Starting phenix.real_space_refine on Sun May 3 01:59:56 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jou_61685/05_2026/9jou_61685.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jou_61685/05_2026/9jou_61685.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.46 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9jou_61685/05_2026/9jou_61685.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jou_61685/05_2026/9jou_61685.map" model { file = "/net/cci-nas-00/data/ceres_data/9jou_61685/05_2026/9jou_61685.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jou_61685/05_2026/9jou_61685.cif" } resolution = 2.46 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= 0.001 sd= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 60 5.16 5 C 6887 2.51 5 N 1415 2.21 5 O 1551 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9913 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 1840 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1840 Classifications: {'peptide': 230} Link IDs: {'PTRANS': 4, 'TRANS': 225} Chain: "B" Number of atoms: 1840 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1840 Classifications: {'peptide': 230} Link IDs: {'PTRANS': 4, 'TRANS': 225} Chain: "C" Number of atoms: 1840 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1840 Classifications: {'peptide': 230} Link IDs: {'PTRANS': 4, 'TRANS': 225} Chain: "D" Number of atoms: 1840 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1840 Classifications: {'peptide': 230} Link IDs: {'PTRANS': 4, 'TRANS': 225} Chain: "E" Number of atoms: 1840 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1840 Classifications: {'peptide': 230} Link IDs: {'PTRANS': 4, 'TRANS': 225} Chain: "A" Number of atoms: 130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 130 Unusual residues: {'D12': 3, 'K3I': 1, 'R16': 2, 'RET': 1} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'RET:plan-5': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 114 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 114 Unusual residues: {'D12': 3, 'K3I': 1, 'R16': 1, 'RET': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'RET:plan-5': 1} Unresolved non-hydrogen planarities: 1 Chain: "C" Number of atoms: 150 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 150 Unusual residues: {'D12': 2, 'K3I': 1, 'R16': 4, 'RET': 1} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'RET:plan-5': 1} Unresolved non-hydrogen planarities: 1 Chain: "D" Number of atoms: 138 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 138 Unusual residues: {'D12': 1, 'K3I': 1, 'R16': 4, 'RET': 1} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'RET:plan-5': 1} Unresolved non-hydrogen planarities: 1 Chain: "E" Number of atoms: 130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 130 Unusual residues: {'D12': 3, 'K3I': 1, 'R16': 2, 'RET': 1} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'RET:plan-5': 1} Unresolved non-hydrogen planarities: 1 Chain: "A" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Classifications: {'water': 8} Link IDs: {None: 7} Chain: "B" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 12 Classifications: {'water': 12} Link IDs: {None: 11} Chain: "C" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 10 Classifications: {'water': 10} Link IDs: {None: 9} Chain: "D" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 11 Classifications: {'water': 11} Link IDs: {None: 10} Chain: "E" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 10 Classifications: {'water': 10} Link IDs: {None: 9} Time building chain proxies: 2.56, per 1000 atoms: 0.26 Number of scatterers: 9913 At special positions: 0 Unit cell: (68.89, 101.26, 103.75, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 60 16.00 O 1551 8.00 N 1415 7.00 C 6887 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=5, symmetry=0 Number of additional bonds: simple=5, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.13 Conformation dependent library (CDL) restraints added in 319.2 milliseconds 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2080 Finding SS restraints... Secondary structure from input PDB file: 54 helices and 0 sheets defined 86.0% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.26 Creating SS restraints... Processing helix chain 'A' and resid 17 through 41 Processing helix chain 'A' and resid 42 through 44 No H-bonds generated for 'chain 'A' and resid 42 through 44' Processing helix chain 'A' and resid 48 through 77 Processing helix chain 'A' and resid 80 through 83 Processing helix chain 'A' and resid 84 through 103 removed outlier: 4.171A pdb=" N LEU A 90 " --> pdb=" O VAL A 86 " (cutoff:3.500A) Proline residue: A 93 - end of helix removed outlier: 3.564A pdb=" N PHE A 99 " --> pdb=" O MET A 95 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N TYR A 100 " --> pdb=" O CYS A 96 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ILE A 102 " --> pdb=" O GLU A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 132 removed outlier: 3.609A pdb=" N MET A 113 " --> pdb=" O LYS A 109 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 159 removed outlier: 3.543A pdb=" N TRP A 141 " --> pdb=" O ASN A 137 " (cutoff:3.500A) Processing helix chain 'A' and resid 159 through 168 Processing helix chain 'A' and resid 170 through 185 Processing helix chain 'A' and resid 188 through 198 Processing helix chain 'A' and resid 211 through 239 removed outlier: 3.694A pdb=" N ASN A 239 " --> pdb=" O VAL A 235 " (cutoff:3.500A) Processing helix chain 'B' and resid 17 through 41 Processing helix chain 'B' and resid 42 through 44 No H-bonds generated for 'chain 'B' and resid 42 through 44' Processing helix chain 'B' and resid 45 through 77 removed outlier: 3.606A pdb=" N ARG B 49 " --> pdb=" O GLU B 45 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N THR B 50 " --> pdb=" O ARG B 46 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N SER B 51 " --> pdb=" O LYS B 47 " (cutoff:3.500A) Processing helix chain 'B' and resid 80 through 83 Processing helix chain 'B' and resid 84 through 103 removed outlier: 4.241A pdb=" N LEU B 90 " --> pdb=" O VAL B 86 " (cutoff:3.500A) Proline residue: B 93 - end of helix removed outlier: 3.531A pdb=" N PHE B 99 " --> pdb=" O MET B 95 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N TYR B 100 " --> pdb=" O CYS B 96 " (cutoff:3.500A) Processing helix chain 'B' and resid 109 through 133 removed outlier: 3.545A pdb=" N MET B 113 " --> pdb=" O LYS B 109 " (cutoff:3.500A) Processing helix chain 'B' and resid 137 through 159 removed outlier: 3.521A pdb=" N TRP B 141 " --> pdb=" O ASN B 137 " (cutoff:3.500A) Processing helix chain 'B' and resid 159 through 169 Processing helix chain 'B' and resid 170 through 185 Processing helix chain 'B' and resid 188 through 198 Processing helix chain 'B' and resid 211 through 239 Processing helix chain 'C' and resid 17 through 41 Processing helix chain 'C' and resid 42 through 44 No H-bonds generated for 'chain 'C' and resid 42 through 44' Processing helix chain 'C' and resid 48 through 77 Processing helix chain 'C' and resid 80 through 83 Processing helix chain 'C' and resid 84 through 103 removed outlier: 4.238A pdb=" N LEU C 90 " --> pdb=" O VAL C 86 " (cutoff:3.500A) Proline residue: C 93 - end of helix removed outlier: 3.537A pdb=" N PHE C 99 " --> pdb=" O MET C 95 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N TYR C 100 " --> pdb=" O CYS C 96 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ILE C 102 " --> pdb=" O GLU C 98 " (cutoff:3.500A) Processing helix chain 'C' and resid 109 through 133 removed outlier: 3.589A pdb=" N MET C 113 " --> pdb=" O LYS C 109 " (cutoff:3.500A) Processing helix chain 'C' and resid 137 through 159 removed outlier: 3.504A pdb=" N TRP C 141 " --> pdb=" O ASN C 137 " (cutoff:3.500A) Processing helix chain 'C' and resid 159 through 169 Processing helix chain 'C' and resid 170 through 185 Processing helix chain 'C' and resid 188 through 198 Processing helix chain 'C' and resid 210 through 239 Processing helix chain 'D' and resid 17 through 41 Processing helix chain 'D' and resid 42 through 44 No H-bonds generated for 'chain 'D' and resid 42 through 44' Processing helix chain 'D' and resid 45 through 77 removed outlier: 3.646A pdb=" N ARG D 49 " --> pdb=" O GLU D 45 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N THR D 50 " --> pdb=" O ARG D 46 " (cutoff:3.500A) removed outlier: 5.322A pdb=" N SER D 51 " --> pdb=" O LYS D 47 " (cutoff:3.500A) Processing helix chain 'D' and resid 80 through 83 Processing helix chain 'D' and resid 84 through 103 removed outlier: 4.240A pdb=" N LEU D 90 " --> pdb=" O VAL D 86 " (cutoff:3.500A) Proline residue: D 93 - end of helix removed outlier: 3.601A pdb=" N PHE D 99 " --> pdb=" O MET D 95 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N TYR D 100 " --> pdb=" O CYS D 96 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ILE D 102 " --> pdb=" O GLU D 98 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LEU D 103 " --> pdb=" O PHE D 99 " (cutoff:3.500A) Processing helix chain 'D' and resid 109 through 132 removed outlier: 3.600A pdb=" N MET D 113 " --> pdb=" O LYS D 109 " (cutoff:3.500A) Processing helix chain 'D' and resid 137 through 159 removed outlier: 3.572A pdb=" N TRP D 141 " --> pdb=" O ASN D 137 " (cutoff:3.500A) Processing helix chain 'D' and resid 159 through 169 removed outlier: 3.705A pdb=" N LYS D 163 " --> pdb=" O GLY D 159 " (cutoff:3.500A) Processing helix chain 'D' and resid 170 through 185 Processing helix chain 'D' and resid 188 through 198 Processing helix chain 'D' and resid 210 through 239 removed outlier: 3.502A pdb=" N ALA D 220 " --> pdb=" O ASN D 216 " (cutoff:3.500A) Processing helix chain 'E' and resid 17 through 41 Processing helix chain 'E' and resid 42 through 44 No H-bonds generated for 'chain 'E' and resid 42 through 44' Processing helix chain 'E' and resid 48 through 77 Processing helix chain 'E' and resid 80 through 103 removed outlier: 3.924A pdb=" N ARG E 84 " --> pdb=" O PRO E 80 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N TYR E 85 " --> pdb=" O VAL E 81 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N VAL E 86 " --> pdb=" O PHE E 82 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N ASP E 87 " --> pdb=" O PHE E 83 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N LEU E 90 " --> pdb=" O VAL E 86 " (cutoff:3.500A) Proline residue: E 93 - end of helix removed outlier: 3.572A pdb=" N PHE E 99 " --> pdb=" O MET E 95 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N TYR E 100 " --> pdb=" O CYS E 96 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ILE E 102 " --> pdb=" O GLU E 98 " (cutoff:3.500A) Processing helix chain 'E' and resid 109 through 132 removed outlier: 3.542A pdb=" N MET E 113 " --> pdb=" O LYS E 109 " (cutoff:3.500A) Processing helix chain 'E' and resid 137 through 159 Processing helix chain 'E' and resid 159 through 169 Processing helix chain 'E' and resid 170 through 185 Processing helix chain 'E' and resid 188 through 198 Processing helix chain 'E' and resid 211 through 239 removed outlier: 3.501A pdb=" N ALA E 220 " --> pdb=" O ASN E 216 " (cutoff:3.500A) 724 hydrogen bonds defined for protein. 2160 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.54 Time building geometry restraints manager: 1.34 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1605 1.33 - 1.46: 3740 1.46 - 1.58: 4712 1.58 - 1.70: 0 1.70 - 1.83: 105 Bond restraints: 10162 Sorted by residual: bond pdb=" CA SER A 120 " pdb=" CB SER A 120 " ideal model delta sigma weight residual 1.529 1.466 0.063 1.55e-02 4.16e+03 1.65e+01 bond pdb=" CA SER E 120 " pdb=" CB SER E 120 " ideal model delta sigma weight residual 1.529 1.468 0.061 1.55e-02 4.16e+03 1.54e+01 bond pdb=" C10 RET D 302 " pdb=" C9 RET D 302 " ideal model delta sigma weight residual 1.359 1.431 -0.072 2.00e-02 2.50e+03 1.29e+01 bond pdb=" C25 K3I D 307 " pdb=" C26 K3I D 307 " ideal model delta sigma weight residual 1.353 1.424 -0.071 2.00e-02 2.50e+03 1.27e+01 bond pdb=" CA SER C 34 " pdb=" CB SER C 34 " ideal model delta sigma weight residual 1.528 1.474 0.055 1.56e-02 4.11e+03 1.24e+01 ... (remaining 10157 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.64: 13128 3.64 - 7.28: 531 7.28 - 10.91: 28 10.91 - 14.55: 7 14.55 - 18.19: 3 Bond angle restraints: 13697 Sorted by residual: angle pdb=" N GLN A 236 " pdb=" CA GLN A 236 " pdb=" CB GLN A 236 " ideal model delta sigma weight residual 110.42 125.05 -14.63 1.62e+00 3.81e-01 8.15e+01 angle pdb=" CG MET D 31 " pdb=" SD MET D 31 " pdb=" CE MET D 31 " ideal model delta sigma weight residual 100.90 82.71 18.19 2.20e+00 2.07e-01 6.84e+01 angle pdb=" CA THR C 178 " pdb=" CB THR C 178 " pdb=" OG1 THR C 178 " ideal model delta sigma weight residual 109.60 97.67 11.93 1.50e+00 4.44e-01 6.33e+01 angle pdb=" OG1 THR E 178 " pdb=" CB THR E 178 " pdb=" CG2 THR E 178 " ideal model delta sigma weight residual 109.30 125.07 -15.77 2.00e+00 2.50e-01 6.21e+01 angle pdb=" CA THR D 178 " pdb=" CB THR D 178 " pdb=" OG1 THR D 178 " ideal model delta sigma weight residual 109.60 97.93 11.67 1.50e+00 4.44e-01 6.05e+01 ... (remaining 13692 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.38: 5483 32.38 - 64.77: 268 64.77 - 97.15: 12 97.15 - 129.53: 8 129.53 - 161.91: 6 Dihedral angle restraints: 5777 sinusoidal: 2487 harmonic: 3290 Sorted by residual: dihedral pdb=" N GLN A 236 " pdb=" C GLN A 236 " pdb=" CA GLN A 236 " pdb=" CB GLN A 236 " ideal model delta harmonic sigma weight residual 122.80 141.04 -18.24 0 2.50e+00 1.60e-01 5.33e+01 dihedral pdb=" C ILE C 102 " pdb=" N ILE C 102 " pdb=" CA ILE C 102 " pdb=" CB ILE C 102 " ideal model delta harmonic sigma weight residual -122.00 -134.53 12.53 0 2.50e+00 1.60e-01 2.51e+01 dihedral pdb=" C5 K3I B 306 " pdb=" C6 K3I B 306 " pdb=" C7 K3I B 306 " pdb=" C8 K3I B 306 " ideal model delta sinusoidal sigma weight residual -50.68 111.23 -161.91 1 3.00e+01 1.11e-03 2.08e+01 ... (remaining 5774 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.124: 1175 0.124 - 0.248: 198 0.248 - 0.372: 20 0.372 - 0.496: 1 0.496 - 0.620: 1 Chirality restraints: 1395 Sorted by residual: chirality pdb=" CA GLN A 236 " pdb=" N GLN A 236 " pdb=" C GLN A 236 " pdb=" CB GLN A 236 " both_signs ideal model delta sigma weight residual False 2.51 1.89 0.62 2.00e-01 2.50e+01 9.62e+00 chirality pdb=" CA LYS B 223 " pdb=" N LYS B 223 " pdb=" C LYS B 223 " pdb=" CB LYS B 223 " both_signs ideal model delta sigma weight residual False 2.51 2.08 0.43 2.00e-01 2.50e+01 4.55e+00 chirality pdb=" CG LEU A 173 " pdb=" CB LEU A 173 " pdb=" CD1 LEU A 173 " pdb=" CD2 LEU A 173 " both_signs ideal model delta sigma weight residual False -2.59 -2.25 -0.34 2.00e-01 2.50e+01 2.90e+00 ... (remaining 1392 not shown) Planarity restraints: 1605 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C12 RET A 301 " 0.130 2.00e-02 2.50e+03 1.49e-01 2.76e+02 pdb=" C13 RET A 301 " -0.033 2.00e-02 2.50e+03 pdb=" C14 RET A 301 " -0.244 2.00e-02 2.50e+03 pdb=" C15 RET A 301 " 0.178 2.00e-02 2.50e+03 pdb=" C20 RET A 301 " -0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C12 RET B 302 " 0.119 2.00e-02 2.50e+03 1.33e-01 2.22e+02 pdb=" C13 RET B 302 " -0.033 2.00e-02 2.50e+03 pdb=" C14 RET B 302 " -0.215 2.00e-02 2.50e+03 pdb=" C15 RET B 302 " 0.162 2.00e-02 2.50e+03 pdb=" C20 RET B 302 " -0.033 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C12 RET D 302 " -0.112 2.00e-02 2.50e+03 1.31e-01 2.15e+02 pdb=" C13 RET D 302 " 0.021 2.00e-02 2.50e+03 pdb=" C14 RET D 302 " 0.219 2.00e-02 2.50e+03 pdb=" C15 RET D 302 " -0.156 2.00e-02 2.50e+03 pdb=" C20 RET D 302 " 0.028 2.00e-02 2.50e+03 ... (remaining 1602 not shown) Histogram of nonbonded interaction distances: 1.97 - 2.55: 95 2.55 - 3.14: 8501 3.14 - 3.73: 15529 3.73 - 4.31: 22262 4.31 - 4.90: 37107 Nonbonded interactions: 83494 Sorted by model distance: nonbonded pdb=" NH1 ARG C 84 " pdb=" O HOH C 401 " model vdw 1.968 3.120 nonbonded pdb=" OD2 ASP B 87 " pdb=" O HOH B 401 " model vdw 1.995 3.040 nonbonded pdb=" OD2 ASP D 219 " pdb=" O HOH D 401 " model vdw 2.077 3.040 nonbonded pdb=" OD2 ASP C 87 " pdb=" O HOH C 402 " model vdw 2.117 3.040 nonbonded pdb=" OD2 ASP E 219 " pdb=" O HOH E 401 " model vdw 2.117 3.040 ... (remaining 83489 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 11 through 240) selection = (chain 'B' and resid 11 through 240) selection = (chain 'C' and resid 11 through 240) selection = (chain 'D' and resid 11 through 240) selection = (chain 'E' and resid 11 through 240) } 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: 0.940 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.130 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 10.670 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:7.480 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8545 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 : 0.011 0.166 10167 Z= 0.710 Angle : 1.665 18.190 13697 Z= 1.063 Chirality : 0.094 0.620 1395 Planarity : 0.015 0.149 1605 Dihedral : 18.541 161.913 3697 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 15.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 7.43 % Allowed : 16.28 % Favored : 76.28 % Cbeta Deviations : 0.29 % 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: -3.03 (0.19), residues: 1140 helix: -2.13 (0.12), residues: 872 sheet: None (None), residues: 0 loop : -0.67 (0.39), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.037 0.004 ARG E 70 TYR 0.037 0.009 TYR B 149 PHE 0.038 0.008 PHE D 37 TRP 0.053 0.006 TRP B 139 HIS 0.021 0.007 HIS C 65 Details of bonding type rmsd covalent geometry : bond 0.01046 (10162) covalent geometry : angle 1.66505 (13697) hydrogen bonds : bond 0.19649 ( 724) hydrogen bonds : angle 8.80029 ( 2160) Misc. bond : bond 0.16159 ( 5) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 227 time to evaluate : 0.329 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 GLU cc_start: 0.9002 (tp30) cc_final: 0.8754 (mm-30) REVERT: A 134 ASP cc_start: 0.8605 (t0) cc_final: 0.8296 (t0) REVERT: C 41 MET cc_start: 0.8745 (ttp) cc_final: 0.8392 (ttm) REVERT: C 78 GLU cc_start: 0.8732 (pp20) cc_final: 0.8236 (pp20) REVERT: C 109 LYS cc_start: 0.8896 (OUTLIER) cc_final: 0.8556 (tptp) REVERT: C 236 GLN cc_start: 0.9043 (mm-40) cc_final: 0.8799 (mp10) REVERT: D 219 ASP cc_start: 0.8375 (m-30) cc_final: 0.8143 (m-30) REVERT: E 46 ARG cc_start: 0.7945 (tpt170) cc_final: 0.7474 (mmm-85) REVERT: E 66 TYR cc_start: 0.8855 (m-80) cc_final: 0.8505 (m-10) REVERT: E 134 ASP cc_start: 0.8217 (t0) cc_final: 0.7809 (t0) REVERT: E 226 PHE cc_start: 0.9277 (OUTLIER) cc_final: 0.8770 (t80) outliers start: 68 outliers final: 31 residues processed: 271 average time/residue: 0.3835 time to fit residues: 114.6748 Evaluate side-chains 226 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 193 time to evaluate : 0.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 SER Chi-restraints excluded: chain A residue 74 SER Chi-restraints excluded: chain A residue 178 THR Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 236 GLN Chi-restraints excluded: chain B residue 34 SER Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain B residue 112 LEU Chi-restraints excluded: chain B residue 223 LYS Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain C residue 34 SER Chi-restraints excluded: chain C residue 57 LEU Chi-restraints excluded: chain C residue 74 SER Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 102 ILE Chi-restraints excluded: chain C residue 109 LYS Chi-restraints excluded: chain C residue 112 LEU Chi-restraints excluded: chain C residue 120 SER Chi-restraints excluded: chain C residue 228 LEU Chi-restraints excluded: chain D residue 112 LEU Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain D residue 134 ASP Chi-restraints excluded: chain D residue 145 SER Chi-restraints excluded: chain D residue 223 LYS Chi-restraints excluded: chain D residue 228 LEU Chi-restraints excluded: chain E residue 74 SER Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 112 LEU Chi-restraints excluded: chain E residue 219 ASP Chi-restraints excluded: chain E residue 226 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 108 optimal weight: 3.9990 chunk 49 optimal weight: 0.6980 chunk 97 optimal weight: 0.9980 chunk 113 optimal weight: 0.8980 chunk 53 optimal weight: 0.8980 chunk 5 optimal weight: 0.7980 chunk 33 optimal weight: 5.9990 chunk 65 optimal weight: 20.0000 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 0.8980 chunk 100 optimal weight: 0.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 216 ASN ** D 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 176 HIS E 222 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4083 r_free = 0.4083 target = 0.116616 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.097833 restraints weight = 23962.294| |-----------------------------------------------------------------------------| r_work (start): 0.3775 rms_B_bonded: 3.16 r_work: 0.3656 rms_B_bonded: 4.24 restraints_weight: 0.5000 r_work (final): 0.3656 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8455 moved from start: 0.1999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 10167 Z= 0.140 Angle : 0.681 10.986 13697 Z= 0.331 Chirality : 0.038 0.217 1395 Planarity : 0.004 0.041 1605 Dihedral : 14.325 127.213 1894 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.35 % Favored : 99.65 % Rotamer: Outliers : 5.79 % Allowed : 20.66 % Favored : 73.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.59 (0.24), residues: 1140 helix: 1.45 (0.17), residues: 886 sheet: None (None), residues: 0 loop : -0.14 (0.41), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 135 TYR 0.023 0.002 TYR B 190 PHE 0.016 0.001 PHE D 150 TRP 0.014 0.001 TRP B 139 HIS 0.007 0.002 HIS E 176 Details of bonding type rmsd covalent geometry : bond 0.00283 (10162) covalent geometry : angle 0.68061 (13697) hydrogen bonds : bond 0.05395 ( 724) hydrogen bonds : angle 4.89341 ( 2160) Misc. bond : bond 0.00036 ( 5) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 247 time to evaluate : 0.346 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 MET cc_start: 0.9016 (OUTLIER) cc_final: 0.8008 (mpp) REVERT: A 34 SER cc_start: 0.9439 (p) cc_final: 0.9225 (p) REVERT: A 78 GLU cc_start: 0.8749 (tp30) cc_final: 0.8442 (mm-30) REVERT: A 87 ASP cc_start: 0.8713 (t0) cc_final: 0.8393 (t0) REVERT: A 134 ASP cc_start: 0.8408 (t0) cc_final: 0.7895 (OUTLIER) REVERT: A 137 ASN cc_start: 0.8336 (t0) cc_final: 0.7989 (t0) REVERT: A 194 TYR cc_start: 0.8841 (t80) cc_final: 0.8553 (t80) REVERT: B 78 GLU cc_start: 0.7819 (OUTLIER) cc_final: 0.7481 (pm20) REVERT: B 84 ARG cc_start: 0.8873 (mtt-85) cc_final: 0.8292 (mtp85) REVERT: B 131 GLU cc_start: 0.7697 (mt-10) cc_final: 0.7108 (mt-10) REVERT: C 34 SER cc_start: 0.9516 (p) cc_final: 0.9232 (p) REVERT: C 78 GLU cc_start: 0.8279 (pp20) cc_final: 0.7843 (pp20) REVERT: C 109 LYS cc_start: 0.8405 (mmtt) cc_final: 0.8192 (tptp) REVERT: C 160 LYS cc_start: 0.8466 (tppt) cc_final: 0.8185 (tppt) REVERT: C 163 LYS cc_start: 0.8988 (mttp) cc_final: 0.8671 (mttp) REVERT: C 210 ASP cc_start: 0.8199 (t0) cc_final: 0.7976 (t0) REVERT: C 236 GLN cc_start: 0.8931 (mm-40) cc_final: 0.8593 (mp10) REVERT: D 109 LYS cc_start: 0.8831 (mtmm) cc_final: 0.8475 (mppt) REVERT: D 131 GLU cc_start: 0.8923 (tp30) cc_final: 0.8624 (mm-30) REVERT: D 134 ASP cc_start: 0.8732 (t0) cc_final: 0.8081 (t0) REVERT: D 137 ASN cc_start: 0.8644 (t0) cc_final: 0.8086 (t0) REVERT: E 66 TYR cc_start: 0.8946 (m-80) cc_final: 0.8574 (m-80) REVERT: E 113 MET cc_start: 0.8678 (tpt) cc_final: 0.8270 (mmm) REVERT: E 134 ASP cc_start: 0.7642 (t0) cc_final: 0.7164 (t0) REVERT: E 219 ASP cc_start: 0.7524 (OUTLIER) cc_final: 0.7303 (m-30) outliers start: 53 outliers final: 15 residues processed: 274 average time/residue: 0.4362 time to fit residues: 130.1075 Evaluate side-chains 231 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 214 time to evaluate : 0.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 MET Chi-restraints excluded: chain A residue 152 ILE Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 236 GLN Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain B residue 78 GLU Chi-restraints excluded: chain B residue 152 ILE Chi-restraints excluded: chain B residue 223 LYS Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain C residue 57 LEU Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain C residue 228 LEU Chi-restraints excluded: chain D residue 40 SER Chi-restraints excluded: chain D residue 228 LEU Chi-restraints excluded: chain E residue 50 THR Chi-restraints excluded: chain E residue 219 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 49 optimal weight: 5.9990 chunk 58 optimal weight: 10.0000 chunk 13 optimal weight: 10.0000 chunk 109 optimal weight: 6.9990 chunk 16 optimal weight: 10.0000 chunk 63 optimal weight: 8.9990 chunk 61 optimal weight: 0.9980 chunk 56 optimal weight: 3.9990 chunk 22 optimal weight: 7.9990 chunk 97 optimal weight: 5.9990 chunk 27 optimal weight: 4.9990 overall best weight: 4.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 216 ASN ** D 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.110211 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.091136 restraints weight = 24720.416| |-----------------------------------------------------------------------------| r_work (start): 0.3672 rms_B_bonded: 3.17 r_work: 0.3540 rms_B_bonded: 4.29 restraints_weight: 0.5000 r_work (final): 0.3540 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8579 moved from start: 0.2176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.075 10167 Z= 0.253 Angle : 0.724 9.637 13697 Z= 0.354 Chirality : 0.042 0.231 1395 Planarity : 0.004 0.048 1605 Dihedral : 13.872 116.790 1857 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 5.90 % Allowed : 23.39 % Favored : 70.71 % 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: 1.99 (0.25), residues: 1140 helix: 1.80 (0.17), residues: 885 sheet: None (None), residues: 0 loop : -0.28 (0.41), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG E 46 TYR 0.021 0.002 TYR C 190 PHE 0.017 0.001 PHE D 36 TRP 0.010 0.001 TRP D 48 HIS 0.007 0.002 HIS B 176 Details of bonding type rmsd covalent geometry : bond 0.00571 (10162) covalent geometry : angle 0.72430 (13697) hydrogen bonds : bond 0.05896 ( 724) hydrogen bonds : angle 5.00230 ( 2160) Misc. bond : bond 0.00238 ( 5) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 209 time to evaluate : 0.336 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 17 ASP cc_start: 0.8539 (t0) cc_final: 0.8217 (t0) REVERT: A 30 MET cc_start: 0.9061 (OUTLIER) cc_final: 0.7978 (mpp) REVERT: A 34 SER cc_start: 0.9449 (p) cc_final: 0.8901 (m) REVERT: A 78 GLU cc_start: 0.8805 (tp30) cc_final: 0.8549 (mm-30) REVERT: A 87 ASP cc_start: 0.8724 (t0) cc_final: 0.8393 (t0) REVERT: A 113 MET cc_start: 0.8881 (OUTLIER) cc_final: 0.8624 (ptt) REVERT: A 134 ASP cc_start: 0.8597 (t0) cc_final: 0.8031 (t0) REVERT: A 137 ASN cc_start: 0.8573 (t0) cc_final: 0.8356 (t0) REVERT: A 194 TYR cc_start: 0.8866 (t80) cc_final: 0.8555 (t80) REVERT: B 78 GLU cc_start: 0.7934 (OUTLIER) cc_final: 0.7576 (pm20) REVERT: B 131 GLU cc_start: 0.7982 (mt-10) cc_final: 0.7666 (mt-10) REVERT: B 149 TYR cc_start: 0.8354 (t80) cc_final: 0.7866 (t80) REVERT: B 155 GLU cc_start: 0.8767 (tp30) cc_final: 0.8534 (tp30) REVERT: C 78 GLU cc_start: 0.8411 (pp20) cc_final: 0.7982 (pp20) REVERT: C 137 ASN cc_start: 0.9059 (m-40) cc_final: 0.8737 (t0) REVERT: C 160 LYS cc_start: 0.8586 (tppt) cc_final: 0.8284 (tppt) REVERT: C 163 LYS cc_start: 0.8958 (mttp) cc_final: 0.8633 (mttp) REVERT: C 210 ASP cc_start: 0.8345 (t0) cc_final: 0.8132 (t0) REVERT: D 131 GLU cc_start: 0.8860 (tp30) cc_final: 0.8497 (mm-30) REVERT: D 134 ASP cc_start: 0.8914 (t0) cc_final: 0.8167 (t0) REVERT: D 137 ASN cc_start: 0.8840 (t0) cc_final: 0.8252 (t0) REVERT: D 194 TYR cc_start: 0.8492 (t80) cc_final: 0.8225 (t80) REVERT: E 134 ASP cc_start: 0.8047 (t0) cc_final: 0.7344 (t0) outliers start: 54 outliers final: 26 residues processed: 238 average time/residue: 0.4313 time to fit residues: 112.0436 Evaluate side-chains 221 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 192 time to evaluate : 0.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 MET Chi-restraints excluded: chain A residue 113 MET Chi-restraints excluded: chain A residue 152 ILE Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 236 GLN Chi-restraints excluded: chain B residue 78 GLU Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain B residue 112 LEU Chi-restraints excluded: chain B residue 152 ILE Chi-restraints excluded: chain B residue 223 LYS Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain C residue 112 LEU Chi-restraints excluded: chain C residue 228 LEU Chi-restraints excluded: chain D residue 40 SER Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain D residue 143 LEU Chi-restraints excluded: chain D residue 183 VAL Chi-restraints excluded: chain D residue 228 LEU Chi-restraints excluded: chain E residue 30 MET Chi-restraints excluded: chain E residue 34 SER Chi-restraints excluded: chain E residue 40 SER Chi-restraints excluded: chain E residue 50 THR Chi-restraints excluded: chain E residue 53 LEU Chi-restraints excluded: chain E residue 90 LEU Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 103 LEU Chi-restraints excluded: chain E residue 112 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 30 optimal weight: 0.7980 chunk 98 optimal weight: 1.9990 chunk 54 optimal weight: 7.9990 chunk 40 optimal weight: 3.9990 chunk 7 optimal weight: 5.9990 chunk 17 optimal weight: 0.9980 chunk 22 optimal weight: 5.9990 chunk 12 optimal weight: 3.9990 chunk 51 optimal weight: 0.9990 chunk 60 optimal weight: 1.9990 chunk 103 optimal weight: 0.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 176 HIS ** D 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.113983 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.095302 restraints weight = 24329.029| |-----------------------------------------------------------------------------| r_work (start): 0.3739 rms_B_bonded: 3.22 r_work: 0.3612 rms_B_bonded: 4.32 restraints_weight: 0.5000 r_work (final): 0.3612 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8504 moved from start: 0.2468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 10167 Z= 0.134 Angle : 0.656 9.035 13697 Z= 0.314 Chirality : 0.038 0.160 1395 Planarity : 0.004 0.046 1605 Dihedral : 12.947 117.138 1853 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.53 % Favored : 99.47 % Rotamer: Outliers : 4.15 % Allowed : 24.81 % Favored : 71.04 % 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: 2.25 (0.25), residues: 1140 helix: 1.97 (0.17), residues: 882 sheet: None (None), residues: 0 loop : -0.14 (0.41), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 135 TYR 0.020 0.001 TYR C 190 PHE 0.009 0.001 PHE D 150 TRP 0.012 0.001 TRP B 139 HIS 0.006 0.001 HIS B 176 Details of bonding type rmsd covalent geometry : bond 0.00287 (10162) covalent geometry : angle 0.65555 (13697) hydrogen bonds : bond 0.05077 ( 724) hydrogen bonds : angle 4.63948 ( 2160) Misc. bond : bond 0.00108 ( 5) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 224 time to evaluate : 0.284 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 MET cc_start: 0.9052 (OUTLIER) cc_final: 0.8028 (mpp) REVERT: A 34 SER cc_start: 0.9454 (p) cc_final: 0.9218 (p) REVERT: A 78 GLU cc_start: 0.8743 (tp30) cc_final: 0.8424 (mm-30) REVERT: A 87 ASP cc_start: 0.8704 (t0) cc_final: 0.8264 (t0) REVERT: A 113 MET cc_start: 0.8815 (OUTLIER) cc_final: 0.8503 (ptt) REVERT: A 134 ASP cc_start: 0.8587 (t0) cc_final: 0.7973 (t0) REVERT: A 137 ASN cc_start: 0.8643 (t0) cc_final: 0.8374 (t0) REVERT: A 194 TYR cc_start: 0.8858 (t80) cc_final: 0.8628 (t80) REVERT: A 236 GLN cc_start: 0.8752 (mm110) cc_final: 0.8543 (mp10) REVERT: B 78 GLU cc_start: 0.7916 (OUTLIER) cc_final: 0.7552 (pm20) REVERT: B 149 TYR cc_start: 0.8320 (t80) cc_final: 0.7904 (t80) REVERT: B 155 GLU cc_start: 0.8803 (tp30) cc_final: 0.8537 (tp30) REVERT: B 226 PHE cc_start: 0.9483 (OUTLIER) cc_final: 0.8651 (t80) REVERT: B 238 THR cc_start: 0.8770 (t) cc_final: 0.8558 (p) REVERT: C 78 GLU cc_start: 0.8392 (pp20) cc_final: 0.7992 (pp20) REVERT: C 137 ASN cc_start: 0.9015 (m-40) cc_final: 0.8774 (t0) REVERT: D 131 GLU cc_start: 0.8770 (tp30) cc_final: 0.8500 (mm-30) REVERT: D 134 ASP cc_start: 0.8802 (t0) cc_final: 0.8088 (t0) REVERT: D 137 ASN cc_start: 0.8848 (t0) cc_final: 0.8300 (t0) REVERT: D 194 TYR cc_start: 0.8455 (t80) cc_final: 0.8206 (t80) REVERT: D 236 GLN cc_start: 0.8477 (tm-30) cc_final: 0.8145 (pp30) REVERT: E 41 MET cc_start: 0.8722 (mtp) cc_final: 0.8310 (ttt) REVERT: E 134 ASP cc_start: 0.8066 (t0) cc_final: 0.7428 (t0) outliers start: 38 outliers final: 18 residues processed: 242 average time/residue: 0.4034 time to fit residues: 107.1704 Evaluate side-chains 228 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 206 time to evaluate : 0.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 MET Chi-restraints excluded: chain A residue 113 MET Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain A residue 131 GLU Chi-restraints excluded: chain A residue 152 ILE Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain B residue 78 GLU Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain B residue 112 LEU Chi-restraints excluded: chain B residue 223 LYS Chi-restraints excluded: chain B residue 226 PHE Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain C residue 112 LEU Chi-restraints excluded: chain C residue 223 LYS Chi-restraints excluded: chain C residue 228 LEU Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain D residue 143 LEU Chi-restraints excluded: chain D residue 183 VAL Chi-restraints excluded: chain D residue 228 LEU Chi-restraints excluded: chain E residue 30 MET Chi-restraints excluded: chain E residue 40 SER Chi-restraints excluded: chain E residue 50 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 12 optimal weight: 0.9980 chunk 69 optimal weight: 10.0000 chunk 87 optimal weight: 0.9980 chunk 20 optimal weight: 10.0000 chunk 48 optimal weight: 6.9990 chunk 112 optimal weight: 1.9990 chunk 57 optimal weight: 0.8980 chunk 41 optimal weight: 10.0000 chunk 95 optimal weight: 10.0000 chunk 90 optimal weight: 0.9990 chunk 8 optimal weight: 3.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 176 HIS ** D 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.114341 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.095567 restraints weight = 24395.403| |-----------------------------------------------------------------------------| r_work (start): 0.3725 rms_B_bonded: 3.24 r_work: 0.3605 rms_B_bonded: 4.30 restraints_weight: 0.5000 r_work (final): 0.3605 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8507 moved from start: 0.2620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 10167 Z= 0.134 Angle : 0.661 9.054 13697 Z= 0.317 Chirality : 0.039 0.199 1395 Planarity : 0.004 0.048 1605 Dihedral : 12.499 115.894 1848 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 10.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.79 % Favored : 99.21 % Rotamer: Outliers : 4.48 % Allowed : 25.68 % Favored : 69.84 % 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: 2.29 (0.25), residues: 1140 helix: 1.96 (0.17), residues: 891 sheet: None (None), residues: 0 loop : 0.00 (0.42), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 135 TYR 0.015 0.001 TYR C 190 PHE 0.011 0.001 PHE A 36 TRP 0.011 0.001 TRP B 139 HIS 0.003 0.001 HIS B 176 Details of bonding type rmsd covalent geometry : bond 0.00297 (10162) covalent geometry : angle 0.66121 (13697) hydrogen bonds : bond 0.04946 ( 724) hydrogen bonds : angle 4.60628 ( 2160) Misc. bond : bond 0.00089 ( 5) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 236 time to evaluate : 0.333 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 MET cc_start: 0.9067 (OUTLIER) cc_final: 0.8076 (mpp) REVERT: A 34 SER cc_start: 0.9405 (p) cc_final: 0.9162 (p) REVERT: A 87 ASP cc_start: 0.8625 (t0) cc_final: 0.8163 (t0) REVERT: A 134 ASP cc_start: 0.8647 (t0) cc_final: 0.8058 (t0) REVERT: A 137 ASN cc_start: 0.8605 (t0) cc_final: 0.8383 (t0) REVERT: A 194 TYR cc_start: 0.8878 (t80) cc_final: 0.8633 (t80) REVERT: B 28 MET cc_start: 0.9305 (tpp) cc_final: 0.9063 (tpp) REVERT: B 78 GLU cc_start: 0.7866 (OUTLIER) cc_final: 0.7551 (pm20) REVERT: B 113 MET cc_start: 0.8668 (mmm) cc_final: 0.8353 (mmm) REVERT: B 131 GLU cc_start: 0.7898 (mt-10) cc_final: 0.7631 (mt-10) REVERT: B 155 GLU cc_start: 0.8824 (tp30) cc_final: 0.8573 (tp30) REVERT: B 226 PHE cc_start: 0.9451 (OUTLIER) cc_final: 0.8584 (t80) REVERT: B 238 THR cc_start: 0.8717 (t) cc_final: 0.8516 (p) REVERT: C 78 GLU cc_start: 0.8378 (pp20) cc_final: 0.8047 (pp20) REVERT: C 137 ASN cc_start: 0.9031 (m-40) cc_final: 0.8811 (t0) REVERT: C 210 ASP cc_start: 0.8315 (t0) cc_final: 0.8099 (t0) REVERT: D 134 ASP cc_start: 0.8792 (t0) cc_final: 0.8098 (t0) REVERT: D 137 ASN cc_start: 0.8778 (t0) cc_final: 0.8307 (t0) REVERT: D 194 TYR cc_start: 0.8447 (t80) cc_final: 0.8047 (t80) REVERT: D 210 ASP cc_start: 0.7638 (t0) cc_final: 0.7341 (t70) REVERT: D 228 LEU cc_start: 0.8824 (OUTLIER) cc_final: 0.8590 (mt) REVERT: E 41 MET cc_start: 0.8714 (OUTLIER) cc_final: 0.8235 (ttt) REVERT: E 134 ASP cc_start: 0.8313 (t0) cc_final: 0.7667 (t0) outliers start: 41 outliers final: 16 residues processed: 257 average time/residue: 0.3834 time to fit residues: 108.6180 Evaluate side-chains 248 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 227 time to evaluate : 0.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 MET Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain B residue 78 GLU Chi-restraints excluded: chain B residue 152 ILE Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain B residue 223 LYS Chi-restraints excluded: chain B residue 226 PHE Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain C residue 112 LEU Chi-restraints excluded: chain C residue 228 LEU Chi-restraints excluded: chain D residue 40 SER Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain D residue 143 LEU Chi-restraints excluded: chain D residue 228 LEU Chi-restraints excluded: chain E residue 30 MET Chi-restraints excluded: chain E residue 40 SER Chi-restraints excluded: chain E residue 41 MET Chi-restraints excluded: chain E residue 42 SER Chi-restraints excluded: chain E residue 53 LEU Chi-restraints excluded: chain E residue 112 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 60 optimal weight: 4.9990 chunk 81 optimal weight: 9.9990 chunk 1 optimal weight: 0.9990 chunk 2 optimal weight: 0.9980 chunk 16 optimal weight: 9.9990 chunk 107 optimal weight: 5.9990 chunk 12 optimal weight: 0.6980 chunk 113 optimal weight: 1.9990 chunk 98 optimal weight: 2.9990 chunk 85 optimal weight: 0.9980 chunk 38 optimal weight: 6.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 176 HIS D 176 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.114676 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.096086 restraints weight = 24469.971| |-----------------------------------------------------------------------------| r_work (start): 0.3752 rms_B_bonded: 3.25 r_work: 0.3629 rms_B_bonded: 4.34 restraints_weight: 0.5000 r_work (final): 0.3629 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8486 moved from start: 0.2812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 10167 Z= 0.136 Angle : 0.669 10.774 13697 Z= 0.323 Chirality : 0.039 0.261 1395 Planarity : 0.004 0.050 1605 Dihedral : 12.352 114.990 1848 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.79 % Favored : 99.21 % Rotamer: Outliers : 4.26 % Allowed : 27.54 % Favored : 68.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.28 (0.25), residues: 1140 helix: 1.98 (0.17), residues: 888 sheet: None (None), residues: 0 loop : -0.10 (0.41), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 135 TYR 0.018 0.001 TYR D 190 PHE 0.043 0.001 PHE D 150 TRP 0.013 0.001 TRP B 139 HIS 0.010 0.002 HIS B 176 Details of bonding type rmsd covalent geometry : bond 0.00303 (10162) covalent geometry : angle 0.66919 (13697) hydrogen bonds : bond 0.04859 ( 724) hydrogen bonds : angle 4.66070 ( 2160) Misc. bond : bond 0.00123 ( 5) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 230 time to evaluate : 0.333 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 MET cc_start: 0.9033 (OUTLIER) cc_final: 0.8053 (mpp) REVERT: A 34 SER cc_start: 0.9418 (p) cc_final: 0.9174 (p) REVERT: A 87 ASP cc_start: 0.8670 (t0) cc_final: 0.8183 (t0) REVERT: A 134 ASP cc_start: 0.8657 (t0) cc_final: 0.8008 (t0) REVERT: A 137 ASN cc_start: 0.8710 (t0) cc_final: 0.8484 (t0) REVERT: A 194 TYR cc_start: 0.8872 (t80) cc_final: 0.8576 (t80) REVERT: B 28 MET cc_start: 0.9339 (tpp) cc_final: 0.9100 (tpp) REVERT: B 44 PHE cc_start: 0.7422 (m-80) cc_final: 0.7143 (m-80) REVERT: B 78 GLU cc_start: 0.7858 (OUTLIER) cc_final: 0.7546 (pm20) REVERT: B 113 MET cc_start: 0.8567 (mmm) cc_final: 0.8326 (mmm) REVERT: B 131 GLU cc_start: 0.7957 (mt-10) cc_final: 0.7663 (mt-10) REVERT: B 149 TYR cc_start: 0.8147 (t80) cc_final: 0.7929 (t80) REVERT: B 155 GLU cc_start: 0.8867 (tp30) cc_final: 0.8596 (tp30) REVERT: B 226 PHE cc_start: 0.9456 (OUTLIER) cc_final: 0.8631 (t80) REVERT: B 238 THR cc_start: 0.8704 (t) cc_final: 0.8449 (p) REVERT: C 78 GLU cc_start: 0.8464 (pp20) cc_final: 0.8054 (pp20) REVERT: C 137 ASN cc_start: 0.9133 (m-40) cc_final: 0.8831 (t0) REVERT: C 210 ASP cc_start: 0.8272 (t0) cc_final: 0.8046 (t0) REVERT: C 228 LEU cc_start: 0.8890 (OUTLIER) cc_final: 0.8690 (mp) REVERT: D 39 LEU cc_start: 0.9300 (mt) cc_final: 0.9062 (mp) REVERT: D 134 ASP cc_start: 0.8755 (t0) cc_final: 0.8032 (t0) REVERT: D 137 ASN cc_start: 0.8817 (t0) cc_final: 0.8373 (t0) REVERT: D 150 PHE cc_start: 0.8769 (t80) cc_final: 0.8546 (t80) REVERT: D 171 ASP cc_start: 0.8289 (p0) cc_final: 0.8029 (p0) REVERT: D 194 TYR cc_start: 0.8489 (t80) cc_final: 0.8059 (t80) REVERT: D 210 ASP cc_start: 0.7711 (t0) cc_final: 0.7439 (t70) REVERT: D 228 LEU cc_start: 0.8879 (OUTLIER) cc_final: 0.8656 (mt) REVERT: D 236 GLN cc_start: 0.8405 (tm-30) cc_final: 0.8161 (pp30) REVERT: E 41 MET cc_start: 0.8711 (OUTLIER) cc_final: 0.8248 (ttt) REVERT: E 113 MET cc_start: 0.8682 (tpt) cc_final: 0.8389 (mmm) REVERT: E 134 ASP cc_start: 0.8311 (t0) cc_final: 0.7727 (t0) REVERT: E 144 PHE cc_start: 0.9233 (m-80) cc_final: 0.8991 (m-80) outliers start: 39 outliers final: 14 residues processed: 246 average time/residue: 0.3984 time to fit residues: 107.5168 Evaluate side-chains 240 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 220 time to evaluate : 0.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 MET Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain B residue 78 GLU Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain B residue 223 LYS Chi-restraints excluded: chain B residue 226 PHE Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain C residue 90 LEU Chi-restraints excluded: chain C residue 95 MET Chi-restraints excluded: chain C residue 223 LYS Chi-restraints excluded: chain C residue 228 LEU Chi-restraints excluded: chain D residue 40 SER Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain D residue 143 LEU Chi-restraints excluded: chain D residue 228 LEU Chi-restraints excluded: chain E residue 40 SER Chi-restraints excluded: chain E residue 41 MET Chi-restraints excluded: chain E residue 53 LEU Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 112 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 84 optimal weight: 6.9990 chunk 25 optimal weight: 3.9990 chunk 74 optimal weight: 3.9990 chunk 64 optimal weight: 1.9990 chunk 86 optimal weight: 2.9990 chunk 3 optimal weight: 7.9990 chunk 83 optimal weight: 0.7980 chunk 26 optimal weight: 5.9990 chunk 73 optimal weight: 0.8980 chunk 63 optimal weight: 0.9980 chunk 11 optimal weight: 3.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 176 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.114094 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.095588 restraints weight = 24154.074| |-----------------------------------------------------------------------------| r_work (start): 0.3747 rms_B_bonded: 3.20 r_work: 0.3625 rms_B_bonded: 4.28 restraints_weight: 0.5000 r_work (final): 0.3625 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8498 moved from start: 0.2859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 10167 Z= 0.144 Angle : 0.678 10.668 13697 Z= 0.329 Chirality : 0.040 0.242 1395 Planarity : 0.004 0.050 1605 Dihedral : 12.357 115.754 1847 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 10.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.96 % Favored : 99.04 % Rotamer: Outliers : 3.39 % Allowed : 28.63 % Favored : 67.98 % 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: 2.29 (0.25), residues: 1140 helix: 1.99 (0.17), residues: 888 sheet: None (None), residues: 0 loop : -0.12 (0.40), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 135 TYR 0.020 0.001 TYR D 18 PHE 0.027 0.001 PHE D 150 TRP 0.009 0.001 TRP B 139 HIS 0.007 0.002 HIS B 176 Details of bonding type rmsd covalent geometry : bond 0.00330 (10162) covalent geometry : angle 0.67773 (13697) hydrogen bonds : bond 0.04920 ( 724) hydrogen bonds : angle 4.65224 ( 2160) Misc. bond : bond 0.00077 ( 5) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 232 time to evaluate : 0.372 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 MET cc_start: 0.9043 (OUTLIER) cc_final: 0.8107 (mpp) REVERT: A 34 SER cc_start: 0.9414 (p) cc_final: 0.9172 (p) REVERT: A 87 ASP cc_start: 0.8691 (t0) cc_final: 0.8216 (t0) REVERT: A 134 ASP cc_start: 0.8669 (t0) cc_final: 0.8040 (t0) REVERT: A 137 ASN cc_start: 0.8682 (t0) cc_final: 0.8472 (t0) REVERT: A 164 LEU cc_start: 0.8824 (OUTLIER) cc_final: 0.8575 (tt) REVERT: B 28 MET cc_start: 0.9335 (tpp) cc_final: 0.9123 (tpp) REVERT: B 44 PHE cc_start: 0.7364 (m-80) cc_final: 0.7160 (m-80) REVERT: B 78 GLU cc_start: 0.7852 (OUTLIER) cc_final: 0.7510 (pm20) REVERT: B 113 MET cc_start: 0.8670 (mmm) cc_final: 0.8362 (mmm) REVERT: B 131 GLU cc_start: 0.7961 (mt-10) cc_final: 0.7676 (mt-10) REVERT: B 155 GLU cc_start: 0.8856 (tp30) cc_final: 0.8597 (tp30) REVERT: B 226 PHE cc_start: 0.9460 (OUTLIER) cc_final: 0.8683 (t80) REVERT: C 78 GLU cc_start: 0.8479 (pp20) cc_final: 0.8108 (pp20) REVERT: C 98 GLU cc_start: 0.8701 (tp30) cc_final: 0.8399 (tp30) REVERT: C 137 ASN cc_start: 0.9176 (m-40) cc_final: 0.8902 (t0) REVERT: C 210 ASP cc_start: 0.8307 (t0) cc_final: 0.8067 (t0) REVERT: D 109 LYS cc_start: 0.8764 (mtmm) cc_final: 0.8403 (mppt) REVERT: D 134 ASP cc_start: 0.8778 (t0) cc_final: 0.8048 (t0) REVERT: D 137 ASN cc_start: 0.8812 (t0) cc_final: 0.8384 (t0) REVERT: D 150 PHE cc_start: 0.8785 (t80) cc_final: 0.8530 (t80) REVERT: D 171 ASP cc_start: 0.8268 (p0) cc_final: 0.8027 (p0) REVERT: D 194 TYR cc_start: 0.8515 (t80) cc_final: 0.8105 (t80) REVERT: D 210 ASP cc_start: 0.7720 (t0) cc_final: 0.7431 (t70) REVERT: D 228 LEU cc_start: 0.8864 (OUTLIER) cc_final: 0.8636 (mt) REVERT: D 236 GLN cc_start: 0.8414 (tm-30) cc_final: 0.8100 (pp30) REVERT: E 41 MET cc_start: 0.8706 (OUTLIER) cc_final: 0.8229 (ttt) REVERT: E 113 MET cc_start: 0.8548 (tpt) cc_final: 0.8145 (mmm) REVERT: E 134 ASP cc_start: 0.8450 (t0) cc_final: 0.7839 (t0) REVERT: E 144 PHE cc_start: 0.9239 (m-80) cc_final: 0.9020 (m-80) outliers start: 31 outliers final: 15 residues processed: 245 average time/residue: 0.4135 time to fit residues: 110.9441 Evaluate side-chains 244 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 223 time to evaluate : 0.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 MET Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain B residue 78 GLU Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain B residue 223 LYS Chi-restraints excluded: chain B residue 226 PHE Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain C residue 90 LEU Chi-restraints excluded: chain C residue 95 MET Chi-restraints excluded: chain C residue 223 LYS Chi-restraints excluded: chain D residue 40 SER Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain D residue 143 LEU Chi-restraints excluded: chain D residue 228 LEU Chi-restraints excluded: chain E residue 30 MET Chi-restraints excluded: chain E residue 40 SER Chi-restraints excluded: chain E residue 41 MET Chi-restraints excluded: chain E residue 42 SER Chi-restraints excluded: chain E residue 53 LEU Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 103 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 101 optimal weight: 9.9990 chunk 58 optimal weight: 4.9990 chunk 82 optimal weight: 7.9990 chunk 35 optimal weight: 5.9990 chunk 61 optimal weight: 7.9990 chunk 40 optimal weight: 4.9990 chunk 98 optimal weight: 9.9990 chunk 66 optimal weight: 5.9990 chunk 105 optimal weight: 10.0000 chunk 107 optimal weight: 4.9990 chunk 50 optimal weight: 0.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.110412 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.091387 restraints weight = 24547.699| |-----------------------------------------------------------------------------| r_work (start): 0.3682 rms_B_bonded: 3.17 r_work: 0.3551 rms_B_bonded: 4.29 restraints_weight: 0.5000 r_work (final): 0.3551 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8576 moved from start: 0.2787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.075 10167 Z= 0.255 Angle : 0.745 11.771 13697 Z= 0.368 Chirality : 0.044 0.300 1395 Planarity : 0.004 0.048 1605 Dihedral : 12.993 116.968 1845 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 11.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 3.72 % Allowed : 29.40 % Favored : 66.89 % 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: 2.17 (0.25), residues: 1140 helix: 1.90 (0.17), residues: 888 sheet: None (None), residues: 0 loop : -0.14 (0.40), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 135 TYR 0.019 0.002 TYR D 190 PHE 0.021 0.001 PHE D 150 TRP 0.010 0.001 TRP D 48 HIS 0.007 0.002 HIS A 65 Details of bonding type rmsd covalent geometry : bond 0.00585 (10162) covalent geometry : angle 0.74539 (13697) hydrogen bonds : bond 0.05620 ( 724) hydrogen bonds : angle 4.89753 ( 2160) Misc. bond : bond 0.00101 ( 5) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 211 time to evaluate : 0.346 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 MET cc_start: 0.9088 (OUTLIER) cc_final: 0.8377 (mpp) REVERT: A 78 GLU cc_start: 0.8806 (tp30) cc_final: 0.8432 (mm-30) REVERT: A 87 ASP cc_start: 0.8742 (t0) cc_final: 0.8354 (t0) REVERT: A 109 LYS cc_start: 0.8746 (mmmm) cc_final: 0.8538 (tptp) REVERT: A 134 ASP cc_start: 0.8650 (t0) cc_final: 0.7924 (t0) REVERT: B 131 GLU cc_start: 0.8107 (mt-10) cc_final: 0.7819 (mt-10) REVERT: B 149 TYR cc_start: 0.8151 (t80) cc_final: 0.7856 (t80) REVERT: B 155 GLU cc_start: 0.8897 (tp30) cc_final: 0.8609 (tp30) REVERT: C 78 GLU cc_start: 0.8496 (pp20) cc_final: 0.8075 (pp20) REVERT: C 137 ASN cc_start: 0.9309 (m-40) cc_final: 0.8955 (t0) REVERT: C 210 ASP cc_start: 0.8280 (t0) cc_final: 0.8069 (t0) REVERT: D 39 LEU cc_start: 0.9369 (mt) cc_final: 0.9102 (mp) REVERT: D 134 ASP cc_start: 0.8838 (t0) cc_final: 0.7999 (t0) REVERT: D 137 ASN cc_start: 0.8884 (t0) cc_final: 0.8377 (t0) REVERT: D 194 TYR cc_start: 0.8647 (t80) cc_final: 0.8345 (t80) REVERT: D 210 ASP cc_start: 0.7760 (t0) cc_final: 0.7494 (t70) REVERT: E 113 MET cc_start: 0.8691 (tpt) cc_final: 0.8381 (mmm) REVERT: E 134 ASP cc_start: 0.8487 (t0) cc_final: 0.7935 (t0) REVERT: E 144 PHE cc_start: 0.9226 (m-80) cc_final: 0.9002 (m-80) outliers start: 34 outliers final: 23 residues processed: 226 average time/residue: 0.4293 time to fit residues: 106.1187 Evaluate side-chains 228 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 204 time to evaluate : 0.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 MET Chi-restraints excluded: chain A residue 66 TYR Chi-restraints excluded: chain A residue 152 ILE Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain B residue 152 ILE Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain B residue 223 LYS Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain C residue 95 MET Chi-restraints excluded: chain C residue 112 LEU Chi-restraints excluded: chain C residue 223 LYS Chi-restraints excluded: chain C residue 228 LEU Chi-restraints excluded: chain D residue 40 SER Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain D residue 143 LEU Chi-restraints excluded: chain D residue 228 LEU Chi-restraints excluded: chain E residue 30 MET Chi-restraints excluded: chain E residue 40 SER Chi-restraints excluded: chain E residue 42 SER Chi-restraints excluded: chain E residue 53 LEU Chi-restraints excluded: chain E residue 90 LEU Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 103 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 13 optimal weight: 9.9990 chunk 88 optimal weight: 8.9990 chunk 68 optimal weight: 6.9990 chunk 55 optimal weight: 0.8980 chunk 30 optimal weight: 1.9990 chunk 34 optimal weight: 4.9990 chunk 37 optimal weight: 0.9980 chunk 57 optimal weight: 3.9990 chunk 50 optimal weight: 2.9990 chunk 110 optimal weight: 3.9990 chunk 4 optimal weight: 0.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4044 r_free = 0.4044 target = 0.113069 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.094464 restraints weight = 24106.035| |-----------------------------------------------------------------------------| r_work (start): 0.3730 rms_B_bonded: 3.17 r_work: 0.3598 rms_B_bonded: 4.32 restraints_weight: 0.5000 r_work (final): 0.3598 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8532 moved from start: 0.2929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 10167 Z= 0.157 Angle : 0.724 11.480 13697 Z= 0.354 Chirality : 0.041 0.259 1395 Planarity : 0.004 0.050 1605 Dihedral : 12.627 116.357 1845 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 11.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Rotamer: Outliers : 2.95 % Allowed : 30.49 % Favored : 66.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.19 (0.25), residues: 1140 helix: 1.92 (0.17), residues: 888 sheet: None (None), residues: 0 loop : -0.16 (0.41), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 46 TYR 0.018 0.001 TYR D 190 PHE 0.018 0.001 PHE D 150 TRP 0.009 0.001 TRP B 139 HIS 0.006 0.001 HIS B 176 Details of bonding type rmsd covalent geometry : bond 0.00365 (10162) covalent geometry : angle 0.72413 (13697) hydrogen bonds : bond 0.05195 ( 724) hydrogen bonds : angle 4.75268 ( 2160) Misc. bond : bond 0.00083 ( 5) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 226 time to evaluate : 0.339 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 MET cc_start: 0.9074 (OUTLIER) cc_final: 0.8038 (mpp) REVERT: A 87 ASP cc_start: 0.8665 (t0) cc_final: 0.8258 (t0) REVERT: A 134 ASP cc_start: 0.8336 (t0) cc_final: 0.7795 (t0) REVERT: B 113 MET cc_start: 0.8677 (mmm) cc_final: 0.8318 (mmm) REVERT: B 131 GLU cc_start: 0.7996 (mt-10) cc_final: 0.7690 (mt-10) REVERT: B 149 TYR cc_start: 0.8122 (t80) cc_final: 0.7828 (t80) REVERT: B 155 GLU cc_start: 0.8887 (tp30) cc_final: 0.8610 (tp30) REVERT: C 78 GLU cc_start: 0.8498 (pp20) cc_final: 0.8084 (pp20) REVERT: C 137 ASN cc_start: 0.9233 (m-40) cc_final: 0.8922 (t0) REVERT: C 210 ASP cc_start: 0.8276 (t0) cc_final: 0.8034 (t0) REVERT: D 134 ASP cc_start: 0.8842 (t0) cc_final: 0.8091 (t0) REVERT: D 137 ASN cc_start: 0.8832 (t0) cc_final: 0.8322 (t0) REVERT: D 171 ASP cc_start: 0.8424 (p0) cc_final: 0.8072 (p0) REVERT: D 194 TYR cc_start: 0.8603 (t80) cc_final: 0.8279 (t80) REVERT: D 210 ASP cc_start: 0.7707 (t0) cc_final: 0.7447 (t70) REVERT: D 219 ASP cc_start: 0.8775 (m-30) cc_final: 0.8416 (m-30) REVERT: E 41 MET cc_start: 0.8616 (OUTLIER) cc_final: 0.8284 (ttt) REVERT: E 113 MET cc_start: 0.8652 (tpt) cc_final: 0.8432 (mmm) REVERT: E 134 ASP cc_start: 0.8434 (t0) cc_final: 0.7845 (t0) outliers start: 27 outliers final: 15 residues processed: 237 average time/residue: 0.4237 time to fit residues: 109.6184 Evaluate side-chains 228 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 211 time to evaluate : 0.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 MET Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain B residue 152 ILE Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain B residue 223 LYS Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain C residue 95 MET Chi-restraints excluded: chain C residue 223 LYS Chi-restraints excluded: chain D residue 40 SER Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain D residue 143 LEU Chi-restraints excluded: chain D residue 228 LEU Chi-restraints excluded: chain E residue 30 MET Chi-restraints excluded: chain E residue 40 SER Chi-restraints excluded: chain E residue 41 MET Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 103 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 52 optimal weight: 10.0000 chunk 70 optimal weight: 0.9990 chunk 28 optimal weight: 0.9980 chunk 113 optimal weight: 5.9990 chunk 92 optimal weight: 1.9990 chunk 91 optimal weight: 3.9990 chunk 88 optimal weight: 7.9990 chunk 19 optimal weight: 7.9990 chunk 65 optimal weight: 4.9990 chunk 111 optimal weight: 7.9990 chunk 82 optimal weight: 6.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.111931 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.093461 restraints weight = 24189.772| |-----------------------------------------------------------------------------| r_work (start): 0.3714 rms_B_bonded: 3.15 r_work: 0.3586 rms_B_bonded: 4.27 restraints_weight: 0.5000 r_work (final): 0.3586 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8551 moved from start: 0.2979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.089 10167 Z= 0.188 Angle : 0.764 11.436 13697 Z= 0.376 Chirality : 0.043 0.268 1395 Planarity : 0.004 0.050 1605 Dihedral : 12.701 116.285 1845 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 11.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 2.19 % Allowed : 32.24 % Favored : 65.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.11 (0.25), residues: 1140 helix: 1.85 (0.17), residues: 888 sheet: None (None), residues: 0 loop : -0.15 (0.40), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 135 TYR 0.022 0.001 TYR A 194 PHE 0.057 0.001 PHE D 150 TRP 0.008 0.001 TRP D 48 HIS 0.005 0.001 HIS A 65 Details of bonding type rmsd covalent geometry : bond 0.00440 (10162) covalent geometry : angle 0.76409 (13697) hydrogen bonds : bond 0.05371 ( 724) hydrogen bonds : angle 4.84924 ( 2160) Misc. bond : bond 0.00088 ( 5) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 216 time to evaluate : 0.324 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 MET cc_start: 0.9113 (OUTLIER) cc_final: 0.8321 (mpp) REVERT: A 34 SER cc_start: 0.9429 (p) cc_final: 0.8818 (m) REVERT: A 87 ASP cc_start: 0.8684 (t0) cc_final: 0.8278 (t0) REVERT: A 134 ASP cc_start: 0.8302 (t0) cc_final: 0.7822 (t0) REVERT: B 113 MET cc_start: 0.8510 (mmm) cc_final: 0.8293 (mmm) REVERT: B 131 GLU cc_start: 0.8013 (mt-10) cc_final: 0.7720 (mt-10) REVERT: B 149 TYR cc_start: 0.8101 (t80) cc_final: 0.7767 (t80) REVERT: B 155 GLU cc_start: 0.8909 (tp30) cc_final: 0.8640 (tp30) REVERT: C 78 GLU cc_start: 0.8505 (pp20) cc_final: 0.8093 (pp20) REVERT: C 137 ASN cc_start: 0.9231 (m-40) cc_final: 0.8887 (t0) REVERT: C 210 ASP cc_start: 0.8322 (t0) cc_final: 0.8099 (t0) REVERT: D 39 LEU cc_start: 0.9332 (mt) cc_final: 0.9115 (mp) REVERT: D 134 ASP cc_start: 0.8864 (t0) cc_final: 0.8111 (t0) REVERT: D 137 ASN cc_start: 0.8844 (t0) cc_final: 0.8328 (t0) REVERT: D 194 TYR cc_start: 0.8619 (t80) cc_final: 0.8307 (t80) REVERT: D 210 ASP cc_start: 0.7710 (t0) cc_final: 0.7446 (t70) REVERT: D 219 ASP cc_start: 0.8823 (m-30) cc_final: 0.8582 (m-30) REVERT: E 41 MET cc_start: 0.8620 (mtp) cc_final: 0.8204 (ttt) REVERT: E 134 ASP cc_start: 0.8420 (t0) cc_final: 0.7865 (t0) outliers start: 20 outliers final: 17 residues processed: 224 average time/residue: 0.4203 time to fit residues: 103.1730 Evaluate side-chains 228 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 210 time to evaluate : 0.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 MET Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain B residue 152 ILE Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain B residue 223 LYS Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain C residue 95 MET Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain C residue 223 LYS Chi-restraints excluded: chain D residue 40 SER Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain D residue 143 LEU Chi-restraints excluded: chain D residue 228 LEU Chi-restraints excluded: chain E residue 30 MET Chi-restraints excluded: chain E residue 40 SER Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 103 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 27 optimal weight: 1.9990 chunk 35 optimal weight: 9.9990 chunk 48 optimal weight: 1.9990 chunk 17 optimal weight: 0.7980 chunk 73 optimal weight: 4.9990 chunk 55 optimal weight: 0.0170 chunk 20 optimal weight: 0.7980 chunk 24 optimal weight: 1.9990 chunk 66 optimal weight: 0.7980 chunk 109 optimal weight: 0.9990 chunk 39 optimal weight: 7.9990 overall best weight: 0.6820 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 216 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4080 r_free = 0.4080 target = 0.115687 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.097467 restraints weight = 23978.760| |-----------------------------------------------------------------------------| r_work (start): 0.3774 rms_B_bonded: 3.21 r_work: 0.3649 rms_B_bonded: 4.31 restraints_weight: 0.5000 r_work (final): 0.3649 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8474 moved from start: 0.3186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.091 10167 Z= 0.146 Angle : 0.746 11.598 13697 Z= 0.366 Chirality : 0.041 0.250 1395 Planarity : 0.004 0.052 1605 Dihedral : 12.263 115.807 1845 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 10.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Rotamer: Outliers : 2.30 % Allowed : 32.13 % Favored : 65.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.11 (0.25), residues: 1140 helix: 1.88 (0.17), residues: 888 sheet: None (None), residues: 0 loop : -0.25 (0.40), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 135 TYR 0.019 0.001 TYR D 190 PHE 0.018 0.001 PHE D 150 TRP 0.015 0.001 TRP B 139 HIS 0.006 0.001 HIS B 176 Details of bonding type rmsd covalent geometry : bond 0.00335 (10162) covalent geometry : angle 0.74567 (13697) hydrogen bonds : bond 0.04885 ( 724) hydrogen bonds : angle 4.73041 ( 2160) Misc. bond : bond 0.00065 ( 5) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3542.27 seconds wall clock time: 61 minutes 16.46 seconds (3676.46 seconds total)