Starting phenix.real_space_refine on Mon Jul 6 00:13:25 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9liz_63128/07_2026/9liz_63128_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9liz_63128/07_2026/9liz_63128.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9liz_63128/07_2026/9liz_63128_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9liz_63128/07_2026/9liz_63128_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9liz_63128/07_2026/9liz_63128.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9liz_63128/07_2026/9liz_63128.map" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 12 5.49 5 S 88 5.16 5 C 10156 2.51 5 N 2684 2.21 5 O 2844 1.98 5 H 15688 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 31472 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 5691 Number of conformers: 1 Conformer: "" Number of residues, atoms: 344, 5691 Classifications: {'peptide': 344} Link IDs: {'PTRANS': 9, 'TRANS': 334} Chain breaks: 1 Chain: "E" Number of atoms: 2130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 2130 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 2, 'TRANS': 141} Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'ASP:plan': 5} Unresolved non-hydrogen planarities: 15 Chain: "B" Number of atoms: 5691 Number of conformers: 1 Conformer: "" Number of residues, atoms: 344, 5691 Classifications: {'peptide': 344} Link IDs: {'PTRANS': 9, 'TRANS': 334} Chain breaks: 1 Chain: "C" Number of atoms: 2130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 2130 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 2, 'TRANS': 141} Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'ASP:plan': 5} Unresolved non-hydrogen planarities: 15 Chain: "D" Number of atoms: 5691 Number of conformers: 1 Conformer: "" Number of residues, atoms: 344, 5691 Classifications: {'peptide': 344} Link IDs: {'PTRANS': 9, 'TRANS': 334} Chain breaks: 1 Chain: "F" Number of atoms: 2130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 2130 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 2, 'TRANS': 141} Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'ASP:plan': 5} Unresolved non-hydrogen planarities: 15 Chain: "G" Number of atoms: 5691 Number of conformers: 1 Conformer: "" Number of residues, atoms: 344, 5691 Classifications: {'peptide': 344} Link IDs: {'PTRANS': 9, 'TRANS': 334} Chain breaks: 1 Chain: "H" Number of atoms: 2130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 2130 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 2, 'TRANS': 141} Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'ASP:plan': 5} Unresolved non-hydrogen planarities: 15 Chain: "A" Number of atoms: 47 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 47 Unusual residues: {'PIO': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 47 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 47 Unusual residues: {'PIO': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 47 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 47 Unusual residues: {'PIO': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 47 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 47 Unusual residues: {'PIO': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.99, per 1000 atoms: 0.19 Number of scatterers: 31472 At special positions: 0 Unit cell: (125.55, 125.55, 120.9, 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) S 88 16.00 P 12 15.00 O 2844 8.00 N 2684 7.00 C 10156 6.00 H 15688 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: 3.26 Conformation dependent library (CDL) restraints added in 798.3 milliseconds 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3640 Finding SS restraints... Secondary structure from input PDB file: 88 helices and 8 sheets defined 82.0% alpha, 0.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.71 Creating SS restraints... Processing helix chain 'A' and resid 103 through 121 Processing helix chain 'A' and resid 124 through 149 removed outlier: 3.514A pdb=" N ILE A 128 " --> pdb=" O GLY A 124 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ILE A 149 " --> pdb=" O VAL A 145 " (cutoff:3.500A) Processing helix chain 'A' and resid 152 through 181 Processing helix chain 'A' and resid 189 through 199 removed outlier: 3.583A pdb=" N GLY A 193 " --> pdb=" O ARG A 189 " (cutoff:3.500A) Processing helix chain 'A' and resid 200 through 223 Processing helix chain 'A' and resid 224 through 235 Processing helix chain 'A' and resid 238 through 246 removed outlier: 4.344A pdb=" N ASP A 246 " --> pdb=" O MET A 242 " (cutoff:3.500A) Processing helix chain 'A' and resid 249 through 262 Processing helix chain 'A' and resid 262 through 289 Processing helix chain 'A' and resid 297 through 310 Processing helix chain 'A' and resid 321 through 363 Proline residue: A 342 - end of helix Processing helix chain 'A' and resid 366 through 384 Processing helix chain 'A' and resid 516 through 541 Processing helix chain 'A' and resid 545 through 576 Processing helix chain 'E' and resid 7 through 22 Processing helix chain 'E' and resid 29 through 39 removed outlier: 3.645A pdb=" N MET E 37 " --> pdb=" O LEU E 33 " (cutoff:3.500A) Processing helix chain 'E' and resid 45 through 55 Processing helix chain 'E' and resid 66 through 75 removed outlier: 3.579A pdb=" N ARG E 75 " --> pdb=" O THR E 71 " (cutoff:3.500A) Processing helix chain 'E' and resid 79 through 92 Processing helix chain 'E' and resid 103 through 113 Processing helix chain 'E' and resid 118 through 128 Processing helix chain 'E' and resid 138 through 147 removed outlier: 3.682A pdb=" N PHE E 142 " --> pdb=" O ASN E 138 " (cutoff:3.500A) Processing helix chain 'B' and resid 104 through 121 Processing helix chain 'B' and resid 124 through 149 removed outlier: 3.514A pdb=" N ILE B 128 " --> pdb=" O GLY B 124 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ILE B 149 " --> pdb=" O VAL B 145 " (cutoff:3.500A) Processing helix chain 'B' and resid 152 through 181 Processing helix chain 'B' and resid 189 through 199 removed outlier: 3.583A pdb=" N GLY B 193 " --> pdb=" O ARG B 189 " (cutoff:3.500A) Processing helix chain 'B' and resid 200 through 223 Processing helix chain 'B' and resid 224 through 235 Processing helix chain 'B' and resid 238 through 246 removed outlier: 4.344A pdb=" N ASP B 246 " --> pdb=" O MET B 242 " (cutoff:3.500A) Processing helix chain 'B' and resid 249 through 262 Processing helix chain 'B' and resid 262 through 289 Processing helix chain 'B' and resid 297 through 310 Processing helix chain 'B' and resid 321 through 363 Proline residue: B 342 - end of helix Processing helix chain 'B' and resid 366 through 384 Processing helix chain 'B' and resid 516 through 541 Processing helix chain 'B' and resid 545 through 576 Processing helix chain 'C' and resid 7 through 22 Processing helix chain 'C' and resid 29 through 39 removed outlier: 3.645A pdb=" N MET C 37 " --> pdb=" O LEU C 33 " (cutoff:3.500A) Processing helix chain 'C' and resid 45 through 55 Processing helix chain 'C' and resid 66 through 75 removed outlier: 3.579A pdb=" N ARG C 75 " --> pdb=" O THR C 71 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 92 Processing helix chain 'C' and resid 103 through 113 Processing helix chain 'C' and resid 118 through 128 Processing helix chain 'C' and resid 138 through 147 removed outlier: 3.682A pdb=" N PHE C 142 " --> pdb=" O ASN C 138 " (cutoff:3.500A) Processing helix chain 'D' and resid 104 through 121 Processing helix chain 'D' and resid 124 through 149 removed outlier: 3.514A pdb=" N ILE D 128 " --> pdb=" O GLY D 124 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ILE D 149 " --> pdb=" O VAL D 145 " (cutoff:3.500A) Processing helix chain 'D' and resid 152 through 181 Processing helix chain 'D' and resid 189 through 199 removed outlier: 3.583A pdb=" N GLY D 193 " --> pdb=" O ARG D 189 " (cutoff:3.500A) Processing helix chain 'D' and resid 200 through 223 Processing helix chain 'D' and resid 224 through 235 Processing helix chain 'D' and resid 238 through 246 removed outlier: 4.344A pdb=" N ASP D 246 " --> pdb=" O MET D 242 " (cutoff:3.500A) Processing helix chain 'D' and resid 249 through 262 Processing helix chain 'D' and resid 262 through 289 Processing helix chain 'D' and resid 297 through 310 Processing helix chain 'D' and resid 321 through 363 Proline residue: D 342 - end of helix Processing helix chain 'D' and resid 366 through 384 Processing helix chain 'D' and resid 516 through 541 Processing helix chain 'D' and resid 545 through 576 Processing helix chain 'F' and resid 7 through 22 Processing helix chain 'F' and resid 29 through 39 removed outlier: 3.645A pdb=" N MET F 37 " --> pdb=" O LEU F 33 " (cutoff:3.500A) Processing helix chain 'F' and resid 45 through 55 Processing helix chain 'F' and resid 66 through 75 removed outlier: 3.579A pdb=" N ARG F 75 " --> pdb=" O THR F 71 " (cutoff:3.500A) Processing helix chain 'F' and resid 79 through 92 Processing helix chain 'F' and resid 103 through 113 Processing helix chain 'F' and resid 118 through 128 Processing helix chain 'F' and resid 138 through 147 removed outlier: 3.682A pdb=" N PHE F 142 " --> pdb=" O ASN F 138 " (cutoff:3.500A) Processing helix chain 'G' and resid 104 through 121 Processing helix chain 'G' and resid 124 through 149 removed outlier: 3.514A pdb=" N ILE G 128 " --> pdb=" O GLY G 124 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ILE G 149 " --> pdb=" O VAL G 145 " (cutoff:3.500A) Processing helix chain 'G' and resid 152 through 181 Processing helix chain 'G' and resid 189 through 199 removed outlier: 3.583A pdb=" N GLY G 193 " --> pdb=" O ARG G 189 " (cutoff:3.500A) Processing helix chain 'G' and resid 200 through 223 Processing helix chain 'G' and resid 224 through 235 Processing helix chain 'G' and resid 238 through 246 removed outlier: 4.344A pdb=" N ASP G 246 " --> pdb=" O MET G 242 " (cutoff:3.500A) Processing helix chain 'G' and resid 249 through 262 Processing helix chain 'G' and resid 262 through 289 Processing helix chain 'G' and resid 297 through 310 Processing helix chain 'G' and resid 321 through 363 Proline residue: G 342 - end of helix Processing helix chain 'G' and resid 366 through 384 Processing helix chain 'G' and resid 516 through 541 Processing helix chain 'G' and resid 545 through 576 Processing helix chain 'H' and resid 7 through 22 Processing helix chain 'H' and resid 29 through 39 removed outlier: 3.645A pdb=" N MET H 37 " --> pdb=" O LEU H 33 " (cutoff:3.500A) Processing helix chain 'H' and resid 45 through 55 Processing helix chain 'H' and resid 66 through 75 removed outlier: 3.579A pdb=" N ARG H 75 " --> pdb=" O THR H 71 " (cutoff:3.500A) Processing helix chain 'H' and resid 79 through 92 Processing helix chain 'H' and resid 103 through 113 Processing helix chain 'H' and resid 118 through 128 Processing helix chain 'H' and resid 138 through 147 removed outlier: 3.682A pdb=" N PHE H 142 " --> pdb=" O ASN H 138 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'E' and resid 27 through 28 Processing sheet with id=AA2, first strand: chain 'E' and resid 101 through 102 removed outlier: 3.717A pdb=" N ILE E 101 " --> pdb=" O VAL E 137 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 27 through 28 Processing sheet with id=AA4, first strand: chain 'C' and resid 101 through 102 removed outlier: 3.717A pdb=" N ILE C 101 " --> pdb=" O VAL C 137 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'F' and resid 27 through 28 Processing sheet with id=AA6, first strand: chain 'F' and resid 101 through 102 removed outlier: 3.717A pdb=" N ILE F 101 " --> pdb=" O VAL F 137 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'H' and resid 27 through 28 Processing sheet with id=AA8, first strand: chain 'H' and resid 101 through 102 removed outlier: 3.717A pdb=" N ILE H 101 " --> pdb=" O VAL H 137 " (cutoff:3.500A) 1221 hydrogen bonds defined for protein. 3651 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: 7.81 Time building geometry restraints manager: 4.25 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: 15656 1.02 - 1.22: 56 1.22 - 1.42: 6696 1.42 - 1.62: 9224 1.62 - 1.81: 160 Bond restraints: 31792 Sorted by residual: bond pdb=" NE ARG A 570 " pdb=" HE ARG A 570 " ideal model delta sigma weight residual 0.860 0.971 -0.111 2.00e-02 2.50e+03 3.07e+01 bond pdb=" NE ARG B 109 " pdb=" HE ARG B 109 " ideal model delta sigma weight residual 0.860 0.970 -0.110 2.00e-02 2.50e+03 3.03e+01 bond pdb=" NE ARG D 109 " pdb=" HE ARG D 109 " ideal model delta sigma weight residual 0.860 0.970 -0.110 2.00e-02 2.50e+03 3.03e+01 bond pdb=" NE ARG D 570 " pdb=" HE ARG D 570 " ideal model delta sigma weight residual 0.860 0.970 -0.110 2.00e-02 2.50e+03 3.03e+01 bond pdb=" NE ARG D 110 " pdb=" HE ARG D 110 " ideal model delta sigma weight residual 0.860 0.970 -0.110 2.00e-02 2.50e+03 3.03e+01 ... (remaining 31787 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.92: 57060 3.92 - 7.84: 132 7.84 - 11.76: 64 11.76 - 15.68: 0 15.68 - 19.59: 4 Bond angle restraints: 57260 Sorted by residual: angle pdb=" O11 PIO D1000 " pdb=" P1 PIO D1000 " pdb=" O12 PIO D1000 " ideal model delta sigma weight residual 121.09 101.50 19.59 3.00e+00 1.11e-01 4.27e+01 angle pdb=" O11 PIO G1000 " pdb=" P1 PIO G1000 " pdb=" O12 PIO G1000 " ideal model delta sigma weight residual 121.09 101.50 19.59 3.00e+00 1.11e-01 4.27e+01 angle pdb=" O11 PIO B1000 " pdb=" P1 PIO B1000 " pdb=" O12 PIO B1000 " ideal model delta sigma weight residual 121.09 101.50 19.59 3.00e+00 1.11e-01 4.27e+01 angle pdb=" O11 PIO A1000 " pdb=" P1 PIO A1000 " pdb=" O12 PIO A1000 " ideal model delta sigma weight residual 121.09 101.50 19.59 3.00e+00 1.11e-01 4.27e+01 angle pdb=" N ARG D 241 " pdb=" CA ARG D 241 " pdb=" C ARG D 241 " ideal model delta sigma weight residual 111.36 106.42 4.94 1.09e+00 8.42e-01 2.05e+01 ... (remaining 57255 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.89: 13108 16.89 - 33.77: 1169 33.77 - 50.66: 367 50.66 - 67.55: 128 67.55 - 84.43: 12 Dihedral angle restraints: 14784 sinusoidal: 7972 harmonic: 6812 Sorted by residual: dihedral pdb=" CB GLU F 105 " pdb=" CG GLU F 105 " pdb=" CD GLU F 105 " pdb=" OE1 GLU F 105 " ideal model delta sinusoidal sigma weight residual 0.00 84.43 -84.43 1 3.00e+01 1.11e-03 9.63e+00 dihedral pdb=" CB GLU C 105 " pdb=" CG GLU C 105 " pdb=" CD GLU C 105 " pdb=" OE1 GLU C 105 " ideal model delta sinusoidal sigma weight residual 0.00 84.43 -84.43 1 3.00e+01 1.11e-03 9.63e+00 dihedral pdb=" CB GLU H 105 " pdb=" CG GLU H 105 " pdb=" CD GLU H 105 " pdb=" OE1 GLU H 105 " ideal model delta sinusoidal sigma weight residual 0.00 84.43 -84.43 1 3.00e+01 1.11e-03 9.63e+00 ... (remaining 14781 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.154: 2436 0.154 - 0.307: 4 0.307 - 0.460: 0 0.460 - 0.614: 0 0.614 - 0.767: 4 Chirality restraints: 2444 Sorted by residual: chirality pdb=" C2C PIO D1000 " pdb=" C1C PIO D1000 " pdb=" C3C PIO D1000 " pdb=" O2C PIO D1000 " both_signs ideal model delta sigma weight residual False -2.56 -1.79 -0.77 2.00e-01 2.50e+01 1.47e+01 chirality pdb=" C2C PIO A1000 " pdb=" C1C PIO A1000 " pdb=" C3C PIO A1000 " pdb=" O2C PIO A1000 " both_signs ideal model delta sigma weight residual False -2.56 -1.79 -0.77 2.00e-01 2.50e+01 1.47e+01 chirality pdb=" C2C PIO G1000 " pdb=" C1C PIO G1000 " pdb=" C3C PIO G1000 " pdb=" O2C PIO G1000 " both_signs ideal model delta sigma weight residual False -2.56 -1.79 -0.77 2.00e-01 2.50e+01 1.47e+01 ... (remaining 2441 not shown) Planarity restraints: 4608 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLN D 112 " 0.124 2.00e-02 2.50e+03 1.36e-01 2.76e+02 pdb=" CD GLN D 112 " -0.010 2.00e-02 2.50e+03 pdb=" OE1 GLN D 112 " -0.118 2.00e-02 2.50e+03 pdb=" NE2 GLN D 112 " 0.005 2.00e-02 2.50e+03 pdb="HE21 GLN D 112 " -0.201 2.00e-02 2.50e+03 pdb="HE22 GLN D 112 " 0.201 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN A 112 " -0.119 2.00e-02 2.50e+03 1.30e-01 2.53e+02 pdb=" CD GLN A 112 " 0.010 2.00e-02 2.50e+03 pdb=" OE1 GLN A 112 " 0.113 2.00e-02 2.50e+03 pdb=" NE2 GLN A 112 " -0.004 2.00e-02 2.50e+03 pdb="HE21 GLN A 112 " 0.192 2.00e-02 2.50e+03 pdb="HE22 GLN A 112 " -0.193 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN G 112 " 0.118 2.00e-02 2.50e+03 1.29e-01 2.49e+02 pdb=" CD GLN G 112 " -0.010 2.00e-02 2.50e+03 pdb=" OE1 GLN G 112 " -0.113 2.00e-02 2.50e+03 pdb=" NE2 GLN G 112 " 0.004 2.00e-02 2.50e+03 pdb="HE21 GLN G 112 " -0.191 2.00e-02 2.50e+03 pdb="HE22 GLN G 112 " 0.191 2.00e-02 2.50e+03 ... (remaining 4605 not shown) Histogram of nonbonded interaction distances: 1.58 - 2.18: 1950 2.18 - 2.79: 65569 2.79 - 3.39: 93568 3.39 - 4.00: 112716 4.00 - 4.60: 178718 Nonbonded interactions: 452521 Sorted by model distance: nonbonded pdb=" HG2 GLU G 164 " pdb="HH12 ARG G 235 " model vdw 1.581 2.270 nonbonded pdb=" HG2 GLU D 164 " pdb="HH12 ARG D 235 " model vdw 1.581 2.270 nonbonded pdb=" HG2 GLU B 164 " pdb="HH12 ARG B 235 " model vdw 1.581 2.270 nonbonded pdb=" HG2 GLU A 164 " pdb="HH12 ARG A 235 " model vdw 1.581 2.270 nonbonded pdb=" O SER D 144 " pdb=" HG SER D 147 " model vdw 1.624 2.450 ... (remaining 452516 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: 0.06 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'D' selection = chain 'G' } ncs_group { reference = chain 'E' selection = chain 'C' selection = chain 'F' selection = chain 'H' } 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 individual isotropic 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: 0.210 Extract box with map and model: 0.540 Check model and map are aligned: 0.100 Set scattering table: 0.080 Process input model: 31.320 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.050 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: 0.010 Load rotamer database and sin/cos tables:1.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6801 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 : 0.006 0.082 16104 Z= 0.318 Angle : 0.918 19.595 21748 Z= 0.452 Chirality : 0.049 0.767 2444 Planarity : 0.003 0.024 2712 Dihedral : 14.408 84.434 5872 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 16.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 0.24 % Allowed : 14.51 % Favored : 85.24 % 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: 1.82 (0.19), residues: 1928 helix: 1.69 (0.13), residues: 1532 sheet: None (None), residues: 0 loop : -0.62 (0.31), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 241 TYR 0.012 0.001 TYR G 271 PHE 0.006 0.001 PHE D 338 TRP 0.008 0.001 TRP D 322 HIS 0.003 0.001 HIS A 362 Details of bonding type rmsd/Z covalent geometry : bond 0.00551 / 0.32 (16104) covalent geometry : angle 0.91795 / 0.45 (21748) hydrogen bonds : bond 0.11860 / 8.10 ( 1221) hydrogen bonds : angle 5.63618 / 4.21 ( 3651) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 95 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 95 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 95 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 95 is missing expected H atoms. Skipping. Evaluate side-chains 273 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 269 time to evaluate : 0.903 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: A 247 ARG cc_start: 0.6751 (ttp-170) cc_final: 0.6095 (tpp-160) REVERT: A 560 MET cc_start: 0.5828 (ptp) cc_final: 0.5458 (ptp) REVERT: B 247 ARG cc_start: 0.6750 (ttp-170) cc_final: 0.6096 (tpp-160) REVERT: B 560 MET cc_start: 0.5843 (ptp) cc_final: 0.5479 (ptp) REVERT: D 160 LEU cc_start: 0.8183 (tp) cc_final: 0.7940 (tt) REVERT: D 247 ARG cc_start: 0.6747 (ttp-170) cc_final: 0.6083 (tpp-160) REVERT: D 560 MET cc_start: 0.5830 (ptp) cc_final: 0.5464 (ptp) REVERT: G 247 ARG cc_start: 0.6754 (ttp-170) cc_final: 0.6089 (tpp-160) REVERT: G 560 MET cc_start: 0.5811 (ptp) cc_final: 0.5443 (ptp) outliers start: 4 outliers final: 4 residues processed: 269 average time/residue: 0.2926 time to fit residues: 118.7273 Evaluate side-chains 222 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 218 time to evaluate : 0.848 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 168 ILE Chi-restraints excluded: chain B residue 168 ILE Chi-restraints excluded: chain D residue 168 ILE Chi-restraints excluded: chain G residue 168 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 98 optimal weight: 0.9980 chunk 107 optimal weight: 10.0000 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 10.0000 chunk 103 optimal weight: 5.9990 chunk 77 optimal weight: 20.0000 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 20.0000 chunk 149 optimal weight: 4.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 112 GLN B 112 GLN D 112 GLN G 112 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4867 r_free = 0.4867 target = 0.250795 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.139157 restraints weight = 57089.873| |-----------------------------------------------------------------------------| r_work (start): 0.3581 rms_B_bonded: 3.91 r_work: 0.3366 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work: 0.3227 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3227 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7233 moved from start: 0.1714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 16104 Z= 0.206 Angle : 0.557 5.636 21748 Z= 0.301 Chirality : 0.036 0.136 2444 Planarity : 0.004 0.043 2712 Dihedral : 7.004 79.603 2216 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 1.34 % Allowed : 16.52 % Favored : 82.13 % 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: 1.95 (0.18), residues: 1928 helix: 1.73 (0.13), residues: 1560 sheet: None (None), residues: 0 loop : -0.51 (0.31), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 542 TYR 0.014 0.002 TYR A 271 PHE 0.018 0.001 PHE D 363 TRP 0.010 0.001 TRP G 322 HIS 0.004 0.001 HIS A 358 Details of bonding type rmsd/Z covalent geometry : bond 0.00448 / 0.21 (16104) covalent geometry : angle 0.55707 / 0.30 (21748) hydrogen bonds : bond 0.05089 / 3.43 ( 1221) hydrogen bonds : angle 4.72370 / 3.51 ( 3651) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 95 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 95 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 95 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 95 is missing expected H atoms. Skipping. Evaluate side-chains 242 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 220 time to evaluate : 0.712 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: A 247 ARG cc_start: 0.6776 (ttp-170) cc_final: 0.5790 (tpp-160) REVERT: A 560 MET cc_start: 0.5751 (ptp) cc_final: 0.5532 (ptp) REVERT: B 247 ARG cc_start: 0.6779 (ttp-170) cc_final: 0.5790 (tpp-160) REVERT: B 560 MET cc_start: 0.5774 (ptp) cc_final: 0.5555 (ptp) REVERT: D 247 ARG cc_start: 0.6766 (ttp-170) cc_final: 0.5777 (tpp-160) REVERT: D 560 MET cc_start: 0.5748 (ptp) cc_final: 0.5532 (ptp) REVERT: G 247 ARG cc_start: 0.6768 (ttp-170) cc_final: 0.5776 (tpp-160) REVERT: G 560 MET cc_start: 0.5725 (ptp) cc_final: 0.5508 (ptp) outliers start: 22 outliers final: 16 residues processed: 230 average time/residue: 0.2777 time to fit residues: 96.5689 Evaluate side-chains 224 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 208 time to evaluate : 0.880 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 168 ILE Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 208 ILE Chi-restraints excluded: chain A residue 294 GLU Chi-restraints excluded: chain B residue 168 ILE Chi-restraints excluded: chain B residue 169 VAL Chi-restraints excluded: chain B residue 208 ILE Chi-restraints excluded: chain B residue 294 GLU Chi-restraints excluded: chain D residue 168 ILE Chi-restraints excluded: chain D residue 169 VAL Chi-restraints excluded: chain D residue 208 ILE Chi-restraints excluded: chain D residue 294 GLU Chi-restraints excluded: chain G residue 168 ILE Chi-restraints excluded: chain G residue 169 VAL Chi-restraints excluded: chain G residue 208 ILE Chi-restraints excluded: chain G residue 294 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 168 optimal weight: 0.5980 chunk 61 optimal weight: 7.9990 chunk 5 optimal weight: 3.9990 chunk 108 optimal weight: 8.9990 chunk 73 optimal weight: 2.9990 chunk 37 optimal weight: 0.3980 chunk 167 optimal weight: 0.7980 chunk 170 optimal weight: 0.9990 chunk 51 optimal weight: 0.9980 chunk 20 optimal weight: 0.5980 chunk 141 optimal weight: 20.0000 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 112 GLN B 112 GLN D 112 GLN G 112 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4889 r_free = 0.4889 target = 0.253539 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.147272 restraints weight = 56937.722| |-----------------------------------------------------------------------------| r_work (start): 0.3644 rms_B_bonded: 4.22 r_work: 0.3417 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3417 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7112 moved from start: 0.2028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.017 16104 Z= 0.119 Angle : 0.479 6.025 21748 Z= 0.258 Chirality : 0.033 0.138 2444 Planarity : 0.003 0.036 2712 Dihedral : 6.622 78.378 2216 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 0.98 % Allowed : 15.79 % Favored : 83.23 % 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: 2.26 (0.19), residues: 1928 helix: 1.97 (0.13), residues: 1560 sheet: None (None), residues: 0 loop : -0.50 (0.32), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 542 TYR 0.009 0.001 TYR A 271 PHE 0.008 0.001 PHE B 165 TRP 0.008 0.001 TRP B 180 HIS 0.002 0.001 HIS G 557 Details of bonding type rmsd/Z covalent geometry : bond 0.00237 / 0.12 (16104) covalent geometry : angle 0.47938 / 0.26 (21748) hydrogen bonds : bond 0.04436 / 3.00 ( 1221) hydrogen bonds : angle 4.39394 / 3.27 ( 3651) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 95 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 95 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 95 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 95 is missing expected H atoms. Skipping. Evaluate side-chains 237 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 221 time to evaluate : 0.737 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: A 247 ARG cc_start: 0.6730 (ttp-170) cc_final: 0.5796 (tpp-160) REVERT: A 268 THR cc_start: 0.8822 (m) cc_final: 0.8381 (m) REVERT: B 247 ARG cc_start: 0.6731 (ttp-170) cc_final: 0.5792 (tpp-160) REVERT: B 268 THR cc_start: 0.8834 (m) cc_final: 0.8389 (m) REVERT: D 247 ARG cc_start: 0.6724 (ttp-170) cc_final: 0.5782 (tpp-160) REVERT: D 268 THR cc_start: 0.8833 (m) cc_final: 0.8392 (m) REVERT: G 247 ARG cc_start: 0.6714 (ttp-170) cc_final: 0.5775 (tpp-160) REVERT: G 268 THR cc_start: 0.8829 (m) cc_final: 0.8391 (m) outliers start: 16 outliers final: 8 residues processed: 229 average time/residue: 0.2852 time to fit residues: 99.1985 Evaluate side-chains 222 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 214 time to evaluate : 0.839 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 208 ILE Chi-restraints excluded: chain B residue 169 VAL Chi-restraints excluded: chain B residue 208 ILE Chi-restraints excluded: chain D residue 169 VAL Chi-restraints excluded: chain D residue 208 ILE Chi-restraints excluded: chain G residue 169 VAL Chi-restraints excluded: chain G residue 208 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 138 optimal weight: 20.0000 chunk 16 optimal weight: 1.9990 chunk 116 optimal weight: 1.9990 chunk 42 optimal weight: 10.0000 chunk 44 optimal weight: 20.0000 chunk 61 optimal weight: 6.9990 chunk 119 optimal weight: 1.9990 chunk 76 optimal weight: 5.9990 chunk 82 optimal weight: 6.9990 chunk 159 optimal weight: 2.9990 chunk 74 optimal weight: 0.4980 overall best weight: 1.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4871 r_free = 0.4871 target = 0.251337 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.145602 restraints weight = 56454.053| |-----------------------------------------------------------------------------| r_work (start): 0.3677 rms_B_bonded: 4.07 r_work: 0.3356 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3356 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7162 moved from start: 0.2276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 16104 Z= 0.162 Angle : 0.494 6.132 21748 Z= 0.267 Chirality : 0.034 0.135 2444 Planarity : 0.003 0.029 2712 Dihedral : 7.163 86.166 2208 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 2.26 % Allowed : 13.72 % Favored : 84.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.20 (0.19), residues: 1928 helix: 1.95 (0.13), residues: 1556 sheet: None (None), residues: 0 loop : -0.62 (0.32), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 563 TYR 0.013 0.001 TYR B 271 PHE 0.009 0.001 PHE B 363 TRP 0.008 0.001 TRP A 322 HIS 0.003 0.001 HIS B 358 Details of bonding type rmsd/Z covalent geometry : bond 0.00349 / 0.16 (16104) covalent geometry : angle 0.49416 / 0.27 (21748) hydrogen bonds : bond 0.04538 / 3.08 ( 1221) hydrogen bonds : angle 4.35097 / 3.24 ( 3651) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 95 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 95 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 95 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 95 is missing expected H atoms. Skipping. Evaluate side-chains 263 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 226 time to evaluate : 0.916 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: A 247 ARG cc_start: 0.6744 (ttp-170) cc_final: 0.5774 (tpp-160) REVERT: E 77 MET cc_start: -0.0278 (OUTLIER) cc_final: -0.0698 (ppp) REVERT: B 247 ARG cc_start: 0.6747 (ttp-170) cc_final: 0.5773 (tpp-160) REVERT: C 77 MET cc_start: -0.0229 (OUTLIER) cc_final: -0.0646 (ppp) REVERT: C 107 ARG cc_start: 0.4799 (ttm-80) cc_final: 0.4298 (tpt170) REVERT: D 247 ARG cc_start: 0.6738 (ttp-170) cc_final: 0.5759 (tpp-160) REVERT: F 77 MET cc_start: -0.0363 (OUTLIER) cc_final: -0.0766 (ppp) REVERT: G 247 ARG cc_start: 0.6739 (ttp-170) cc_final: 0.5766 (tpp-160) REVERT: H 77 MET cc_start: -0.0387 (OUTLIER) cc_final: -0.0798 (ppp) outliers start: 37 outliers final: 17 residues processed: 245 average time/residue: 0.3077 time to fit residues: 112.1969 Evaluate side-chains 233 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 212 time to evaluate : 0.840 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 168 ILE Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 294 GLU Chi-restraints excluded: chain E residue 77 MET Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 169 VAL Chi-restraints excluded: chain B residue 294 GLU Chi-restraints excluded: chain B residue 537 PHE Chi-restraints excluded: chain C residue 77 MET Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 168 ILE Chi-restraints excluded: chain D residue 169 VAL Chi-restraints excluded: chain D residue 294 GLU Chi-restraints excluded: chain F residue 77 MET Chi-restraints excluded: chain F residue 131 ILE Chi-restraints excluded: chain G residue 160 LEU Chi-restraints excluded: chain G residue 168 ILE Chi-restraints excluded: chain G residue 169 VAL Chi-restraints excluded: chain G residue 294 GLU Chi-restraints excluded: chain H residue 77 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 38 optimal weight: 30.0000 chunk 49 optimal weight: 7.9990 chunk 6 optimal weight: 4.9990 chunk 137 optimal weight: 30.0000 chunk 176 optimal weight: 8.9990 chunk 127 optimal weight: 1.9990 chunk 93 optimal weight: 20.0000 chunk 1 optimal weight: 0.8980 chunk 142 optimal weight: 20.0000 chunk 110 optimal weight: 6.9990 chunk 42 optimal weight: 9.9990 overall best weight: 4.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 112 GLN A 360 GLN E 42 GLN B 112 GLN B 360 GLN C 42 GLN D 112 GLN F 42 GLN G 112 GLN G 360 GLN H 42 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4833 r_free = 0.4833 target = 0.246679 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.146957 restraints weight = 56314.233| |-----------------------------------------------------------------------------| r_work (start): 0.3697 rms_B_bonded: 3.89 r_work: 0.3328 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3328 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7240 moved from start: 0.2596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.055 16104 Z= 0.305 Angle : 0.571 6.007 21748 Z= 0.314 Chirality : 0.039 0.149 2444 Planarity : 0.004 0.028 2712 Dihedral : 7.788 68.913 2208 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 2.62 % Allowed : 12.80 % Favored : 84.57 % 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: 1.65 (0.18), residues: 1928 helix: 1.58 (0.13), residues: 1548 sheet: None (None), residues: 0 loop : -0.80 (0.31), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 563 TYR 0.017 0.002 TYR G 285 PHE 0.010 0.001 PHE A 350 TRP 0.010 0.002 TRP A 322 HIS 0.004 0.001 HIS D 358 Details of bonding type rmsd/Z covalent geometry : bond 0.00687 / 0.30 (16104) covalent geometry : angle 0.57111 / 0.31 (21748) hydrogen bonds : bond 0.05219 / 3.53 ( 1221) hydrogen bonds : angle 4.66499 / 3.48 ( 3651) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 95 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 95 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 95 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 95 is missing expected H atoms. Skipping. Evaluate side-chains 268 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 225 time to evaluate : 0.897 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: A 247 ARG cc_start: 0.6824 (ttp-170) cc_final: 0.5596 (tpp-160) REVERT: E 77 MET cc_start: -0.0218 (OUTLIER) cc_final: -0.0666 (ppp) REVERT: E 107 ARG cc_start: 0.4842 (ttm-80) cc_final: 0.4392 (ttm-80) REVERT: B 247 ARG cc_start: 0.6830 (ttp-170) cc_final: 0.5604 (tpp-160) REVERT: B 367 ARG cc_start: 0.5492 (OUTLIER) cc_final: 0.4114 (mtm-85) REVERT: C 77 MET cc_start: -0.0180 (OUTLIER) cc_final: -0.0625 (ppp) REVERT: C 107 ARG cc_start: 0.4778 (ttm-80) cc_final: 0.4330 (ttm-80) REVERT: D 247 ARG cc_start: 0.6813 (ttp-170) cc_final: 0.5599 (tpp-160) REVERT: D 367 ARG cc_start: 0.5375 (OUTLIER) cc_final: 0.3991 (mtp-110) REVERT: F 77 MET cc_start: -0.0275 (OUTLIER) cc_final: -0.0722 (ppp) REVERT: F 107 ARG cc_start: 0.4780 (ttm-80) cc_final: 0.4328 (ttm-80) REVERT: G 247 ARG cc_start: 0.6821 (ttp-170) cc_final: 0.5599 (tpp-160) REVERT: G 367 ARG cc_start: 0.5365 (OUTLIER) cc_final: 0.3955 (mtp-110) REVERT: H 77 MET cc_start: -0.0343 (OUTLIER) cc_final: -0.0785 (ppp) REVERT: H 107 ARG cc_start: 0.4777 (ttm-80) cc_final: 0.4325 (ttm-80) outliers start: 43 outliers final: 24 residues processed: 242 average time/residue: 0.3251 time to fit residues: 115.2089 Evaluate side-chains 251 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 220 time to evaluate : 0.862 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 173 LEU Chi-restraints excluded: chain A residue 294 GLU Chi-restraints excluded: chain A residue 341 LEU Chi-restraints excluded: chain E residue 77 MET Chi-restraints excluded: chain E residue 131 ILE Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 169 VAL Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain B residue 294 GLU Chi-restraints excluded: chain B residue 367 ARG Chi-restraints excluded: chain B residue 537 PHE Chi-restraints excluded: chain C residue 77 MET Chi-restraints excluded: chain C residue 131 ILE Chi-restraints excluded: chain D residue 128 ILE Chi-restraints excluded: chain D residue 169 VAL Chi-restraints excluded: chain D residue 173 LEU Chi-restraints excluded: chain D residue 294 GLU Chi-restraints excluded: chain D residue 367 ARG Chi-restraints excluded: chain F residue 51 ASP Chi-restraints excluded: chain F residue 77 MET Chi-restraints excluded: chain F residue 131 ILE Chi-restraints excluded: chain G residue 128 ILE Chi-restraints excluded: chain G residue 169 VAL Chi-restraints excluded: chain G residue 173 LEU Chi-restraints excluded: chain G residue 294 GLU Chi-restraints excluded: chain G residue 367 ARG Chi-restraints excluded: chain H residue 51 ASP Chi-restraints excluded: chain H residue 77 MET Chi-restraints excluded: chain H residue 131 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 182 optimal weight: 0.8980 chunk 128 optimal weight: 5.9990 chunk 142 optimal weight: 30.0000 chunk 1 optimal weight: 8.9990 chunk 97 optimal weight: 3.9990 chunk 5 optimal weight: 0.3980 chunk 125 optimal weight: 30.0000 chunk 117 optimal weight: 0.7980 chunk 20 optimal weight: 0.7980 chunk 6 optimal weight: 4.9990 chunk 45 optimal weight: 6.9990 overall best weight: 1.3782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 112 GLN B 112 GLN D 112 GLN D 360 GLN G 112 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4861 r_free = 0.4861 target = 0.250344 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.150082 restraints weight = 56275.656| |-----------------------------------------------------------------------------| r_work (start): 0.3702 rms_B_bonded: 4.85 r_work: 0.3362 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3362 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7181 moved from start: 0.2688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 16104 Z= 0.139 Angle : 0.486 6.636 21748 Z= 0.262 Chirality : 0.034 0.137 2444 Planarity : 0.003 0.029 2712 Dihedral : 7.434 73.197 2208 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 2.13 % Allowed : 14.02 % Favored : 83.84 % 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: 2.02 (0.19), residues: 1928 helix: 1.88 (0.13), residues: 1544 sheet: None (None), residues: 0 loop : -0.87 (0.30), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 366 TYR 0.009 0.001 TYR D 271 PHE 0.005 0.001 PHE D 171 TRP 0.008 0.001 TRP B 322 HIS 0.002 0.001 HIS G 557 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.14 (16104) covalent geometry : angle 0.48614 / 0.26 (21748) hydrogen bonds : bond 0.04426 / 3.00 ( 1221) hydrogen bonds : angle 4.40471 / 3.28 ( 3651) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 95 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 95 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 95 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 95 is missing expected H atoms. Skipping. Evaluate side-chains 258 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 223 time to evaluate : 0.881 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: A 247 ARG cc_start: 0.6710 (ttp-170) cc_final: 0.5540 (tpp-160) REVERT: A 366 ARG cc_start: 0.5357 (OUTLIER) cc_final: 0.5149 (mmt-90) REVERT: A 367 ARG cc_start: 0.5464 (OUTLIER) cc_final: 0.4064 (mtp-110) REVERT: E 107 ARG cc_start: 0.4763 (ttm-80) cc_final: 0.4258 (tpt170) REVERT: B 247 ARG cc_start: 0.6715 (ttp-170) cc_final: 0.5553 (tpp-160) REVERT: B 367 ARG cc_start: 0.5513 (OUTLIER) cc_final: 0.4190 (mtp-110) REVERT: C 107 ARG cc_start: 0.4776 (ttm-80) cc_final: 0.4269 (tpt170) REVERT: D 247 ARG cc_start: 0.6682 (ttp-170) cc_final: 0.5542 (tpp-160) REVERT: F 107 ARG cc_start: 0.4775 (ttm-80) cc_final: 0.4261 (tpt170) REVERT: G 247 ARG cc_start: 0.6682 (ttp-170) cc_final: 0.5531 (tpp-160) REVERT: H 107 ARG cc_start: 0.4756 (ttm-80) cc_final: 0.4238 (tpt170) outliers start: 35 outliers final: 23 residues processed: 236 average time/residue: 0.3222 time to fit residues: 111.8280 Evaluate side-chains 243 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 217 time to evaluate : 0.866 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 167 MET Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 366 ARG Chi-restraints excluded: chain A residue 367 ARG Chi-restraints excluded: chain E residue 131 ILE Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 167 MET Chi-restraints excluded: chain B residue 169 VAL Chi-restraints excluded: chain B residue 367 ARG Chi-restraints excluded: chain B residue 537 PHE Chi-restraints excluded: chain C residue 131 ILE Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 167 MET Chi-restraints excluded: chain D residue 169 VAL Chi-restraints excluded: chain D residue 208 ILE Chi-restraints excluded: chain F residue 131 ILE Chi-restraints excluded: chain G residue 128 ILE Chi-restraints excluded: chain G residue 160 LEU Chi-restraints excluded: chain G residue 167 MET Chi-restraints excluded: chain G residue 169 VAL Chi-restraints excluded: chain G residue 208 ILE Chi-restraints excluded: chain G residue 341 LEU Chi-restraints excluded: chain H residue 131 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 15 optimal weight: 0.9980 chunk 164 optimal weight: 1.9990 chunk 29 optimal weight: 30.0000 chunk 71 optimal weight: 1.9990 chunk 161 optimal weight: 0.6980 chunk 14 optimal weight: 3.9990 chunk 21 optimal weight: 1.9990 chunk 188 optimal weight: 20.0000 chunk 61 optimal weight: 0.9990 chunk 49 optimal weight: 3.9990 chunk 42 optimal weight: 20.0000 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 112 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4864 r_free = 0.4864 target = 0.251158 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.148979 restraints weight = 57155.191| |-----------------------------------------------------------------------------| r_work (start): 0.3684 rms_B_bonded: 4.13 r_work: 0.3372 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3372 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7140 moved from start: 0.2851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 16104 Z= 0.137 Angle : 0.475 6.515 21748 Z= 0.255 Chirality : 0.034 0.139 2444 Planarity : 0.003 0.029 2712 Dihedral : 7.159 77.495 2208 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 2.07 % Allowed : 14.15 % Favored : 83.78 % 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: 2.34 (0.19), residues: 1928 helix: 2.09 (0.13), residues: 1552 sheet: None (None), residues: 0 loop : -0.73 (0.31), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 563 TYR 0.010 0.001 TYR A 271 PHE 0.008 0.001 PHE D 236 TRP 0.008 0.001 TRP A 378 HIS 0.002 0.001 HIS B 358 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.14 (16104) covalent geometry : angle 0.47494 / 0.26 (21748) hydrogen bonds : bond 0.04255 / 2.89 ( 1221) hydrogen bonds : angle 4.28744 / 3.19 ( 3651) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 95 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 95 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 95 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 95 is missing expected H atoms. Skipping. Evaluate side-chains 257 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 223 time to evaluate : 0.871 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: A 247 ARG cc_start: 0.6676 (ttp-170) cc_final: 0.5545 (tpp-160) REVERT: A 367 ARG cc_start: 0.5429 (OUTLIER) cc_final: 0.4082 (mtp-110) REVERT: E 107 ARG cc_start: 0.4818 (ttm-80) cc_final: 0.4224 (tpt170) REVERT: B 247 ARG cc_start: 0.6674 (ttp-170) cc_final: 0.5541 (tpp-160) REVERT: B 367 ARG cc_start: 0.5471 (OUTLIER) cc_final: 0.4238 (mtm-85) REVERT: C 107 ARG cc_start: 0.4826 (ttm-80) cc_final: 0.4231 (tpt170) REVERT: D 247 ARG cc_start: 0.6677 (ttp-170) cc_final: 0.5454 (tpp-160) REVERT: D 367 ARG cc_start: 0.5368 (OUTLIER) cc_final: 0.4170 (mtp-110) REVERT: F 107 ARG cc_start: 0.4779 (ttm-80) cc_final: 0.4223 (tpt170) REVERT: G 247 ARG cc_start: 0.6569 (ttp-170) cc_final: 0.5346 (tpp-160) REVERT: G 367 ARG cc_start: 0.5386 (OUTLIER) cc_final: 0.4178 (mtp-110) REVERT: H 107 ARG cc_start: 0.4824 (ttm-80) cc_final: 0.4223 (tpt170) outliers start: 34 outliers final: 22 residues processed: 239 average time/residue: 0.3165 time to fit residues: 111.4718 Evaluate side-chains 236 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 210 time to evaluate : 0.865 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 167 MET Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 367 ARG Chi-restraints excluded: chain A residue 537 PHE Chi-restraints excluded: chain E residue 131 ILE Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 167 MET Chi-restraints excluded: chain B residue 169 VAL Chi-restraints excluded: chain B residue 341 LEU Chi-restraints excluded: chain B residue 367 ARG Chi-restraints excluded: chain C residue 131 ILE Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 167 MET Chi-restraints excluded: chain D residue 169 VAL Chi-restraints excluded: chain D residue 341 LEU Chi-restraints excluded: chain D residue 367 ARG Chi-restraints excluded: chain F residue 51 ASP Chi-restraints excluded: chain F residue 131 ILE Chi-restraints excluded: chain G residue 160 LEU Chi-restraints excluded: chain G residue 167 MET Chi-restraints excluded: chain G residue 169 VAL Chi-restraints excluded: chain G residue 341 LEU Chi-restraints excluded: chain G residue 367 ARG Chi-restraints excluded: chain H residue 51 ASP Chi-restraints excluded: chain H residue 131 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 90 optimal weight: 8.9990 chunk 174 optimal weight: 9.9990 chunk 129 optimal weight: 20.0000 chunk 87 optimal weight: 50.0000 chunk 109 optimal weight: 6.9990 chunk 26 optimal weight: 6.9990 chunk 186 optimal weight: 10.0000 chunk 190 optimal weight: 9.9990 chunk 157 optimal weight: 6.9990 chunk 45 optimal weight: 20.0000 chunk 139 optimal weight: 20.0000 overall best weight: 7.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 112 GLN B 112 GLN D 112 GLN G 112 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4803 r_free = 0.4803 target = 0.243659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.145862 restraints weight = 56483.216| |-----------------------------------------------------------------------------| r_work (start): 0.3674 rms_B_bonded: 5.39 r_work: 0.3271 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3271 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7365 moved from start: 0.3137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.091 16104 Z= 0.501 Angle : 0.699 6.620 21748 Z= 0.388 Chirality : 0.049 0.191 2444 Planarity : 0.005 0.044 2712 Dihedral : 8.213 70.589 2208 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 2.26 % Allowed : 14.57 % Favored : 83.17 % 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: 1.04 (0.18), residues: 1928 helix: 1.14 (0.12), residues: 1548 sheet: None (None), residues: 0 loop : -0.96 (0.31), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG G 563 TYR 0.025 0.003 TYR D 553 PHE 0.012 0.002 PHE A 350 TRP 0.013 0.003 TRP B 303 HIS 0.006 0.002 HIS B 358 Details of bonding type rmsd/Z covalent geometry : bond 0.01146 / 0.50 (16104) covalent geometry : angle 0.69947 / 0.39 (21748) hydrogen bonds : bond 0.05927 / 4.00 ( 1221) hydrogen bonds : angle 5.01019 / 3.73 ( 3651) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 95 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 95 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 95 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 95 is missing expected H atoms. Skipping. Evaluate side-chains 261 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 224 time to evaluate : 0.864 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: A 247 ARG cc_start: 0.6975 (ttp-170) cc_final: 0.5748 (tpp-160) REVERT: A 367 ARG cc_start: 0.5544 (OUTLIER) cc_final: 0.4002 (mtp-110) REVERT: E 107 ARG cc_start: 0.4913 (ttm-80) cc_final: 0.4330 (tpt170) REVERT: B 247 ARG cc_start: 0.7079 (ttp-170) cc_final: 0.5867 (tpp-160) REVERT: B 367 ARG cc_start: 0.5536 (OUTLIER) cc_final: 0.4102 (mtm-85) REVERT: C 107 ARG cc_start: 0.4926 (ttm-80) cc_final: 0.4342 (tpt170) REVERT: D 367 ARG cc_start: 0.5477 (OUTLIER) cc_final: 0.4041 (mtp-110) REVERT: F 107 ARG cc_start: 0.4921 (ttm-80) cc_final: 0.4335 (tpt170) REVERT: G 247 ARG cc_start: 0.6971 (ttp-170) cc_final: 0.5734 (tpp-160) REVERT: G 367 ARG cc_start: 0.5480 (OUTLIER) cc_final: 0.4031 (mtp-110) REVERT: H 107 ARG cc_start: 0.4917 (ttm-80) cc_final: 0.4328 (tpt170) outliers start: 37 outliers final: 31 residues processed: 241 average time/residue: 0.3149 time to fit residues: 112.1928 Evaluate side-chains 251 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 216 time to evaluate : 0.834 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 167 MET Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 173 LEU Chi-restraints excluded: chain A residue 294 GLU Chi-restraints excluded: chain A residue 367 ARG Chi-restraints excluded: chain A residue 537 PHE Chi-restraints excluded: chain E residue 131 ILE Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 167 MET Chi-restraints excluded: chain B residue 169 VAL Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain B residue 294 GLU Chi-restraints excluded: chain B residue 341 LEU Chi-restraints excluded: chain B residue 367 ARG Chi-restraints excluded: chain B residue 537 PHE Chi-restraints excluded: chain C residue 131 ILE Chi-restraints excluded: chain D residue 128 ILE Chi-restraints excluded: chain D residue 167 MET Chi-restraints excluded: chain D residue 169 VAL Chi-restraints excluded: chain D residue 173 LEU Chi-restraints excluded: chain D residue 294 GLU Chi-restraints excluded: chain D residue 341 LEU Chi-restraints excluded: chain D residue 367 ARG Chi-restraints excluded: chain F residue 51 ASP Chi-restraints excluded: chain F residue 131 ILE Chi-restraints excluded: chain G residue 128 ILE Chi-restraints excluded: chain G residue 167 MET Chi-restraints excluded: chain G residue 169 VAL Chi-restraints excluded: chain G residue 173 LEU Chi-restraints excluded: chain G residue 294 GLU Chi-restraints excluded: chain G residue 341 LEU Chi-restraints excluded: chain G residue 367 ARG Chi-restraints excluded: chain H residue 51 ASP Chi-restraints excluded: chain H residue 131 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 147 optimal weight: 0.9980 chunk 93 optimal weight: 1.9990 chunk 187 optimal weight: 20.0000 chunk 125 optimal weight: 40.0000 chunk 9 optimal weight: 0.7980 chunk 103 optimal weight: 6.9990 chunk 99 optimal weight: 0.6980 chunk 55 optimal weight: 6.9990 chunk 43 optimal weight: 20.0000 chunk 115 optimal weight: 0.5980 chunk 127 optimal weight: 6.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 112 GLN B 112 GLN D 112 GLN G 112 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4864 r_free = 0.4864 target = 0.250984 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.142667 restraints weight = 57266.462| |-----------------------------------------------------------------------------| r_work (start): 0.3608 rms_B_bonded: 4.12 r_work: 0.3371 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work: 0.3225 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3225 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7255 moved from start: 0.3023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 16104 Z= 0.138 Angle : 0.500 7.330 21748 Z= 0.268 Chirality : 0.034 0.134 2444 Planarity : 0.003 0.030 2712 Dihedral : 7.566 74.346 2208 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 1.46 % Allowed : 15.61 % Favored : 82.93 % 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: 1.94 (0.19), residues: 1928 helix: 1.81 (0.13), residues: 1552 sheet: None (None), residues: 0 loop : -0.88 (0.30), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 563 TYR 0.009 0.001 TYR B 553 PHE 0.008 0.001 PHE A 274 TRP 0.008 0.001 TRP D 378 HIS 0.002 0.001 HIS A 557 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.14 (16104) covalent geometry : angle 0.49951 / 0.27 (21748) hydrogen bonds : bond 0.04361 / 2.95 ( 1221) hydrogen bonds : angle 4.47217 / 3.32 ( 3651) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 95 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 95 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 95 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 95 is missing expected H atoms. Skipping. Evaluate side-chains 240 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 216 time to evaluate : 0.871 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: A 232 ARG cc_start: 0.7618 (mtt180) cc_final: 0.7070 (tmt170) REVERT: A 247 ARG cc_start: 0.6818 (ttp-170) cc_final: 0.5427 (tpp-160) REVERT: A 367 ARG cc_start: 0.5583 (OUTLIER) cc_final: 0.4176 (mtp-110) REVERT: E 107 ARG cc_start: 0.4898 (ttm-80) cc_final: 0.4317 (tpt170) REVERT: B 247 ARG cc_start: 0.6917 (ttp-170) cc_final: 0.5539 (tpp-160) REVERT: B 367 ARG cc_start: 0.5561 (OUTLIER) cc_final: 0.4203 (mtm-85) REVERT: C 107 ARG cc_start: 0.4921 (ttm-80) cc_final: 0.4332 (tpt170) REVERT: D 247 ARG cc_start: 0.6783 (ttp-170) cc_final: 0.5397 (tpp-160) REVERT: D 367 ARG cc_start: 0.5453 (OUTLIER) cc_final: 0.4181 (mtp-110) REVERT: F 107 ARG cc_start: 0.4924 (ttm-80) cc_final: 0.4330 (tpt170) REVERT: G 247 ARG cc_start: 0.6776 (ttp-170) cc_final: 0.5389 (tpp-160) REVERT: G 367 ARG cc_start: 0.5460 (OUTLIER) cc_final: 0.4213 (mtm-85) REVERT: H 107 ARG cc_start: 0.4897 (ttm-80) cc_final: 0.4309 (tpt170) outliers start: 24 outliers final: 20 residues processed: 224 average time/residue: 0.3233 time to fit residues: 105.0520 Evaluate side-chains 239 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 215 time to evaluate : 0.827 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 167 MET Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 208 ILE Chi-restraints excluded: chain A residue 367 ARG Chi-restraints excluded: chain A residue 537 PHE Chi-restraints excluded: chain E residue 131 ILE Chi-restraints excluded: chain B residue 167 MET Chi-restraints excluded: chain B residue 169 VAL Chi-restraints excluded: chain B residue 208 ILE Chi-restraints excluded: chain B residue 341 LEU Chi-restraints excluded: chain B residue 367 ARG Chi-restraints excluded: chain B residue 537 PHE Chi-restraints excluded: chain C residue 131 ILE Chi-restraints excluded: chain D residue 128 ILE Chi-restraints excluded: chain D residue 167 MET Chi-restraints excluded: chain D residue 169 VAL Chi-restraints excluded: chain D residue 367 ARG Chi-restraints excluded: chain F residue 51 ASP Chi-restraints excluded: chain F residue 131 ILE Chi-restraints excluded: chain G residue 167 MET Chi-restraints excluded: chain G residue 169 VAL Chi-restraints excluded: chain G residue 367 ARG Chi-restraints excluded: chain H residue 51 ASP Chi-restraints excluded: chain H residue 131 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 37 optimal weight: 20.0000 chunk 43 optimal weight: 20.0000 chunk 117 optimal weight: 0.9990 chunk 67 optimal weight: 0.7980 chunk 4 optimal weight: 0.5980 chunk 131 optimal weight: 20.0000 chunk 15 optimal weight: 0.0870 chunk 122 optimal weight: 3.9990 chunk 69 optimal weight: 0.7980 chunk 137 optimal weight: 30.0000 chunk 98 optimal weight: 0.7980 overall best weight: 0.6158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4870 r_free = 0.4870 target = 0.251403 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.151145 restraints weight = 56363.402| |-----------------------------------------------------------------------------| r_work (start): 0.3731 rms_B_bonded: 4.20 r_work: 0.3416 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3416 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7136 moved from start: 0.3130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 16104 Z= 0.117 Angle : 0.486 7.956 21748 Z= 0.257 Chirality : 0.033 0.139 2444 Planarity : 0.003 0.030 2712 Dihedral : 7.008 79.091 2208 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 1.46 % Allowed : 15.24 % Favored : 83.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 2.37 (0.19), residues: 1928 helix: 2.18 (0.13), residues: 1544 sheet: None (None), residues: 0 loop : -0.99 (0.30), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 563 TYR 0.009 0.001 TYR D 271 PHE 0.007 0.001 PHE B 274 TRP 0.009 0.001 TRP A 378 HIS 0.002 0.001 HIS D 362 Details of bonding type rmsd/Z covalent geometry : bond 0.00238 / 0.12 (16104) covalent geometry : angle 0.48555 / 0.26 (21748) hydrogen bonds : bond 0.04080 / 2.77 ( 1221) hydrogen bonds : angle 4.28224 / 3.18 ( 3651) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 95 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 95 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 95 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 95 is missing expected H atoms. Skipping. Evaluate side-chains 241 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 217 time to evaluate : 0.623 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: A 232 ARG cc_start: 0.7717 (mtt180) cc_final: 0.7104 (tmt170) REVERT: A 247 ARG cc_start: 0.6673 (ttp-170) cc_final: 0.5395 (tpp-160) REVERT: A 367 ARG cc_start: 0.5423 (OUTLIER) cc_final: 0.4215 (mtp-110) REVERT: E 52 MET cc_start: -0.0542 (tpt) cc_final: -0.0816 (mmm) REVERT: E 107 ARG cc_start: 0.4875 (ttm-80) cc_final: 0.4281 (tpt170) REVERT: B 232 ARG cc_start: 0.7701 (mtt180) cc_final: 0.7104 (tmt170) REVERT: B 247 ARG cc_start: 0.6674 (ttp-170) cc_final: 0.5393 (tpp-160) REVERT: C 107 ARG cc_start: 0.4894 (ttm-80) cc_final: 0.4299 (tpt170) REVERT: D 232 ARG cc_start: 0.7694 (mtt180) cc_final: 0.7076 (tmt170) REVERT: D 247 ARG cc_start: 0.6666 (ttp-170) cc_final: 0.5373 (tpp-160) REVERT: D 367 ARG cc_start: 0.5367 (OUTLIER) cc_final: 0.4274 (mtm-85) REVERT: F 107 ARG cc_start: 0.4890 (ttm-80) cc_final: 0.4292 (tpt170) REVERT: G 247 ARG cc_start: 0.6657 (ttp-170) cc_final: 0.5370 (tpp-160) REVERT: H 107 ARG cc_start: 0.4881 (ttm-80) cc_final: 0.4278 (tpt170) outliers start: 24 outliers final: 15 residues processed: 229 average time/residue: 0.3462 time to fit residues: 112.5261 Evaluate side-chains 230 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 213 time to evaluate : 0.840 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 167 MET Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 367 ARG Chi-restraints excluded: chain A residue 537 PHE Chi-restraints excluded: chain E residue 131 ILE Chi-restraints excluded: chain B residue 167 MET Chi-restraints excluded: chain B residue 169 VAL Chi-restraints excluded: chain B residue 341 LEU Chi-restraints excluded: chain C residue 131 ILE Chi-restraints excluded: chain D residue 167 MET Chi-restraints excluded: chain D residue 169 VAL Chi-restraints excluded: chain D residue 341 LEU Chi-restraints excluded: chain D residue 367 ARG Chi-restraints excluded: chain F residue 131 ILE Chi-restraints excluded: chain G residue 167 MET Chi-restraints excluded: chain G residue 169 VAL Chi-restraints excluded: chain H residue 131 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 83 optimal weight: 8.9990 chunk 191 optimal weight: 10.0000 chunk 190 optimal weight: 6.9990 chunk 71 optimal weight: 2.9990 chunk 44 optimal weight: 30.0000 chunk 9 optimal weight: 5.9990 chunk 128 optimal weight: 10.0000 chunk 10 optimal weight: 0.9990 chunk 13 optimal weight: 0.9990 chunk 47 optimal weight: 8.9990 chunk 105 optimal weight: 0.2980 overall best weight: 2.2588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4856 r_free = 0.4856 target = 0.249664 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.142071 restraints weight = 56417.078| |-----------------------------------------------------------------------------| r_work (start): 0.3622 rms_B_bonded: 4.13 r_work: 0.3378 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.3237 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3237 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7246 moved from start: 0.3137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 16104 Z= 0.179 Angle : 0.508 7.811 21748 Z= 0.274 Chirality : 0.035 0.134 2444 Planarity : 0.003 0.030 2712 Dihedral : 7.181 76.740 2208 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 1.28 % Allowed : 15.49 % Favored : 83.23 % 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: 2.34 (0.19), residues: 1928 helix: 2.12 (0.13), residues: 1544 sheet: None (None), residues: 0 loop : -0.84 (0.31), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 563 TYR 0.011 0.001 TYR G 271 PHE 0.007 0.001 PHE D 282 TRP 0.009 0.001 TRP A 322 HIS 0.002 0.001 HIS A 358 Details of bonding type rmsd/Z covalent geometry : bond 0.00388 / 0.18 (16104) covalent geometry : angle 0.50838 / 0.27 (21748) hydrogen bonds : bond 0.04445 / 3.02 ( 1221) hydrogen bonds : angle 4.36212 / 3.24 ( 3651) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11285.95 seconds wall clock time: 191 minutes 40.54 seconds (11500.54 seconds total)