-02 2.50e+03 1.31e+01 ... (remaining 16145 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.56: 28983 6.56 - 13.13: 21 13.13 - 19.69: 5 19.69 - 26.26: 1 26.26 - 32.82: 4 Bond angle restraints: 29014 Sorted by residual: angle pdb=" CA GLU A 81 " pdb=" CB GLU A 81 " pdb=" HB2 GLU A 81 " ideal model delta sigma weight residual 109.00 76.18 32.82 3.00e+00 1.11e-01 1.20e+02 angle pdb=" CA GLU A 81 " pdb=" CB GLU A 81 " pdb=" HB3 GLU A 81 " ideal model delta sigma weight residual 109.00 77.25 31.75 3.00e+00 1.11e-01 1.12e+02 angle pdb=" HB2 GLU A 81 " pdb=" CB GLU A 81 " pdb=" HB3 GLU A 81 " ideal model delta sigma weight residual 110.00 138.13 -28.13 3.00e+00 1.11e-01 8.79e+01 angle pdb=" CG GLU A 81 " pdb=" CB GLU A 81 " pdb=" HB2 GLU A 81 " ideal model delta sigma weight residual 108.00 81.68 26.32 3.00e+00 1.11e-01 7.70e+01 angle pdb=" CG GLU A 81 " pdb=" CB GLU A 81 " pdb=" HB3 GLU A 81 " ideal model delta sigma weight residual 108.00 83.18 24.82 3.00e+00 1.11e-01 6.85e+01 ... (remaining 29009 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.69: 6763 16.69 - 33.38: 562 33.38 - 50.07: 185 50.07 - 66.76: 78 66.76 - 83.45: 18 Dihedral angle restraints: 7606 sinusoidal: 4286 harmonic: 3320 Sorted by residual: dihedral pdb=" N GLU H 81 " pdb=" CA GLU H 81 " pdb=" CB GLU H 81 " pdb=" CG GLU H 81 " ideal model delta sinusoidal sigma weight residual 180.00 129.59 50.41 3 1.50e+01 4.44e-03 8.90e+00 dihedral pdb=" N GLU D 81 " pdb=" CA GLU D 81 " pdb=" CB GLU D 81 " pdb=" CG GLU D 81 " ideal model delta sinusoidal sigma weight residual 180.00 129.61 50.39 3 1.50e+01 4.44e-03 8.89e+00 dihedral pdb=" N GLU B 81 " pdb=" CA GLU B 81 " pdb=" CB GLU B 81 " pdb=" CG GLU B 81 " ideal model delta sinusoidal sigma weight residual 180.00 129.61 50.39 3 1.50e+01 4.44e-03 8.89e+00 ... (remaining 7603 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 683 0.034 - 0.067: 325 0.067 - 0.100: 172 0.100 - 0.134: 84 0.134 - 0.167: 32 Chirality restraints: 1296 Sorted by residual: chirality pdb=" CB VAL C 117 " pdb=" CA VAL C 117 " pdb=" CG1 VAL C 117 " pdb=" CG2 VAL C 117 " both_signs ideal model delta sigma weight residual False -2.63 -2.46 -0.17 2.00e-01 2.50e+01 6.98e-01 chirality pdb=" CB VAL E 117 " pdb=" CA VAL E 117 " pdb=" CG1 VAL E 117 " pdb=" CG2 VAL E 117 " both_signs ideal model delta sigma weight residual False -2.63 -2.46 -0.16 2.00e-01 2.50e+01 6.80e-01 chirality pdb=" CA PRO E 80 " pdb=" N PRO E 80 " pdb=" C PRO E 80 " pdb=" CB PRO E 80 " both_signs ideal model delta sigma weight residual False 2.72 2.55 0.16 2.00e-01 2.50e+01 6.71e-01 ... (remaining 1293 not shown) Planarity restraints: 2320 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE B 43 " 0.015 2.00e-02 2.50e+03 1.41e-02 6.00e+00 pdb=" CG PHE B 43 " -0.039 2.00e-02 2.50e+03 pdb=" CD1 PHE B 43 " 0.022 2.00e-02 2.50e+03 pdb=" CD2 PHE B 43 " 0.003 2.00e-02 2.50e+03 pdb=" CE1 PHE B 43 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 PHE B 43 " -0.005 2.00e-02 2.50e+03 pdb=" CZ PHE B 43 " 0.004 2.00e-02 2.50e+03 pdb=" HD1 PHE B 43 " -0.005 2.00e-02 2.50e+03 pdb=" HD2 PHE B 43 " 0.002 2.00e-02 2.50e+03 pdb=" HE1 PHE B 43 " -0.005 2.00e-02 2.50e+03 pdb=" HE2 PHE B 43 " 0.004 2.00e-02 2.50e+03 pdb=" HZ PHE B 43 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE E 43 " -0.014 2.00e-02 2.50e+03 1.39e-02 5.81e+00 pdb=" CG PHE E 43 " 0.039 2.00e-02 2.50e+03 pdb=" CD1 PHE E 43 " -0.022 2.00e-02 2.50e+03 pdb=" CD2 PHE E 43 " -0.003 2.00e-02 2.50e+03 pdb=" CE1 PHE E 43 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 PHE E 43 " 0.003 2.00e-02 2.50e+03 pdb=" CZ PHE E 43 " -0.004 2.00e-02 2.50e+03 pdb=" HD1 PHE E 43 " 0.005 2.00e-02 2.50e+03 pdb=" HD2 PHE E 43 " -0.001 2.00e-02 2.50e+03 pdb=" HE1 PHE E 43 " 0.005 2.00e-02 2.50e+03 pdb=" HE2 PHE E 43 " -0.005 2.00e-02 2.50e+03 pdb=" HZ PHE E 43 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE D 43 " 0.016 2.00e-02 2.50e+03 1.37e-02 5.60e+00 pdb=" CG PHE D 43 " -0.039 2.00e-02 2.50e+03 pdb=" CD1 PHE D 43 " 0.019 2.00e-02 2.50e+03 pdb=" CD2 PHE D 43 " 0.006 2.00e-02 2.50e+03 pdb=" CE1 PHE D 43 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE D 43 " -0.003 2.00e-02 2.50e+03 pdb=" CZ PHE D 43 " 0.003 2.00e-02 2.50e+03 pdb=" HD1 PHE D 43 " -0.006 2.00e-02 2.50e+03 pdb=" HD2 PHE D 43 " 0.001 2.00e-02 2.50e+03 pdb=" HE1 PHE D 43 " 0.001 2.00e-02 2.50e+03 pdb=" HE2 PHE D 43 " 0.004 2.00e-02 2.50e+03 pdb=" HZ PHE D 43 " -0.002 2.00e-02 2.50e+03 ... (remaining 2317 not shown) Histogram of nonbonded interaction distances: 1.40 - 2.04: 188 2.04 - 2.68: 25536 2.68 - 3.32: 46659 3.32 - 3.96: 59609 3.96 - 4.60: 94945 Nonbonded interactions: 226937 Sorted by model distance: nonbonded pdb=" O TYR A 58 " pdb=" HG1 THR A 62 " model vdw 1.397 2.450 nonbonded pdb=" O TYR B 58 " pdb=" HG1 THR B 62 " model vdw 1.483 2.450 nonbonded pdb=" O TYR C 58 " pdb=" HG1 THR C 62 " model vdw 1.504 2.450 nonbonded pdb=" O TYR G 58 " pdb=" HG1 THR G 62 " model vdw 1.534 2.450 nonbonded pdb=" O THR G 92 " pdb=" HG SER G 93 " model vdw 1.539 2.450 ... (remaining 226932 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' and (resid 7 through 83 or (resid 84 and (name N or name CA or name C \ or name O or name CB or name SG or name H or name HA or name HB2 or name HB3)) \ or resid 85 through 401)) selection = (chain 'B' and (resid 7 through 83 or (resid 84 and (name N or name CA or name C \ or name O or name CB or name SG or name H or name HA or name HB2 or name HB3)) \ or resid 85 through 107 or (resid 108 and (name N or name CA or name C or name O \ or name CB or name OG1 or name CG2 or name H or name HA or name HB or name HG21 \ or name HG22 or name HG23)) or resid 109 through 401)) selection = (chain 'C' and (resid 7 through 83 or (resid 84 and (name N or name CA or name C \ or name O or name CB or name SG or name H or name HA or name HB2 or name HB3)) \ or resid 85 through 107 or (resid 108 and (name N or name CA or name C or name O \ or name CB or name OG1 or name CG2 or name H or name HA or name HB or name HG21 \ or name HG22 or name HG23)) or resid 109 through 401)) selection = (chain 'D' and (resid 7 through 83 or (resid 84 and (name N or name CA or name C \ or name O or name CB or name SG or name H or name HA or name HB2 or name HB3)) \ or resid 85 through 107 or (resid 108 and (name N or name CA or name C or name O \ or name CB or name OG1 or name CG2 or name H or name HA or name HB or name HG21 \ or name HG22 or name HG23)) or resid 109 through 401)) selection = (chain 'E' and (resid 7 through 83 or (resid 84 and (name N or name CA or name C \ or name O or name CB or name SG or name H or name HA or name HB2 or name HB3)) \ or resid 85 through 107 or (resid 108 and (name N or name CA or name C or name O \ or name CB or name OG1 or name CG2 or name H or name HA or name HB or name HG21 \ or name HG22 or name HG23)) or resid 109 through 401)) selection = (chain 'F' and (resid 7 through 107 or (resid 108 and (name N or name CA or name \ C or name O or name CB or name OG1 or name CG2 or name H or name HA or name HB \ or name HG21 or name HG22 or name HG23)) or resid 109 through 401)) selection = (chain 'G' and (resid 7 through 83 or (resid 84 and (name N or name CA or name C \ or name O or name CB or name SG or name H or name HA or name HB2 or name HB3)) \ or resid 85 through 107 or (resid 108 and (name N or name CA or name C or name O \ or name CB or name OG1 or name CG2 or name H or name HA or name HB or name HG21 \ or name HG22 or name HG23)) or resid 109 through 401)) selection = (chain 'H' and (resid 7 through 83 or (resid 84 and (name N or name CA or name C \ or name O or name CB or name SG or name H or name HA or name HB2 or name HB3)) \ or resid 85 through 107 or (resid 108 and (name N or name CA or name C or name O \ or name CB or name OG1 or name CG2 or name H or name HA or name HB or name HG21 \ or name HG22 or name HG23)) or resid 109 through 401)) } 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: 1.060 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.080 Extract box with map and model: 0.270 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 14.880 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5250 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 0.083 8208 Z= 0.496 Angle : 1.120 9.615 11096 Z= 0.621 Chirality : 0.057 0.167 1296 Planarity : 0.006 0.023 1368 Dihedral : 15.974 83.454 3168 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 0.89 % Allowed : 5.36 % Favored : 93.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.34 (0.23), residues: 960 helix: -1.09 (0.16), residues: 584 sheet: None (None), residues: 0 loop : -0.24 (0.32), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.025 0.003 ARG C 40 TYR 0.016 0.004 TYR E 111 PHE 0.040 0.005 PHE B 43 HIS 0.018 0.005 HIS G 46 Details of bonding type rmsd covalent geometry : bond 0.01165 ( 8208) covalent geometry : angle 1.11999 (11096) hydrogen bonds : bond 0.15243 ( 497) hydrogen bonds : angle 6.18163 ( 1443) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1920 Ramachandran restraints generated. 960 Oldfield, 0 Emsley, 960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1920 Ramachandran restraints generated. 960 Oldfield, 0 Emsley, 960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 108 is missing expected H atoms. Skipping. Evaluate side-chains 307 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 299 time to evaluate : 0.405 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 30 ILE cc_start: 0.6263 (mt) cc_final: 0.5828 (mt) REVERT: D 105 VAL cc_start: 0.6413 (t) cc_final: 0.6169 (t) REVERT: F 30 ILE cc_start: 0.5868 (mt) cc_final: 0.5547 (mt) REVERT: G 33 ASP cc_start: 0.4361 (p0) cc_final: 0.4087 (p0) outliers start: 8 outliers final: 2 residues processed: 304 average time/residue: 0.1968 time to fit residues: 80.3051 Evaluate side-chains 166 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 164 time to evaluate : 0.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 81 GLU Chi-restraints excluded: chain E residue 81 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 49 optimal weight: 0.7980 chunk 53 optimal weight: 0.8980 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 3.9990 chunk 65 optimal weight: 0.6980 chunk 62 optimal weight: 0.6980 chunk 51 optimal weight: 0.7980 chunk 38 optimal weight: 0.9990 chunk 61 optimal weight: 0.5980 chunk 45 optimal weight: 2.9990 chunk 74 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 21 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4826 r_free = 0.4826 target = 0.191890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4542 r_free = 0.4542 target = 0.164106 restraints weight = 25564.652| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4625 r_free = 0.4625 target = 0.171992 restraints weight = 9951.789| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.4675 r_free = 0.4675 target = 0.176888 restraints weight = 5065.335| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.4704 r_free = 0.4704 target = 0.179818 restraints weight = 3050.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.4724 r_free = 0.4724 target = 0.181805 restraints weight = 2119.773| |-----------------------------------------------------------------------------| r_work (final): 0.4733 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5479 moved from start: 0.4224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 8208 Z= 0.130 Angle : 0.555 9.099 11096 Z= 0.305 Chirality : 0.042 0.154 1296 Planarity : 0.003 0.025 1368 Dihedral : 6.165 45.622 1286 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 1.79 % Allowed : 15.29 % Favored : 82.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.33 (0.27), residues: 960 helix: 1.40 (0.21), residues: 600 sheet: None (None), residues: 0 loop : 0.13 (0.33), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 44 TYR 0.016 0.002 TYR E 58 PHE 0.018 0.001 PHE H 124 HIS 0.004 0.001 HIS H 46 Details of bonding type rmsd covalent geometry : bond 0.00274 ( 8208) covalent geometry : angle 0.55452 (11096) hydrogen bonds : bond 0.04344 ( 497) hydrogen bonds : angle 4.35903 ( 1443) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1920 Ramachandran restraints generated. 960 Oldfield, 0 Emsley, 960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1920 Ramachandran restraints generated. 960 Oldfield, 0 Emsley, 960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 108 is missing expected H atoms. Skipping. Evaluate side-chains 208 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 192 time to evaluate : 0.342 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 75 ASP cc_start: 0.4609 (p0) cc_final: 0.4306 (m-30) REVERT: C 24 ARG cc_start: 0.7930 (mtt180) cc_final: 0.7400 (mtm-85) REVERT: C 30 ILE cc_start: 0.6591 (mt) cc_final: 0.6223 (tp) REVERT: C 86 LEU cc_start: 0.7748 (mt) cc_final: 0.7505 (mt) REVERT: C 113 GLN cc_start: 0.6601 (mt0) cc_final: 0.6391 (mm-40) REVERT: D 30 ILE cc_start: 0.6619 (mt) cc_final: 0.6327 (mt) REVERT: G 106 MET cc_start: 0.6329 (ttt) cc_final: 0.5923 (ttt) REVERT: H 75 ASP cc_start: 0.4976 (t70) cc_final: 0.4738 (m-30) outliers start: 16 outliers final: 7 residues processed: 203 average time/residue: 0.1673 time to fit residues: 48.5658 Evaluate side-chains 171 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 164 time to evaluate : 0.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 128 SER Chi-restraints excluded: chain D residue 81 GLU Chi-restraints excluded: chain F residue 101 ASN Chi-restraints excluded: chain G residue 54 SER Chi-restraints excluded: chain G residue 116 HIS Chi-restraints excluded: chain H residue 9 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 88 optimal weight: 3.9990 chunk 52 optimal weight: 1.9990 chunk 2 optimal weight: 4.9990 chunk 23 optimal weight: 0.8980 chunk 20 optimal weight: 1.9990 chunk 32 optimal weight: 3.9990 chunk 14 optimal weight: 3.9990 chunk 70 optimal weight: 1.9990 chunk 35 optimal weight: 3.9990 chunk 48 optimal weight: 2.9990 chunk 3 optimal weight: 1.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 79 ASN C 21 ASN C 79 ASN D 23 ASN D 42 GLN F 96 ASN G 113 GLN H 79 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4713 r_free = 0.4713 target = 0.180450 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4415 r_free = 0.4415 target = 0.153419 restraints weight = 28102.347| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.4499 r_free = 0.4499 target = 0.160755 restraints weight = 11314.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4546 r_free = 0.4546 target = 0.165176 restraints weight = 5867.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 50)----------------| | r_work = 0.4577 r_free = 0.4577 target = 0.168004 restraints weight = 3610.286| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.4596 r_free = 0.4596 target = 0.169764 restraints weight = 2506.787| |-----------------------------------------------------------------------------| r_work (final): 0.4609 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5837 moved from start: 0.5711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 8208 Z= 0.183 Angle : 0.621 7.422 11096 Z= 0.340 Chirality : 0.044 0.172 1296 Planarity : 0.005 0.050 1368 Dihedral : 7.866 63.626 1283 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 11.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 2.23 % Allowed : 16.29 % Favored : 81.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.15 (0.27), residues: 960 helix: 1.29 (0.21), residues: 600 sheet: None (None), residues: 0 loop : 0.01 (0.33), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG F 98 TYR 0.020 0.003 TYR E 58 PHE 0.014 0.002 PHE B 43 HIS 0.006 0.002 HIS F 14 Details of bonding type rmsd covalent geometry : bond 0.00405 ( 8208) covalent geometry : angle 0.62054 (11096) hydrogen bonds : bond 0.04750 ( 497) hydrogen bonds : angle 4.53592 ( 1443) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1920 Ramachandran restraints generated. 960 Oldfield, 0 Emsley, 960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1920 Ramachandran restraints generated. 960 Oldfield, 0 Emsley, 960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 108 is missing expected H atoms. Skipping. Evaluate side-chains 193 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 173 time to evaluate : 0.442 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 24 ARG cc_start: 0.7921 (mtt180) cc_final: 0.7474 (mtm-85) REVERT: D 30 ILE cc_start: 0.6678 (mt) cc_final: 0.6442 (mt) REVERT: H 103 MET cc_start: 0.7925 (tmm) cc_final: 0.7599 (ptm) outliers start: 20 outliers final: 15 residues processed: 187 average time/residue: 0.1639 time to fit residues: 44.0315 Evaluate side-chains 173 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 158 time to evaluate : 0.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 ILE Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 128 SER Chi-restraints excluded: chain B residue 54 SER Chi-restraints excluded: chain B residue 63 ASP Chi-restraints excluded: chain B residue 93 SER Chi-restraints excluded: chain C residue 81 GLU Chi-restraints excluded: chain F residue 30 ILE Chi-restraints excluded: chain F residue 54 SER Chi-restraints excluded: chain G residue 54 SER Chi-restraints excluded: chain G residue 70 SER Chi-restraints excluded: chain G residue 116 HIS Chi-restraints excluded: chain H residue 9 ILE Chi-restraints excluded: chain H residue 22 LEU Chi-restraints excluded: chain H residue 54 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 74 optimal weight: 3.9990 chunk 39 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 chunk 28 optimal weight: 8.9990 chunk 59 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 chunk 40 optimal weight: 0.9980 chunk 71 optimal weight: 0.6980 chunk 10 optimal weight: 2.9990 chunk 76 optimal weight: 0.8980 chunk 25 optimal weight: 3.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4721 r_free = 0.4721 target = 0.181459 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4419 r_free = 0.4419 target = 0.154140 restraints weight = 27996.469| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.4504 r_free = 0.4504 target = 0.161557 restraints weight = 11445.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.4554 r_free = 0.4554 target = 0.166155 restraints weight = 6033.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.4584 r_free = 0.4584 target = 0.168933 restraints weight = 3709.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.4602 r_free = 0.4602 target = 0.170676 restraints weight = 2582.761| |-----------------------------------------------------------------------------| r_work (final): 0.4599 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5797 moved from start: 0.6217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8208 Z= 0.138 Angle : 0.537 8.498 11096 Z= 0.294 Chirality : 0.042 0.154 1296 Planarity : 0.003 0.034 1368 Dihedral : 6.915 54.752 1280 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 10.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 1.67 % Allowed : 17.41 % Favored : 80.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.38 (0.27), residues: 960 helix: 1.53 (0.21), residues: 600 sheet: None (None), residues: 0 loop : -0.02 (0.33), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 28 TYR 0.015 0.002 TYR E 58 PHE 0.013 0.001 PHE F 124 HIS 0.004 0.001 HIS H 46 Details of bonding type rmsd covalent geometry : bond 0.00303 ( 8208) covalent geometry : angle 0.53739 (11096) hydrogen bonds : bond 0.03953 ( 497) hydrogen bonds : angle 4.33287 ( 1443) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1920 Ramachandran restraints generated. 960 Oldfield, 0 Emsley, 960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1920 Ramachandran restraints generated. 960 Oldfield, 0 Emsley, 960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 108 is missing expected H atoms. Skipping. Evaluate side-chains 190 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 175 time to evaluate : 0.451 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 24 ARG cc_start: 0.7998 (mtt180) cc_final: 0.7493 (mtm-85) REVERT: C 113 GLN cc_start: 0.6715 (mt0) cc_final: 0.6442 (mm-40) REVERT: D 30 ILE cc_start: 0.6658 (mt) cc_final: 0.6450 (mt) REVERT: D 103 MET cc_start: 0.6883 (mmt) cc_final: 0.6393 (mpp) REVERT: F 106 MET cc_start: 0.4289 (ttt) cc_final: 0.3844 (mtt) REVERT: H 22 LEU cc_start: 0.6236 (OUTLIER) cc_final: 0.5845 (tt) REVERT: H 110 MET cc_start: 0.6612 (mtm) cc_final: 0.6329 (mtt) outliers start: 15 outliers final: 11 residues processed: 183 average time/residue: 0.1641 time to fit residues: 43.1129 Evaluate side-chains 176 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 164 time to evaluate : 0.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 ILE Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 128 SER Chi-restraints excluded: chain B residue 54 SER Chi-restraints excluded: chain E residue 81 GLU Chi-restraints excluded: chain F residue 30 ILE Chi-restraints excluded: chain F residue 54 SER Chi-restraints excluded: chain G residue 54 SER Chi-restraints excluded: chain G residue 70 SER Chi-restraints excluded: chain H residue 22 LEU Chi-restraints excluded: chain H residue 54 SER Chi-restraints excluded: chain H residue 128 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 55 optimal weight: 1.9990 chunk 18 optimal weight: 3.9990 chunk 12 optimal weight: 4.9990 chunk 13 optimal weight: 0.7980 chunk 5 optimal weight: 0.8980 chunk 4 optimal weight: 0.9990 chunk 43 optimal weight: 0.4980 chunk 76 optimal weight: 7.9990 chunk 45 optimal weight: 4.9990 chunk 9 optimal weight: 0.5980 chunk 14 optimal weight: 1.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4823 r_free = 0.4823 target = 0.190241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4523 r_free = 0.4523 target = 0.162866 restraints weight = 26326.519| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4610 r_free = 0.4610 target = 0.170681 restraints weight = 10333.233| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4660 r_free = 0.4660 target = 0.175397 restraints weight = 5233.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.4690 r_free = 0.4690 target = 0.178318 restraints weight = 3133.139| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.4709 r_free = 0.4709 target = 0.180155 restraints weight = 2135.532| |-----------------------------------------------------------------------------| r_work (final): 0.4718 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5773 moved from start: 0.6587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 8208 Z= 0.110 Angle : 0.501 8.845 11096 Z= 0.272 Chirality : 0.041 0.144 1296 Planarity : 0.003 0.032 1368 Dihedral : 6.697 53.848 1280 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 2.01 % Allowed : 16.74 % Favored : 81.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.74 (0.27), residues: 960 helix: 1.80 (0.21), residues: 600 sheet: None (None), residues: 0 loop : 0.13 (0.33), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 28 TYR 0.015 0.002 TYR A 58 PHE 0.011 0.001 PHE C 83 HIS 0.003 0.001 HIS H 46 Details of bonding type rmsd covalent geometry : bond 0.00239 ( 8208) covalent geometry : angle 0.50088 (11096) hydrogen bonds : bond 0.03544 ( 497) hydrogen bonds : angle 4.20015 ( 1443) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1920 Ramachandran restraints generated. 960 Oldfield, 0 Emsley, 960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1920 Ramachandran restraints generated. 960 Oldfield, 0 Emsley, 960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 108 is missing expected H atoms. Skipping. Evaluate side-chains 196 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 178 time to evaluate : 0.415 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 24 ARG cc_start: 0.7929 (mtt180) cc_final: 0.7501 (mtm-85) REVERT: C 113 GLN cc_start: 0.6723 (mt0) cc_final: 0.6461 (mm-40) REVERT: D 29 ASP cc_start: 0.6033 (m-30) cc_final: 0.5347 (t0) REVERT: D 30 ILE cc_start: 0.6712 (mt) cc_final: 0.6493 (mt) REVERT: D 103 MET cc_start: 0.6977 (mmt) cc_final: 0.6530 (mpp) REVERT: F 106 MET cc_start: 0.4341 (ttt) cc_final: 0.3888 (mtt) REVERT: H 22 LEU cc_start: 0.6139 (OUTLIER) cc_final: 0.5743 (tt) outliers start: 18 outliers final: 13 residues processed: 189 average time/residue: 0.1806 time to fit residues: 47.8404 Evaluate side-chains 177 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 163 time to evaluate : 0.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 ILE Chi-restraints excluded: chain A residue 114 MET Chi-restraints excluded: chain A residue 128 SER Chi-restraints excluded: chain B residue 54 SER Chi-restraints excluded: chain E residue 54 SER Chi-restraints excluded: chain E residue 81 GLU Chi-restraints excluded: chain F residue 30 ILE Chi-restraints excluded: chain F residue 54 SER Chi-restraints excluded: chain F residue 96 ASN Chi-restraints excluded: chain G residue 54 SER Chi-restraints excluded: chain G residue 70 SER Chi-restraints excluded: chain H residue 22 LEU Chi-restraints excluded: chain H residue 54 SER Chi-restraints excluded: chain H residue 128 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 44 optimal weight: 5.9990 chunk 34 optimal weight: 2.9990 chunk 24 optimal weight: 3.9990 chunk 43 optimal weight: 0.8980 chunk 81 optimal weight: 2.9990 chunk 1 optimal weight: 2.9990 chunk 46 optimal weight: 0.6980 chunk 74 optimal weight: 2.9990 chunk 2 optimal weight: 2.9990 chunk 90 optimal weight: 6.9990 chunk 6 optimal weight: 0.7980 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 96 ASN G 96 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4746 r_free = 0.4746 target = 0.182831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4437 r_free = 0.4437 target = 0.155670 restraints weight = 27228.107| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4524 r_free = 0.4524 target = 0.163209 restraints weight = 10552.960| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.4574 r_free = 0.4574 target = 0.167720 restraints weight = 5316.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.4604 r_free = 0.4604 target = 0.170442 restraints weight = 3201.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.4618 r_free = 0.4618 target = 0.171832 restraints weight = 2220.019| |-----------------------------------------------------------------------------| r_work (final): 0.4619 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5892 moved from start: 0.7158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 8208 Z= 0.167 Angle : 0.588 7.942 11096 Z= 0.319 Chirality : 0.043 0.164 1296 Planarity : 0.004 0.040 1368 Dihedral : 7.550 70.638 1280 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 12.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 2.90 % Allowed : 16.85 % Favored : 80.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.46 (0.27), residues: 960 helix: 1.60 (0.21), residues: 600 sheet: None (None), residues: 0 loop : -0.01 (0.33), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 44 TYR 0.021 0.002 TYR C 58 PHE 0.012 0.002 PHE H 61 HIS 0.006 0.001 HIS H 14 Details of bonding type rmsd covalent geometry : bond 0.00369 ( 8208) covalent geometry : angle 0.58834 (11096) hydrogen bonds : bond 0.04075 ( 497) hydrogen bonds : angle 4.45915 ( 1443) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1920 Ramachandran restraints generated. 960 Oldfield, 0 Emsley, 960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1920 Ramachandran restraints generated. 960 Oldfield, 0 Emsley, 960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 108 is missing expected H atoms. Skipping. Evaluate side-chains 201 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 175 time to evaluate : 0.431 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 24 ARG cc_start: 0.8016 (mtt180) cc_final: 0.7551 (mtm-85) REVERT: D 29 ASP cc_start: 0.6317 (m-30) cc_final: 0.5739 (t0) REVERT: D 30 ILE cc_start: 0.6848 (mt) cc_final: 0.6646 (mt) REVERT: D 103 MET cc_start: 0.6918 (mmt) cc_final: 0.6470 (mpp) REVERT: E 68 ASN cc_start: 0.5013 (p0) cc_final: 0.4778 (t0) REVERT: F 106 MET cc_start: 0.4449 (ttt) cc_final: 0.3984 (mtt) REVERT: G 106 MET cc_start: 0.6127 (ttt) cc_final: 0.5904 (ttt) REVERT: H 22 LEU cc_start: 0.6190 (OUTLIER) cc_final: 0.5816 (tt) REVERT: H 103 MET cc_start: 0.7904 (tmm) cc_final: 0.7511 (ptm) outliers start: 26 outliers final: 20 residues processed: 186 average time/residue: 0.1785 time to fit residues: 46.1547 Evaluate side-chains 183 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 162 time to evaluate : 0.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 ILE Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 102 ILE Chi-restraints excluded: chain A residue 114 MET Chi-restraints excluded: chain A residue 128 SER Chi-restraints excluded: chain B residue 54 SER Chi-restraints excluded: chain B residue 93 SER Chi-restraints excluded: chain E residue 54 SER Chi-restraints excluded: chain F residue 30 ILE Chi-restraints excluded: chain F residue 54 SER Chi-restraints excluded: chain F residue 81 GLU Chi-restraints excluded: chain G residue 54 SER Chi-restraints excluded: chain G residue 70 SER Chi-restraints excluded: chain G residue 116 HIS Chi-restraints excluded: chain G residue 124 PHE Chi-restraints excluded: chain H residue 22 LEU Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 54 SER Chi-restraints excluded: chain H residue 102 ILE Chi-restraints excluded: chain H residue 128 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 64 optimal weight: 2.9990 chunk 91 optimal weight: 1.9990 chunk 89 optimal weight: 0.7980 chunk 47 optimal weight: 5.9990 chunk 71 optimal weight: 2.9990 chunk 43 optimal weight: 0.6980 chunk 95 optimal weight: 0.9990 chunk 56 optimal weight: 0.7980 chunk 53 optimal weight: 1.9990 chunk 80 optimal weight: 1.9990 chunk 76 optimal weight: 0.8980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 101 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4779 r_free = 0.4779 target = 0.186731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4485 r_free = 0.4485 target = 0.160193 restraints weight = 26793.832| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.4568 r_free = 0.4568 target = 0.167602 restraints weight = 10528.477| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4615 r_free = 0.4615 target = 0.172002 restraints weight = 5338.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.4644 r_free = 0.4644 target = 0.174732 restraints weight = 3253.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4657 r_free = 0.4657 target = 0.176088 restraints weight = 2253.649| |-----------------------------------------------------------------------------| r_work (final): 0.4667 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5865 moved from start: 0.7486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8208 Z= 0.115 Angle : 0.536 9.004 11096 Z= 0.286 Chirality : 0.041 0.142 1296 Planarity : 0.003 0.038 1368 Dihedral : 7.041 80.591 1280 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 10.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 1.90 % Allowed : 18.86 % Favored : 79.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.80 (0.27), residues: 960 helix: 1.89 (0.21), residues: 600 sheet: None (None), residues: 0 loop : 0.07 (0.33), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 122 TYR 0.018 0.002 TYR F 58 PHE 0.014 0.001 PHE C 83 HIS 0.004 0.001 HIS H 46 Details of bonding type rmsd covalent geometry : bond 0.00253 ( 8208) covalent geometry : angle 0.53578 (11096) hydrogen bonds : bond 0.03436 ( 497) hydrogen bonds : angle 4.25519 ( 1443) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1920 Ramachandran restraints generated. 960 Oldfield, 0 Emsley, 960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1920 Ramachandran restraints generated. 960 Oldfield, 0 Emsley, 960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 108 is missing expected H atoms. Skipping. Evaluate side-chains 189 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 172 time to evaluate : 0.433 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 24 ARG cc_start: 0.8002 (mtt180) cc_final: 0.7560 (mtm-85) REVERT: D 29 ASP cc_start: 0.6044 (m-30) cc_final: 0.5683 (t0) REVERT: D 103 MET cc_start: 0.6966 (mmt) cc_final: 0.6508 (mpp) REVERT: E 63 ASP cc_start: 0.7678 (t0) cc_final: 0.7403 (m-30) REVERT: F 106 MET cc_start: 0.4638 (ttt) cc_final: 0.4084 (mtt) REVERT: G 106 MET cc_start: 0.6189 (ttt) cc_final: 0.5909 (ttt) REVERT: H 22 LEU cc_start: 0.6164 (OUTLIER) cc_final: 0.5828 (tt) REVERT: H 103 MET cc_start: 0.7854 (tmm) cc_final: 0.7525 (ptm) REVERT: H 110 MET cc_start: 0.6666 (mtm) cc_final: 0.6257 (mtt) outliers start: 17 outliers final: 14 residues processed: 182 average time/residue: 0.1806 time to fit residues: 45.3395 Evaluate side-chains 178 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 163 time to evaluate : 0.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 114 MET Chi-restraints excluded: chain A residue 128 SER Chi-restraints excluded: chain B residue 54 SER Chi-restraints excluded: chain B residue 93 SER Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain E residue 54 SER Chi-restraints excluded: chain F residue 30 ILE Chi-restraints excluded: chain F residue 54 SER Chi-restraints excluded: chain F residue 96 ASN Chi-restraints excluded: chain G residue 54 SER Chi-restraints excluded: chain G residue 70 SER Chi-restraints excluded: chain G residue 116 HIS Chi-restraints excluded: chain H residue 22 LEU Chi-restraints excluded: chain H residue 117 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 69 optimal weight: 0.9980 chunk 94 optimal weight: 2.9990 chunk 19 optimal weight: 0.8980 chunk 21 optimal weight: 0.1980 chunk 91 optimal weight: 0.5980 chunk 0 optimal weight: 5.9990 chunk 83 optimal weight: 0.9980 chunk 44 optimal weight: 0.1980 chunk 90 optimal weight: 4.9990 chunk 8 optimal weight: 2.9990 chunk 58 optimal weight: 3.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4804 r_free = 0.4804 target = 0.189009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4509 r_free = 0.4509 target = 0.162188 restraints weight = 26812.847| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4593 r_free = 0.4593 target = 0.169713 restraints weight = 10502.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4639 r_free = 0.4639 target = 0.174132 restraints weight = 5320.169| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.4668 r_free = 0.4668 target = 0.176879 restraints weight = 3225.410| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.4680 r_free = 0.4680 target = 0.178221 restraints weight = 2236.737| |-----------------------------------------------------------------------------| r_work (final): 0.4688 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5833 moved from start: 0.7651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 8208 Z= 0.103 Angle : 0.517 8.954 11096 Z= 0.274 Chirality : 0.041 0.137 1296 Planarity : 0.003 0.046 1368 Dihedral : 6.993 84.361 1280 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 1.23 % Allowed : 19.87 % Favored : 78.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.19 (0.27), residues: 960 helix: 2.19 (0.21), residues: 600 sheet: None (None), residues: 0 loop : 0.26 (0.34), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 122 TYR 0.018 0.002 TYR A 58 PHE 0.017 0.001 PHE B 124 HIS 0.003 0.001 HIS F 46 Details of bonding type rmsd covalent geometry : bond 0.00228 ( 8208) covalent geometry : angle 0.51746 (11096) hydrogen bonds : bond 0.03205 ( 497) hydrogen bonds : angle 4.15967 ( 1443) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1920 Ramachandran restraints generated. 960 Oldfield, 0 Emsley, 960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1920 Ramachandran restraints generated. 960 Oldfield, 0 Emsley, 960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 108 is missing expected H atoms. Skipping. Evaluate side-chains 185 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 174 time to evaluate : 0.500 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 24 ARG cc_start: 0.7984 (mtt180) cc_final: 0.7535 (mtm-85) REVERT: D 29 ASP cc_start: 0.6001 (m-30) cc_final: 0.5678 (t0) REVERT: D 103 MET cc_start: 0.6938 (mmt) cc_final: 0.6489 (mpp) REVERT: E 63 ASP cc_start: 0.7538 (t0) cc_final: 0.7261 (m-30) REVERT: F 106 MET cc_start: 0.4548 (ttt) cc_final: 0.4121 (mtt) REVERT: H 22 LEU cc_start: 0.6131 (OUTLIER) cc_final: 0.5783 (tt) REVERT: H 103 MET cc_start: 0.7777 (tmm) cc_final: 0.7524 (ptp) REVERT: H 110 MET cc_start: 0.6617 (mtm) cc_final: 0.6188 (mtt) outliers start: 11 outliers final: 10 residues processed: 182 average time/residue: 0.1842 time to fit residues: 46.6090 Evaluate side-chains 176 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 165 time to evaluate : 0.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 114 MET Chi-restraints excluded: chain A residue 128 SER Chi-restraints excluded: chain B residue 54 SER Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain E residue 54 SER Chi-restraints excluded: chain F residue 96 ASN Chi-restraints excluded: chain G residue 54 SER Chi-restraints excluded: chain H residue 22 LEU Chi-restraints excluded: chain H residue 117 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 55 optimal weight: 0.5980 chunk 75 optimal weight: 0.6980 chunk 54 optimal weight: 2.9990 chunk 68 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 69 optimal weight: 0.9980 chunk 11 optimal weight: 1.9990 chunk 36 optimal weight: 0.2980 chunk 64 optimal weight: 1.9990 chunk 62 optimal weight: 0.6980 chunk 39 optimal weight: 2.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4813 r_free = 0.4813 target = 0.189811 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4518 r_free = 0.4518 target = 0.162776 restraints weight = 26952.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4601 r_free = 0.4601 target = 0.170286 restraints weight = 10680.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4649 r_free = 0.4649 target = 0.174833 restraints weight = 5458.827| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.4677 r_free = 0.4677 target = 0.177587 restraints weight = 3306.919| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.4691 r_free = 0.4691 target = 0.179099 restraints weight = 2297.378| |-----------------------------------------------------------------------------| r_work (final): 0.4699 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5829 moved from start: 0.7841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 8208 Z= 0.108 Angle : 0.526 8.924 11096 Z= 0.279 Chirality : 0.041 0.143 1296 Planarity : 0.004 0.114 1368 Dihedral : 7.081 87.415 1280 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 11.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 1.56 % Allowed : 19.20 % Favored : 79.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.27 (0.27), residues: 960 helix: 2.24 (0.21), residues: 600 sheet: None (None), residues: 0 loop : 0.32 (0.34), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG C 28 TYR 0.016 0.002 TYR A 58 PHE 0.013 0.001 PHE C 83 HIS 0.003 0.001 HIS H 46 Details of bonding type rmsd covalent geometry : bond 0.00243 ( 8208) covalent geometry : angle 0.52612 (11096) hydrogen bonds : bond 0.03227 ( 497) hydrogen bonds : angle 4.14303 ( 1443) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1920 Ramachandran restraints generated. 960 Oldfield, 0 Emsley, 960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1920 Ramachandran restraints generated. 960 Oldfield, 0 Emsley, 960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 108 is missing expected H atoms. Skipping. Evaluate side-chains 188 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 174 time to evaluate : 0.532 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 24 ARG cc_start: 0.7984 (mtt180) cc_final: 0.7559 (mtm-85) REVERT: D 29 ASP cc_start: 0.6056 (m-30) cc_final: 0.5804 (t0) REVERT: D 103 MET cc_start: 0.6951 (mmt) cc_final: 0.6515 (mpp) REVERT: F 106 MET cc_start: 0.4573 (ttt) cc_final: 0.4087 (mtt) REVERT: H 22 LEU cc_start: 0.6054 (OUTLIER) cc_final: 0.5729 (tt) REVERT: H 110 MET cc_start: 0.6578 (mtm) cc_final: 0.6166 (mtt) outliers start: 14 outliers final: 12 residues processed: 183 average time/residue: 0.1693 time to fit residues: 43.8580 Evaluate side-chains 181 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 168 time to evaluate : 0.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 ILE Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 114 MET Chi-restraints excluded: chain A residue 128 SER Chi-restraints excluded: chain B residue 54 SER Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain E residue 54 SER Chi-restraints excluded: chain F residue 96 ASN Chi-restraints excluded: chain G residue 54 SER Chi-restraints excluded: chain G residue 116 HIS Chi-restraints excluded: chain H residue 22 LEU Chi-restraints excluded: chain H residue 117 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 60 optimal weight: 0.5980 chunk 21 optimal weight: 1.9990 chunk 28 optimal weight: 3.9990 chunk 64 optimal weight: 1.9990 chunk 4 optimal weight: 3.9990 chunk 24 optimal weight: 0.7980 chunk 57 optimal weight: 0.9980 chunk 14 optimal weight: 0.3980 chunk 39 optimal weight: 1.9990 chunk 82 optimal weight: 2.9990 chunk 61 optimal weight: 0.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4811 r_free = 0.4811 target = 0.189392 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4514 r_free = 0.4514 target = 0.162305 restraints weight = 26882.094| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.4597 r_free = 0.4597 target = 0.169808 restraints weight = 10692.641| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.4644 r_free = 0.4644 target = 0.174229 restraints weight = 5466.131| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.4669 r_free = 0.4669 target = 0.176753 restraints weight = 3343.217| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.4688 r_free = 0.4688 target = 0.178662 restraints weight = 2377.783| |-----------------------------------------------------------------------------| r_work (final): 0.4688 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5846 moved from start: 0.7946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 8208 Z= 0.110 Angle : 0.528 9.122 11096 Z= 0.280 Chirality : 0.041 0.140 1296 Planarity : 0.004 0.108 1368 Dihedral : 7.192 89.720 1280 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 11.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 1.56 % Allowed : 19.87 % Favored : 78.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.28 (0.27), residues: 960 helix: 2.25 (0.21), residues: 600 sheet: None (None), residues: 0 loop : 0.31 (0.34), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG C 28 TYR 0.016 0.002 TYR A 58 PHE 0.013 0.001 PHE C 83 HIS 0.003 0.001 HIS H 46 Details of bonding type rmsd covalent geometry : bond 0.00247 ( 8208) covalent geometry : angle 0.52791 (11096) hydrogen bonds : bond 0.03212 ( 497) hydrogen bonds : angle 4.15367 ( 1443) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1920 Ramachandran restraints generated. 960 Oldfield, 0 Emsley, 960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1920 Ramachandran restraints generated. 960 Oldfield, 0 Emsley, 960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 108 is missing expected H atoms. Skipping. Evaluate side-chains 182 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 168 time to evaluate : 0.426 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 24 ARG cc_start: 0.7983 (mtt180) cc_final: 0.7563 (mtm-85) REVERT: D 32 THR cc_start: 0.5840 (t) cc_final: 0.5579 (t) REVERT: D 103 MET cc_start: 0.6961 (mmt) cc_final: 0.6514 (mpp) REVERT: D 114 MET cc_start: 0.7796 (ttm) cc_final: 0.7454 (ttm) REVERT: F 106 MET cc_start: 0.4611 (ttt) cc_final: 0.4133 (mtt) REVERT: G 106 MET cc_start: 0.6183 (ttt) cc_final: 0.5864 (ttt) REVERT: H 22 LEU cc_start: 0.6047 (OUTLIER) cc_final: 0.5688 (tt) REVERT: H 110 MET cc_start: 0.6578 (mtm) cc_final: 0.6134 (mtt) outliers start: 14 outliers final: 13 residues processed: 176 average time/residue: 0.1735 time to fit residues: 43.2951 Evaluate side-chains 180 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 166 time to evaluate : 0.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 ILE Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 114 MET Chi-restraints excluded: chain A residue 128 SER Chi-restraints excluded: chain B residue 54 SER Chi-restraints excluded: chain D residue 25 LEU Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain E residue 54 SER Chi-restraints excluded: chain F residue 96 ASN Chi-restraints excluded: chain G residue 54 SER Chi-restraints excluded: chain G residue 116 HIS Chi-restraints excluded: chain H residue 22 LEU Chi-restraints excluded: chain H residue 117 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 11 optimal weight: 2.9990 chunk 24 optimal weight: 0.7980 chunk 84 optimal weight: 4.9990 chunk 45 optimal weight: 3.9990 chunk 26 optimal weight: 8.9990 chunk 6 optimal weight: 0.7980 chunk 61 optimal weight: 3.9990 chunk 63 optimal weight: 0.0870 chunk 55 optimal weight: 0.4980 chunk 83 optimal weight: 0.8980 chunk 43 optimal weight: 0.6980 overall best weight: 0.5758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4931 r_free = 0.4931 target = 0.203336 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4692 r_free = 0.4692 target = 0.180774 restraints weight = 27339.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.4752 r_free = 0.4752 target = 0.186727 restraints weight = 12464.345| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.4788 r_free = 0.4788 target = 0.190282 restraints weight = 6885.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 54)----------------| | r_work = 0.4809 r_free = 0.4809 target = 0.192481 restraints weight = 4436.818| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4818 r_free = 0.4818 target = 0.193484 restraints weight = 3221.277| |-----------------------------------------------------------------------------| r_work (final): 0.4715 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5870 moved from start: 0.8032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 8208 Z= 0.102 Angle : 0.523 9.067 11096 Z= 0.275 Chirality : 0.041 0.135 1296 Planarity : 0.004 0.097 1368 Dihedral : 7.105 86.698 1280 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 11.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 1.23 % Allowed : 20.31 % Favored : 78.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.42 (0.27), residues: 960 helix: 2.37 (0.21), residues: 600 sheet: None (None), residues: 0 loop : 0.35 (0.34), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG C 28 TYR 0.017 0.001 TYR A 58 PHE 0.012 0.001 PHE C 83 HIS 0.003 0.001 HIS F 46 Details of bonding type rmsd covalent geometry : bond 0.00230 ( 8208) covalent geometry : angle 0.52301 (11096) hydrogen bonds : bond 0.03063 ( 497) hydrogen bonds : angle 4.08415 ( 1443) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2931.42 seconds wall clock time: 50 minutes 30.88 seconds (3030.88 seconds total)