Starting phenix.real_space_refine on Fri Mar 14 03:11:50 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8j8v_36081/03_2025/8j8v_36081.cif Found real_map, /net/cci-nas-00/data/ceres_data/8j8v_36081/03_2025/8j8v_36081.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.22 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8j8v_36081/03_2025/8j8v_36081.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8j8v_36081/03_2025/8j8v_36081.map" model { file = "/net/cci-nas-00/data/ceres_data/8j8v_36081/03_2025/8j8v_36081.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8j8v_36081/03_2025/8j8v_36081.cif" } resolution = 3.22 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.029 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: 5 Type Number sf(0) Gaussians P 14 5.49 5 S 20 5.16 5 C 5963 2.51 5 N 1616 2.21 5 O 1824 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 39 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 9437 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 2890 Number of conformers: 1 Conformer: "" Number of residues, atoms: 365, 2890 Classifications: {'peptide': 365} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 2, 'PTRANS': 24, 'TRANS': 338} Chain breaks: 1 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "B" Number of atoms: 908 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 908 Classifications: {'peptide': 117} Link IDs: {'CIS': 1, 'PTRANS': 2, 'TRANS': 113} Chain: "C" Number of atoms: 800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 800 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 100} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'GLN:plan1': 2} Unresolved non-hydrogen planarities: 8 Chain: "D" Number of atoms: 914 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 914 Classifications: {'peptide': 118} Link IDs: {'CIS': 1, 'PTRANS': 2, 'TRANS': 114} Chain: "E" Number of atoms: 805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 805 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 100} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "F" Number of atoms: 2890 Number of conformers: 1 Conformer: "" Number of residues, atoms: 365, 2890 Classifications: {'peptide': 365} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 2, 'PTRANS': 24, 'TRANS': 338} Chain breaks: 1 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "G" Number of atoms: 115 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 115 Classifications: {'peptide': 13} Link IDs: {'TRANS': 12} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'TPO:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "H" Number of atoms: 115 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 115 Classifications: {'peptide': 13} Link IDs: {'TRANS': 12} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'TPO:plan-1': 1} Unresolved non-hydrogen planarities: 1 Time building chain proxies: 6.76, per 1000 atoms: 0.72 Number of scatterers: 9437 At special positions: 0 Unit cell: (135.569, 86.3707, 104.957, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 20 16.00 P 14 15.00 O 1824 8.00 N 1616 7.00 C 5963 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS B 25 " - pdb=" SG CYS B 99 " distance=2.03 Simple disulfide: pdb=" SG CYS C 24 " - pdb=" SG CYS C 89 " distance=2.03 Simple disulfide: pdb=" SG CYS D 25 " - pdb=" SG CYS D 99 " distance=2.03 Simple disulfide: pdb=" SG CYS E 24 " - pdb=" SG CYS E 89 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.21 Conformation dependent library (CDL) restraints added in 1.0 seconds 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2258 Finding SS restraints... Secondary structure from input PDB file: 6 helices and 22 sheets defined 5.5% alpha, 46.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.59 Creating SS restraints... Processing helix chain 'A' and resid 99 through 110 Processing helix chain 'A' and resid 393 through 408 removed outlier: 3.514A pdb=" N LYS A 408 " --> pdb=" O ARG A 404 " (cutoff:3.500A) Processing helix chain 'B' and resid 90 through 94 removed outlier: 4.056A pdb=" N THR B 94 " --> pdb=" O ALA B 91 " (cutoff:3.500A) Processing helix chain 'D' and resid 90 through 94 removed outlier: 4.042A pdb=" N THR D 94 " --> pdb=" O ALA D 91 " (cutoff:3.500A) Processing helix chain 'F' and resid 99 through 110 Processing helix chain 'F' and resid 393 through 408 Processing sheet with id=AA1, first strand: chain 'A' and resid 113 through 118 Processing sheet with id=AA2, first strand: chain 'A' and resid 27 through 29 removed outlier: 4.003A pdb=" N PHE A 145 " --> pdb=" O ILE A 169 " (cutoff:3.500A) removed outlier: 7.831A pdb=" N LYS A 171 " --> pdb=" O VAL A 143 " (cutoff:3.500A) removed outlier: 10.298A pdb=" N VAL A 143 " --> pdb=" O LYS A 171 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ASP A 144 " --> pdb=" O ALA A 61 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N PHE A 88 " --> pdb=" O VAL A 54 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N VAL A 56 " --> pdb=" O GLN A 86 " (cutoff:3.500A) removed outlier: 5.386A pdb=" N GLN A 86 " --> pdb=" O VAL A 56 " (cutoff:3.500A) removed outlier: 7.241A pdb=" N LEU A 58 " --> pdb=" O ASN A 84 " (cutoff:3.500A) removed outlier: 5.823A pdb=" N ASN A 84 " --> pdb=" O LEU A 58 " (cutoff:3.500A) removed outlier: 7.897A pdb=" N VAL A 60 " --> pdb=" O ILE A 82 " (cutoff:3.500A) removed outlier: 6.014A pdb=" N ILE A 82 " --> pdb=" O VAL A 60 " (cutoff:3.500A) removed outlier: 8.446A pdb=" N PHE A 62 " --> pdb=" O LEU A 80 " (cutoff:3.500A) removed outlier: 7.313A pdb=" N LEU A 80 " --> pdb=" O PHE A 62 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 27 through 29 removed outlier: 4.003A pdb=" N PHE A 145 " --> pdb=" O ILE A 169 " (cutoff:3.500A) removed outlier: 7.831A pdb=" N LYS A 171 " --> pdb=" O VAL A 143 " (cutoff:3.500A) removed outlier: 10.298A pdb=" N VAL A 143 " --> pdb=" O LYS A 171 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 184 through 190 removed outlier: 3.655A pdb=" N SER A 203 " --> pdb=" O ASN A 218 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ASN A 223 " --> pdb=" O SER A 267 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 208 through 209 removed outlier: 3.600A pdb=" N VAL A 336 " --> pdb=" O LEU A 328 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N PHE A 342 " --> pdb=" O TYR A 322 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N TYR A 322 " --> pdb=" O PHE A 342 " (cutoff:3.500A) removed outlier: 7.699A pdb=" N LEU A 344 " --> pdb=" O VAL A 320 " (cutoff:3.500A) removed outlier: 9.411A pdb=" N VAL A 320 " --> pdb=" O LEU A 344 " (cutoff:3.500A) removed outlier: 7.631A pdb=" N ILE A 232 " --> pdb=" O GLU A 258 " (cutoff:3.500A) removed outlier: 5.013A pdb=" N GLU A 258 " --> pdb=" O ILE A 232 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N VAL A 234 " --> pdb=" O GLN A 256 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N GLN A 256 " --> pdb=" O VAL A 234 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N VAL A 236 " --> pdb=" O VAL A 254 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 6 through 10 Processing sheet with id=AA7, first strand: chain 'B' and resid 13 through 14 removed outlier: 6.504A pdb=" N GLY B 13 " --> pdb=" O THR B 120 " (cutoff:3.500A) removed outlier: 8.713A pdb=" N SER B 35 " --> pdb=" O SER B 55 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N SER B 55 " --> pdb=" O SER B 35 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N ILE B 37 " --> pdb=" O SER B 53 " (cutoff:3.500A) removed outlier: 4.729A pdb=" N SER B 53 " --> pdb=" O ILE B 37 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N TRP B 39 " --> pdb=" O VAL B 51 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 13 through 14 removed outlier: 6.504A pdb=" N GLY B 13 " --> pdb=" O THR B 120 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N TYR B 112 " --> pdb=" O ARG B 101 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 5 through 8 removed outlier: 3.611A pdb=" N VAL C 20 " --> pdb=" O ILE C 76 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 11 through 13 removed outlier: 3.531A pdb=" N LEU C 12 " --> pdb=" O LYS C 104 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N VAL C 34 " --> pdb=" O TYR C 50 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N TYR C 50 " --> pdb=" O VAL C 34 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N TRP C 36 " --> pdb=" O LEU C 48 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 11 through 13 removed outlier: 3.531A pdb=" N LEU C 12 " --> pdb=" O LYS C 104 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N THR C 98 " --> pdb=" O GLN C 91 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 6 through 10 removed outlier: 3.544A pdb=" N VAL D 8 " --> pdb=" O ALA D 26 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 13 through 15 removed outlier: 6.521A pdb=" N GLY D 13 " --> pdb=" O THR D 120 " (cutoff:3.500A) removed outlier: 8.702A pdb=" N SER D 35 " --> pdb=" O SER D 55 " (cutoff:3.500A) removed outlier: 6.173A pdb=" N SER D 55 " --> pdb=" O SER D 35 " (cutoff:3.500A) removed outlier: 7.054A pdb=" N ILE D 37 " --> pdb=" O SER D 53 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N SER D 53 " --> pdb=" O ILE D 37 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N TRP D 39 " --> pdb=" O VAL D 51 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 13 through 15 removed outlier: 6.521A pdb=" N GLY D 13 " --> pdb=" O THR D 120 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N TYR D 112 " --> pdb=" O ARG D 101 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 5 through 8 removed outlier: 3.603A pdb=" N VAL E 20 " --> pdb=" O ILE E 76 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 11 through 13 removed outlier: 3.539A pdb=" N LEU E 12 " --> pdb=" O LYS E 104 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N VAL E 34 " --> pdb=" O TYR E 50 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N TYR E 50 " --> pdb=" O VAL E 34 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N TRP E 36 " --> pdb=" O LEU E 48 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 11 through 13 removed outlier: 3.539A pdb=" N LEU E 12 " --> pdb=" O LYS E 104 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N THR E 98 " --> pdb=" O GLN E 91 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 113 through 118 Processing sheet with id=AC1, first strand: chain 'F' and resid 27 through 29 removed outlier: 4.019A pdb=" N PHE F 145 " --> pdb=" O ILE F 169 " (cutoff:3.500A) removed outlier: 7.830A pdb=" N LYS F 171 " --> pdb=" O VAL F 143 " (cutoff:3.500A) removed outlier: 10.325A pdb=" N VAL F 143 " --> pdb=" O LYS F 171 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ASP F 144 " --> pdb=" O ALA F 61 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N PHE F 88 " --> pdb=" O VAL F 54 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N VAL F 56 " --> pdb=" O GLN F 86 " (cutoff:3.500A) removed outlier: 5.343A pdb=" N GLN F 86 " --> pdb=" O VAL F 56 " (cutoff:3.500A) removed outlier: 7.214A pdb=" N LEU F 58 " --> pdb=" O ASN F 84 " (cutoff:3.500A) removed outlier: 5.798A pdb=" N ASN F 84 " --> pdb=" O LEU F 58 " (cutoff:3.500A) removed outlier: 7.855A pdb=" N VAL F 60 " --> pdb=" O ILE F 82 " (cutoff:3.500A) removed outlier: 5.985A pdb=" N ILE F 82 " --> pdb=" O VAL F 60 " (cutoff:3.500A) removed outlier: 8.440A pdb=" N PHE F 62 " --> pdb=" O LEU F 80 " (cutoff:3.500A) removed outlier: 7.282A pdb=" N LEU F 80 " --> pdb=" O PHE F 62 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 27 through 29 removed outlier: 4.019A pdb=" N PHE F 145 " --> pdb=" O ILE F 169 " (cutoff:3.500A) removed outlier: 7.830A pdb=" N LYS F 171 " --> pdb=" O VAL F 143 " (cutoff:3.500A) removed outlier: 10.325A pdb=" N VAL F 143 " --> pdb=" O LYS F 171 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 184 through 190 removed outlier: 3.880A pdb=" N SER F 203 " --> pdb=" O ASN F 218 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ASN F 223 " --> pdb=" O SER F 267 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 208 through 209 removed outlier: 3.637A pdb=" N VAL F 336 " --> pdb=" O LEU F 328 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N PHE F 342 " --> pdb=" O TYR F 322 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N TYR F 322 " --> pdb=" O PHE F 342 " (cutoff:3.500A) removed outlier: 7.704A pdb=" N LEU F 344 " --> pdb=" O VAL F 320 " (cutoff:3.500A) removed outlier: 9.392A pdb=" N VAL F 320 " --> pdb=" O LEU F 344 " (cutoff:3.500A) removed outlier: 7.618A pdb=" N ILE F 232 " --> pdb=" O GLU F 258 " (cutoff:3.500A) removed outlier: 4.982A pdb=" N GLU F 258 " --> pdb=" O ILE F 232 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N VAL F 234 " --> pdb=" O GLN F 256 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N GLN F 256 " --> pdb=" O VAL F 234 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N VAL F 236 " --> pdb=" O VAL F 254 " (cutoff:3.500A) 384 hydrogen bonds defined for protein. 999 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.21 Time building geometry restraints manager: 2.65 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3026 1.34 - 1.46: 1903 1.46 - 1.58: 4652 1.58 - 1.69: 42 1.69 - 1.81: 28 Bond restraints: 9651 Sorted by residual: bond pdb=" OG1 TPO H 354 " pdb=" P TPO H 354 " ideal model delta sigma weight residual 1.717 1.608 0.109 2.00e-02 2.50e+03 2.97e+01 bond pdb=" OG1 TPO G 354 " pdb=" P TPO G 354 " ideal model delta sigma weight residual 1.717 1.609 0.108 2.00e-02 2.50e+03 2.92e+01 bond pdb=" O1P SEP H 345 " pdb=" P SEP H 345 " ideal model delta sigma weight residual 1.610 1.513 0.097 2.00e-02 2.50e+03 2.34e+01 bond pdb=" O1P SEP G 343 " pdb=" P SEP G 343 " ideal model delta sigma weight residual 1.610 1.514 0.096 2.00e-02 2.50e+03 2.30e+01 bond pdb=" O2P SEP H 345 " pdb=" P SEP H 345 " ideal model delta sigma weight residual 1.610 1.515 0.095 2.00e-02 2.50e+03 2.27e+01 ... (remaining 9646 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.54: 12917 2.54 - 5.08: 181 5.08 - 7.61: 13 7.61 - 10.15: 8 10.15 - 12.69: 3 Bond angle restraints: 13122 Sorted by residual: angle pdb=" N LEU F 49 " pdb=" CA LEU F 49 " pdb=" C LEU F 49 " ideal model delta sigma weight residual 110.55 97.86 12.69 1.35e+00 5.49e-01 8.83e+01 angle pdb=" N LYS F 50 " pdb=" CA LYS F 50 " pdb=" C LYS F 50 " ideal model delta sigma weight residual 112.12 103.01 9.11 1.34e+00 5.57e-01 4.62e+01 angle pdb=" N VAL A 315 " pdb=" CA VAL A 315 " pdb=" C VAL A 315 " ideal model delta sigma weight residual 106.21 112.51 -6.30 1.07e+00 8.73e-01 3.47e+01 angle pdb=" C LEU A 49 " pdb=" N LYS A 50 " pdb=" CA LYS A 50 " ideal model delta sigma weight residual 120.72 111.56 9.16 1.67e+00 3.59e-01 3.01e+01 angle pdb=" N PHE A 245 " pdb=" CA PHE A 245 " pdb=" C PHE A 245 " ideal model delta sigma weight residual 114.75 108.37 6.38 1.26e+00 6.30e-01 2.56e+01 ... (remaining 13117 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.67: 5348 17.67 - 35.33: 363 35.33 - 53.00: 67 53.00 - 70.66: 13 70.66 - 88.33: 15 Dihedral angle restraints: 5806 sinusoidal: 2297 harmonic: 3509 Sorted by residual: dihedral pdb=" CA SER F 75 " pdb=" C SER F 75 " pdb=" N PHE F 76 " pdb=" CA PHE F 76 " ideal model delta harmonic sigma weight residual 180.00 159.85 20.15 0 5.00e+00 4.00e-02 1.62e+01 dihedral pdb=" CA LEU F 244 " pdb=" C LEU F 244 " pdb=" N PHE F 245 " pdb=" CA PHE F 245 " ideal model delta harmonic sigma weight residual 180.00 160.87 19.13 0 5.00e+00 4.00e-02 1.46e+01 dihedral pdb=" CA SER A 75 " pdb=" C SER A 75 " pdb=" N PHE A 76 " pdb=" CA PHE A 76 " ideal model delta harmonic sigma weight residual 180.00 161.26 18.74 0 5.00e+00 4.00e-02 1.40e+01 ... (remaining 5803 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.070: 1284 0.070 - 0.140: 173 0.140 - 0.210: 7 0.210 - 0.279: 1 0.279 - 0.349: 2 Chirality restraints: 1467 Sorted by residual: chirality pdb=" CA LEU A 49 " pdb=" N LEU A 49 " pdb=" C LEU A 49 " pdb=" CB LEU A 49 " both_signs ideal model delta sigma weight residual False 2.51 2.86 -0.35 2.00e-01 2.50e+01 3.05e+00 chirality pdb=" CA LEU F 49 " pdb=" N LEU F 49 " pdb=" C LEU F 49 " pdb=" CB LEU F 49 " both_signs ideal model delta sigma weight residual False 2.51 2.85 -0.34 2.00e-01 2.50e+01 2.93e+00 chirality pdb=" CA LYS F 50 " pdb=" N LYS F 50 " pdb=" C LYS F 50 " pdb=" CB LYS F 50 " both_signs ideal model delta sigma weight residual False 2.51 2.77 -0.26 2.00e-01 2.50e+01 1.68e+00 ... (remaining 1464 not shown) Planarity restraints: 1672 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TYR F 48 " -0.018 2.00e-02 2.50e+03 3.77e-02 1.42e+01 pdb=" C TYR F 48 " 0.065 2.00e-02 2.50e+03 pdb=" O TYR F 48 " -0.025 2.00e-02 2.50e+03 pdb=" N LEU F 49 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA HIS F 350 " -0.010 2.00e-02 2.50e+03 2.02e-02 4.06e+00 pdb=" C HIS F 350 " 0.035 2.00e-02 2.50e+03 pdb=" O HIS F 350 " -0.013 2.00e-02 2.50e+03 pdb=" N ASP F 351 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR A 48 " 0.009 2.00e-02 2.50e+03 1.82e-02 3.32e+00 pdb=" C TYR A 48 " -0.032 2.00e-02 2.50e+03 pdb=" O TYR A 48 " 0.011 2.00e-02 2.50e+03 pdb=" N LEU A 49 " 0.011 2.00e-02 2.50e+03 ... (remaining 1669 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 1311 2.76 - 3.30: 8412 3.30 - 3.83: 14735 3.83 - 4.37: 17043 4.37 - 4.90: 31706 Nonbonded interactions: 73207 Sorted by model distance: nonbonded pdb=" OD1 ASP A 205 " pdb=" OH TYR A 209 " model vdw 2.228 3.040 nonbonded pdb=" OD1 ASP F 205 " pdb=" OH TYR F 209 " model vdw 2.230 3.040 nonbonded pdb=" OD2 ASP F 261 " pdb=" OH TYR F 273 " model vdw 2.267 3.040 nonbonded pdb=" OD2 ASP A 261 " pdb=" OH TYR A 273 " model vdw 2.270 3.040 nonbonded pdb=" NZ LYS F 293 " pdb=" OG1 THR F 299 " model vdw 2.277 3.120 ... (remaining 73202 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'F' } ncs_group { reference = chain 'B' selection = (chain 'D' and resid 5 through 121) } ncs_group { reference = chain 'C' selection = (chain 'E' and (resid 1 through 3 or (resid 4 and (name N or name CA or name C o \ r name O or name CB )) or resid 5 through 65 or (resid 66 and (name N or name CA \ or name C or name O or name CB )) or resid 67 through 107)) } ncs_group { reference = chain 'G' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 24.530 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: 0.020 Extract box with map and model: 0.380 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 25.230 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7786 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 : 0.005 0.109 9651 Z= 0.332 Angle : 0.718 12.689 13122 Z= 0.399 Chirality : 0.046 0.349 1467 Planarity : 0.004 0.045 1672 Dihedral : 13.272 88.326 3536 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 0.98 % Allowed : 0.59 % Favored : 98.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.76 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.23 (0.25), residues: 1163 helix: 2.76 (0.69), residues: 52 sheet: 0.66 (0.23), residues: 521 loop : -0.54 (0.26), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 50 HIS 0.003 0.001 HIS A 346 PHE 0.009 0.001 PHE A 116 TYR 0.010 0.001 TYR E 50 ARG 0.005 0.000 ARG A 406 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 124 time to evaluate : 1.003 Fit side-chains REVERT: A 350 HIS cc_start: 0.5562 (m90) cc_final: 0.5345 (m170) REVERT: B 76 ASP cc_start: 0.7148 (t0) cc_final: 0.6899 (t0) REVERT: D 76 ASP cc_start: 0.7074 (t0) cc_final: 0.6860 (t0) REVERT: F 52 ARG cc_start: 0.5797 (OUTLIER) cc_final: 0.4918 (mtp180) REVERT: F 351 ASP cc_start: 0.4956 (OUTLIER) cc_final: 0.4301 (t0) outliers start: 10 outliers final: 6 residues processed: 131 average time/residue: 0.2359 time to fit residues: 42.2515 Evaluate side-chains 106 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 98 time to evaluate : 1.029 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 295 LYS Chi-restraints excluded: chain A residue 351 ASP Chi-restraints excluded: chain C residue 101 GLN Chi-restraints excluded: chain E residue 101 GLN Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 52 ARG Chi-restraints excluded: chain F residue 351 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 97 optimal weight: 4.9990 chunk 87 optimal weight: 0.9990 chunk 48 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 90 optimal weight: 0.9990 chunk 35 optimal weight: 0.7980 chunk 55 optimal weight: 0.0470 chunk 67 optimal weight: 1.9990 chunk 105 optimal weight: 0.9980 overall best weight: 0.7682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 112 HIS A 160 HIS B 87 ASN F 112 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.160714 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.127704 restraints weight = 12915.452| |-----------------------------------------------------------------------------| r_work (start): 0.3522 rms_B_bonded: 2.78 r_work: 0.3296 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3296 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8050 moved from start: 0.1085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9651 Z= 0.215 Angle : 0.574 10.106 13122 Z= 0.296 Chirality : 0.045 0.150 1467 Planarity : 0.004 0.047 1672 Dihedral : 8.343 78.733 1377 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 1.56 % Allowed : 6.34 % Favored : 92.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.76 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.30 (0.25), residues: 1163 helix: 2.80 (0.69), residues: 54 sheet: 0.68 (0.23), residues: 514 loop : -0.45 (0.26), residues: 595 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 50 HIS 0.007 0.001 HIS F 199 PHE 0.011 0.002 PHE A 117 TYR 0.013 0.001 TYR F 273 ARG 0.004 0.000 ARG A 406 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 107 time to evaluate : 1.223 Fit side-chains REVERT: A 351 ASP cc_start: 0.6113 (OUTLIER) cc_final: 0.5810 (t70) REVERT: C 25 ARG cc_start: 0.8215 (tpt170) cc_final: 0.7922 (tpp-160) REVERT: E 25 ARG cc_start: 0.8227 (tpt170) cc_final: 0.7942 (tpp-160) REVERT: F 351 ASP cc_start: 0.5802 (OUTLIER) cc_final: 0.4923 (t0) outliers start: 16 outliers final: 12 residues processed: 114 average time/residue: 0.2451 time to fit residues: 40.2830 Evaluate side-chains 115 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 101 time to evaluate : 1.090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 HIS Chi-restraints excluded: chain A residue 200 LEU Chi-restraints excluded: chain A residue 260 ASP Chi-restraints excluded: chain A residue 351 ASP Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain C residue 101 GLN Chi-restraints excluded: chain D residue 117 THR Chi-restraints excluded: chain E residue 4 GLN Chi-restraints excluded: chain E residue 101 GLN Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 51 ASP Chi-restraints excluded: chain F residue 190 HIS Chi-restraints excluded: chain F residue 200 LEU Chi-restraints excluded: chain F residue 351 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 15 optimal weight: 10.0000 chunk 47 optimal weight: 0.4980 chunk 107 optimal weight: 2.9990 chunk 60 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 18 optimal weight: 5.9990 chunk 38 optimal weight: 0.8980 chunk 84 optimal weight: 4.9990 chunk 51 optimal weight: 0.8980 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 112 HIS B 87 ASN F 112 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.151100 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.120901 restraints weight = 12702.795| |-----------------------------------------------------------------------------| r_work (start): 0.3423 rms_B_bonded: 2.33 r_work: 0.3213 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3213 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 moved from start: 0.1348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 9651 Z= 0.307 Angle : 0.594 12.135 13122 Z= 0.304 Chirality : 0.045 0.161 1467 Planarity : 0.005 0.045 1672 Dihedral : 8.068 78.205 1367 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 2.24 % Allowed : 8.68 % Favored : 89.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.76 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.20 (0.25), residues: 1163 helix: 2.70 (0.69), residues: 54 sheet: 0.49 (0.22), residues: 550 loop : -0.43 (0.27), residues: 559 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 50 HIS 0.007 0.001 HIS A 199 PHE 0.014 0.002 PHE A 117 TYR 0.014 0.002 TYR C 92 ARG 0.003 0.000 ARG A 406 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 98 time to evaluate : 0.976 Fit side-chains REVERT: F 351 ASP cc_start: 0.6273 (OUTLIER) cc_final: 0.5306 (t0) outliers start: 23 outliers final: 16 residues processed: 110 average time/residue: 0.2142 time to fit residues: 33.5314 Evaluate side-chains 115 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 98 time to evaluate : 1.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 HIS Chi-restraints excluded: chain A residue 200 LEU Chi-restraints excluded: chain A residue 260 ASP Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain A residue 351 ASP Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain C residue 101 GLN Chi-restraints excluded: chain D residue 117 THR Chi-restraints excluded: chain E residue 43 LYS Chi-restraints excluded: chain E residue 101 GLN Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 51 ASP Chi-restraints excluded: chain F residue 190 HIS Chi-restraints excluded: chain F residue 200 LEU Chi-restraints excluded: chain F residue 260 ASP Chi-restraints excluded: chain F residue 306 ILE Chi-restraints excluded: chain F residue 351 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 30 optimal weight: 0.7980 chunk 66 optimal weight: 0.5980 chunk 84 optimal weight: 0.9990 chunk 92 optimal weight: 1.9990 chunk 1 optimal weight: 0.6980 chunk 65 optimal weight: 3.9990 chunk 32 optimal weight: 2.9990 chunk 67 optimal weight: 0.7980 chunk 56 optimal weight: 0.8980 chunk 4 optimal weight: 2.9990 chunk 115 optimal weight: 6.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 112 HIS A 350 HIS F 112 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.152253 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.122618 restraints weight = 12592.114| |-----------------------------------------------------------------------------| r_work (start): 0.3456 rms_B_bonded: 2.26 r_work: 0.3246 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3246 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8081 moved from start: 0.1500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9651 Z= 0.208 Angle : 0.530 10.578 13122 Z= 0.273 Chirality : 0.043 0.146 1467 Planarity : 0.004 0.046 1672 Dihedral : 7.855 77.005 1367 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer: Outliers : 2.44 % Allowed : 10.73 % Favored : 86.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.76 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.23 (0.25), residues: 1163 helix: 2.77 (0.70), residues: 54 sheet: 0.53 (0.22), residues: 550 loop : -0.43 (0.27), residues: 559 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 50 HIS 0.008 0.001 HIS A 350 PHE 0.012 0.001 PHE A 116 TYR 0.010 0.001 TYR B 98 ARG 0.004 0.000 ARG E 25 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 103 time to evaluate : 1.009 Fit side-chains REVERT: A 351 ASP cc_start: 0.6178 (OUTLIER) cc_final: 0.5730 (t70) REVERT: F 230 LYS cc_start: 0.8089 (ttpt) cc_final: 0.7814 (mmmm) REVERT: F 351 ASP cc_start: 0.6396 (OUTLIER) cc_final: 0.5597 (t0) outliers start: 25 outliers final: 18 residues processed: 117 average time/residue: 0.2156 time to fit residues: 35.7200 Evaluate side-chains 117 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 97 time to evaluate : 0.997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 HIS Chi-restraints excluded: chain A residue 200 LEU Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain A residue 351 ASP Chi-restraints excluded: chain B residue 93 ASP Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 101 GLN Chi-restraints excluded: chain D residue 117 THR Chi-restraints excluded: chain E residue 4 GLN Chi-restraints excluded: chain E residue 98 THR Chi-restraints excluded: chain E residue 101 GLN Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 51 ASP Chi-restraints excluded: chain F residue 190 HIS Chi-restraints excluded: chain F residue 200 LEU Chi-restraints excluded: chain F residue 260 ASP Chi-restraints excluded: chain F residue 306 ILE Chi-restraints excluded: chain F residue 351 ASP Chi-restraints excluded: chain G residue 352 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 64 optimal weight: 3.9990 chunk 50 optimal weight: 0.9990 chunk 44 optimal weight: 2.9990 chunk 83 optimal weight: 3.9990 chunk 100 optimal weight: 0.9990 chunk 11 optimal weight: 0.7980 chunk 68 optimal weight: 1.9990 chunk 104 optimal weight: 0.8980 chunk 19 optimal weight: 2.9990 chunk 56 optimal weight: 0.6980 chunk 90 optimal weight: 1.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 112 HIS A 160 HIS B 87 ASN F 112 HIS F 211 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.151557 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.122114 restraints weight = 12678.887| |-----------------------------------------------------------------------------| r_work (start): 0.3452 rms_B_bonded: 2.26 r_work: 0.3239 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3239 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 0.1623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 9651 Z= 0.230 Angle : 0.539 10.290 13122 Z= 0.277 Chirality : 0.044 0.151 1467 Planarity : 0.004 0.045 1672 Dihedral : 7.746 76.344 1367 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.67 % Favored : 94.33 % Rotamer: Outliers : 2.05 % Allowed : 11.71 % Favored : 86.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.76 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.24 (0.25), residues: 1163 helix: 2.79 (0.70), residues: 54 sheet: 0.58 (0.22), residues: 552 loop : -0.50 (0.26), residues: 557 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 50 HIS 0.006 0.001 HIS A 199 PHE 0.012 0.001 PHE A 116 TYR 0.011 0.001 TYR B 98 ARG 0.004 0.000 ARG E 25 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 92 time to evaluate : 1.011 Fit side-chains REVERT: A 351 ASP cc_start: 0.6212 (OUTLIER) cc_final: 0.5795 (t70) REVERT: F 230 LYS cc_start: 0.8079 (ttpt) cc_final: 0.7798 (mmmm) outliers start: 21 outliers final: 17 residues processed: 102 average time/residue: 0.2145 time to fit residues: 31.1134 Evaluate side-chains 110 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 92 time to evaluate : 1.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 HIS Chi-restraints excluded: chain A residue 200 LEU Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain A residue 351 ASP Chi-restraints excluded: chain B residue 93 ASP Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 101 GLN Chi-restraints excluded: chain D residue 117 THR Chi-restraints excluded: chain E residue 4 GLN Chi-restraints excluded: chain E residue 98 THR Chi-restraints excluded: chain E residue 101 GLN Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 51 ASP Chi-restraints excluded: chain F residue 190 HIS Chi-restraints excluded: chain F residue 200 LEU Chi-restraints excluded: chain F residue 306 ILE Chi-restraints excluded: chain G residue 352 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 91 optimal weight: 0.6980 chunk 5 optimal weight: 2.9990 chunk 94 optimal weight: 0.9990 chunk 81 optimal weight: 5.9990 chunk 114 optimal weight: 6.9990 chunk 50 optimal weight: 0.9980 chunk 111 optimal weight: 0.5980 chunk 4 optimal weight: 3.9990 chunk 45 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 83 optimal weight: 4.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 112 HIS B 87 ASN F 112 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.150824 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.120893 restraints weight = 12564.851| |-----------------------------------------------------------------------------| r_work (start): 0.3422 rms_B_bonded: 2.33 r_work: 0.3212 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3212 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 moved from start: 0.1725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 9651 Z= 0.264 Angle : 0.553 10.182 13122 Z= 0.284 Chirality : 0.044 0.153 1467 Planarity : 0.004 0.046 1672 Dihedral : 7.605 75.607 1365 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.67 % Favored : 94.33 % Rotamer: Outliers : 2.44 % Allowed : 12.00 % Favored : 85.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.76 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.21 (0.25), residues: 1163 helix: 2.73 (0.69), residues: 54 sheet: 0.56 (0.22), residues: 552 loop : -0.50 (0.26), residues: 557 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 50 HIS 0.007 0.001 HIS A 199 PHE 0.014 0.002 PHE A 117 TYR 0.012 0.001 TYR B 98 ARG 0.005 0.000 ARG C 25 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 96 time to evaluate : 1.000 Fit side-chains REVERT: F 230 LYS cc_start: 0.8087 (ttpt) cc_final: 0.7810 (mmmm) outliers start: 25 outliers final: 18 residues processed: 112 average time/residue: 0.2118 time to fit residues: 34.0269 Evaluate side-chains 114 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 96 time to evaluate : 0.977 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 HIS Chi-restraints excluded: chain A residue 200 LEU Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain B residue 93 ASP Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 101 GLN Chi-restraints excluded: chain D residue 93 ASP Chi-restraints excluded: chain D residue 117 THR Chi-restraints excluded: chain E residue 4 GLN Chi-restraints excluded: chain E residue 98 THR Chi-restraints excluded: chain E residue 101 GLN Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 190 HIS Chi-restraints excluded: chain F residue 200 LEU Chi-restraints excluded: chain F residue 306 ILE Chi-restraints excluded: chain F residue 393 THR Chi-restraints excluded: chain G residue 352 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 54 optimal weight: 3.9990 chunk 63 optimal weight: 3.9990 chunk 42 optimal weight: 1.9990 chunk 114 optimal weight: 6.9990 chunk 29 optimal weight: 2.9990 chunk 107 optimal weight: 0.8980 chunk 81 optimal weight: 4.9990 chunk 24 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 38 optimal weight: 0.9990 chunk 65 optimal weight: 2.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 112 HIS A 122 GLN B 87 ASN F 112 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.148905 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.118742 restraints weight = 12722.228| |-----------------------------------------------------------------------------| r_work (start): 0.3394 rms_B_bonded: 2.34 r_work: 0.3179 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3179 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8158 moved from start: 0.1884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.040 9651 Z= 0.408 Angle : 0.636 10.987 13122 Z= 0.326 Chirality : 0.047 0.237 1467 Planarity : 0.005 0.049 1672 Dihedral : 7.683 75.565 1363 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.28 % Favored : 93.64 % Rotamer: Outliers : 2.54 % Allowed : 12.59 % Favored : 84.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.76 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.04 (0.25), residues: 1163 helix: 2.50 (0.67), residues: 54 sheet: 0.46 (0.23), residues: 540 loop : -0.59 (0.26), residues: 569 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 50 HIS 0.009 0.001 HIS A 199 PHE 0.016 0.002 PHE A 117 TYR 0.017 0.002 TYR C 92 ARG 0.004 0.000 ARG C 25 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 99 time to evaluate : 1.821 Fit side-chains REVERT: F 230 LYS cc_start: 0.8143 (ttpt) cc_final: 0.7897 (mmmm) outliers start: 26 outliers final: 24 residues processed: 113 average time/residue: 0.2702 time to fit residues: 43.4561 Evaluate side-chains 120 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 96 time to evaluate : 1.745 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 HIS Chi-restraints excluded: chain A residue 200 LEU Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain B residue 93 ASP Chi-restraints excluded: chain B residue 111 ASP Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 101 GLN Chi-restraints excluded: chain D residue 56 SER Chi-restraints excluded: chain D residue 93 ASP Chi-restraints excluded: chain D residue 111 ASP Chi-restraints excluded: chain D residue 117 THR Chi-restraints excluded: chain E residue 4 GLN Chi-restraints excluded: chain E residue 79 LEU Chi-restraints excluded: chain E residue 98 THR Chi-restraints excluded: chain E residue 101 GLN Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 51 ASP Chi-restraints excluded: chain F residue 190 HIS Chi-restraints excluded: chain F residue 200 LEU Chi-restraints excluded: chain F residue 306 ILE Chi-restraints excluded: chain F residue 329 VAL Chi-restraints excluded: chain F residue 393 THR Chi-restraints excluded: chain G residue 352 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 52 optimal weight: 0.8980 chunk 33 optimal weight: 0.6980 chunk 36 optimal weight: 3.9990 chunk 97 optimal weight: 0.9990 chunk 98 optimal weight: 0.6980 chunk 103 optimal weight: 3.9990 chunk 14 optimal weight: 3.9990 chunk 40 optimal weight: 0.5980 chunk 31 optimal weight: 0.5980 chunk 45 optimal weight: 0.6980 chunk 108 optimal weight: 3.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 112 HIS B 87 ASN F 112 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.151481 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.121780 restraints weight = 12735.357| |-----------------------------------------------------------------------------| r_work (start): 0.3445 rms_B_bonded: 2.28 r_work: 0.3228 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3228 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8101 moved from start: 0.1873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9651 Z= 0.198 Angle : 0.537 9.519 13122 Z= 0.275 Chirality : 0.043 0.191 1467 Planarity : 0.004 0.049 1672 Dihedral : 7.482 74.470 1363 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.76 % Favored : 94.24 % Rotamer: Outliers : 2.44 % Allowed : 12.88 % Favored : 84.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.76 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.18 (0.25), residues: 1163 helix: 2.73 (0.69), residues: 54 sheet: 0.56 (0.23), residues: 540 loop : -0.53 (0.26), residues: 569 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 50 HIS 0.005 0.001 HIS F 199 PHE 0.012 0.001 PHE A 116 TYR 0.010 0.001 TYR B 98 ARG 0.002 0.000 ARG C 25 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 95 time to evaluate : 2.075 Fit side-chains REVERT: B 5 VAL cc_start: 0.7998 (t) cc_final: 0.7691 (p) REVERT: F 51 ASP cc_start: 0.5814 (OUTLIER) cc_final: 0.5534 (p0) REVERT: F 230 LYS cc_start: 0.8100 (ttpt) cc_final: 0.7861 (mmmm) outliers start: 25 outliers final: 22 residues processed: 110 average time/residue: 0.2735 time to fit residues: 43.3605 Evaluate side-chains 116 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 93 time to evaluate : 1.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 HIS Chi-restraints excluded: chain A residue 200 LEU Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain B residue 93 ASP Chi-restraints excluded: chain B residue 94 THR Chi-restraints excluded: chain B residue 111 ASP Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 101 GLN Chi-restraints excluded: chain D residue 93 ASP Chi-restraints excluded: chain D residue 94 THR Chi-restraints excluded: chain D residue 117 THR Chi-restraints excluded: chain E residue 4 GLN Chi-restraints excluded: chain E residue 98 THR Chi-restraints excluded: chain E residue 101 GLN Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 51 ASP Chi-restraints excluded: chain F residue 59 THR Chi-restraints excluded: chain F residue 190 HIS Chi-restraints excluded: chain F residue 200 LEU Chi-restraints excluded: chain F residue 306 ILE Chi-restraints excluded: chain F residue 393 THR Chi-restraints excluded: chain G residue 352 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 55 optimal weight: 2.9990 chunk 73 optimal weight: 2.9990 chunk 69 optimal weight: 4.9990 chunk 16 optimal weight: 1.9990 chunk 46 optimal weight: 0.8980 chunk 81 optimal weight: 5.9990 chunk 94 optimal weight: 1.9990 chunk 26 optimal weight: 0.6980 chunk 49 optimal weight: 3.9990 chunk 108 optimal weight: 4.9990 chunk 91 optimal weight: 0.0370 overall best weight: 1.1262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 112 HIS B 87 ASN D 87 ASN F 112 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.150216 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.120155 restraints weight = 12615.967| |-----------------------------------------------------------------------------| r_work (start): 0.3425 rms_B_bonded: 2.34 r_work: 0.3210 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3210 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8127 moved from start: 0.1924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 9651 Z= 0.278 Angle : 0.576 10.078 13122 Z= 0.293 Chirality : 0.044 0.171 1467 Planarity : 0.004 0.046 1672 Dihedral : 7.463 74.124 1363 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.76 % Favored : 94.24 % Rotamer: Outliers : 2.63 % Allowed : 12.59 % Favored : 84.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.76 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.13 (0.25), residues: 1163 helix: 2.67 (0.69), residues: 54 sheet: 0.51 (0.23), residues: 540 loop : -0.54 (0.26), residues: 569 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 50 HIS 0.006 0.001 HIS A 199 PHE 0.013 0.002 PHE A 117 TYR 0.013 0.002 TYR B 98 ARG 0.003 0.000 ARG C 25 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 94 time to evaluate : 1.033 Fit side-chains REVERT: B 5 VAL cc_start: 0.7900 (t) cc_final: 0.7642 (p) REVERT: F 51 ASP cc_start: 0.5872 (OUTLIER) cc_final: 0.5594 (p0) REVERT: F 230 LYS cc_start: 0.8114 (ttpt) cc_final: 0.7868 (mmmm) outliers start: 27 outliers final: 25 residues processed: 111 average time/residue: 0.2095 time to fit residues: 33.3694 Evaluate side-chains 120 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 94 time to evaluate : 0.948 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 HIS Chi-restraints excluded: chain A residue 200 LEU Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain B residue 56 SER Chi-restraints excluded: chain B residue 93 ASP Chi-restraints excluded: chain B residue 94 THR Chi-restraints excluded: chain B residue 111 ASP Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 101 GLN Chi-restraints excluded: chain D residue 93 ASP Chi-restraints excluded: chain D residue 111 ASP Chi-restraints excluded: chain D residue 117 THR Chi-restraints excluded: chain E residue 4 GLN Chi-restraints excluded: chain E residue 98 THR Chi-restraints excluded: chain E residue 101 GLN Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 51 ASP Chi-restraints excluded: chain F residue 59 THR Chi-restraints excluded: chain F residue 190 HIS Chi-restraints excluded: chain F residue 200 LEU Chi-restraints excluded: chain F residue 306 ILE Chi-restraints excluded: chain F residue 329 VAL Chi-restraints excluded: chain F residue 393 THR Chi-restraints excluded: chain G residue 352 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 83 optimal weight: 4.9990 chunk 63 optimal weight: 3.9990 chunk 98 optimal weight: 1.9990 chunk 105 optimal weight: 0.9990 chunk 47 optimal weight: 0.8980 chunk 60 optimal weight: 3.9990 chunk 107 optimal weight: 0.9990 chunk 9 optimal weight: 1.9990 chunk 115 optimal weight: 7.9990 chunk 77 optimal weight: 0.7980 chunk 45 optimal weight: 0.6980 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 112 HIS B 87 ASN F 112 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.150999 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.121218 restraints weight = 12703.448| |-----------------------------------------------------------------------------| r_work (start): 0.3439 rms_B_bonded: 2.28 r_work: 0.3224 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3224 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 moved from start: 0.1967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 9651 Z= 0.233 Angle : 0.555 9.653 13122 Z= 0.283 Chirality : 0.043 0.162 1467 Planarity : 0.004 0.046 1672 Dihedral : 7.343 73.338 1363 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.28 % Favored : 93.72 % Rotamer: Outliers : 2.63 % Allowed : 12.59 % Favored : 84.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.76 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (0.25), residues: 1163 helix: 2.75 (0.69), residues: 54 sheet: 0.54 (0.23), residues: 540 loop : -0.53 (0.26), residues: 569 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 50 HIS 0.006 0.001 HIS A 199 PHE 0.012 0.001 PHE A 116 TYR 0.011 0.001 TYR B 98 ARG 0.003 0.000 ARG C 25 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 94 time to evaluate : 1.521 Fit side-chains REVERT: B 5 VAL cc_start: 0.7968 (t) cc_final: 0.7693 (p) REVERT: F 51 ASP cc_start: 0.5931 (OUTLIER) cc_final: 0.5656 (p0) REVERT: F 230 LYS cc_start: 0.8102 (ttpt) cc_final: 0.7859 (mmmm) outliers start: 27 outliers final: 25 residues processed: 111 average time/residue: 0.2686 time to fit residues: 42.0716 Evaluate side-chains 120 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 94 time to evaluate : 1.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 HIS Chi-restraints excluded: chain A residue 200 LEU Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain B residue 93 ASP Chi-restraints excluded: chain B residue 94 THR Chi-restraints excluded: chain B residue 111 ASP Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 101 GLN Chi-restraints excluded: chain D residue 93 ASP Chi-restraints excluded: chain D residue 94 THR Chi-restraints excluded: chain D residue 111 ASP Chi-restraints excluded: chain D residue 117 THR Chi-restraints excluded: chain E residue 4 GLN Chi-restraints excluded: chain E residue 98 THR Chi-restraints excluded: chain E residue 101 GLN Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 51 ASP Chi-restraints excluded: chain F residue 59 THR Chi-restraints excluded: chain F residue 190 HIS Chi-restraints excluded: chain F residue 200 LEU Chi-restraints excluded: chain F residue 306 ILE Chi-restraints excluded: chain F residue 329 VAL Chi-restraints excluded: chain F residue 393 THR Chi-restraints excluded: chain G residue 352 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 23 optimal weight: 3.9990 chunk 15 optimal weight: 10.0000 chunk 47 optimal weight: 0.7980 chunk 51 optimal weight: 1.9990 chunk 59 optimal weight: 0.7980 chunk 78 optimal weight: 5.9990 chunk 70 optimal weight: 0.7980 chunk 30 optimal weight: 0.0010 chunk 71 optimal weight: 0.5980 chunk 25 optimal weight: 1.9990 chunk 87 optimal weight: 0.0170 overall best weight: 0.4424 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 112 HIS A 211 HIS B 87 ASN ** C 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 87 ASN ** E 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 112 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.152852 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.122707 restraints weight = 12611.045| |-----------------------------------------------------------------------------| r_work (start): 0.3458 rms_B_bonded: 2.37 r_work: 0.3241 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3241 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 moved from start: 0.1992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 9651 Z= 0.160 Angle : 0.518 8.880 13122 Z= 0.263 Chirality : 0.042 0.164 1467 Planarity : 0.004 0.046 1672 Dihedral : 7.051 71.963 1363 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 2.54 % Allowed : 12.78 % Favored : 84.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.76 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.30 (0.25), residues: 1163 helix: 2.91 (0.70), residues: 54 sheet: 0.57 (0.22), residues: 558 loop : -0.42 (0.27), residues: 551 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 36 HIS 0.004 0.001 HIS F 199 PHE 0.012 0.001 PHE A 116 TYR 0.008 0.001 TYR C 50 ARG 0.002 0.000 ARG C 25 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4724.27 seconds wall clock time: 85 minutes 38.62 seconds (5138.62 seconds total)