Starting phenix.real_space_refine on Wed Jan 22 01:08:42 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8rt9_19483/01_2025/8rt9_19483.cif Found real_map, /net/cci-nas-00/data/ceres_data/8rt9_19483/01_2025/8rt9_19483.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.97 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8rt9_19483/01_2025/8rt9_19483.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8rt9_19483/01_2025/8rt9_19483.map" model { file = "/net/cci-nas-00/data/ceres_data/8rt9_19483/01_2025/8rt9_19483.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8rt9_19483/01_2025/8rt9_19483.cif" } resolution = 2.97 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= 0.007 sd= 0.033 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 11349 2.51 5 N 3083 2.21 5 O 3374 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 63 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 17866 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 1599 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 1599 Classifications: {'peptide': 207} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 3, 'TRANS': 203} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2} Unresolved non-hydrogen planarities: 8 Chain: "B" Number of atoms: 1599 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 1599 Classifications: {'peptide': 207} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 3, 'TRANS': 203} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2} Unresolved non-hydrogen planarities: 8 Chain: "C" Number of atoms: 1599 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 1599 Classifications: {'peptide': 207} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 3, 'TRANS': 203} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2} Unresolved non-hydrogen planarities: 8 Chain: "D" Number of atoms: 1599 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 1599 Classifications: {'peptide': 207} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 3, 'TRANS': 203} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2} Unresolved non-hydrogen planarities: 8 Chain: "E" Number of atoms: 1599 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 1599 Classifications: {'peptide': 207} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 3, 'TRANS': 203} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2} Unresolved non-hydrogen planarities: 8 Chain: "F" Number of atoms: 1963 Number of conformers: 1 Conformer: "A" Number of residues, atoms: 272, 1963 Classifications: {'peptide': 272} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 8, 'TRANS': 263} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 52 Unresolved non-hydrogen angles: 66 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 5, 'GLU:plan': 1, 'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 35 Chain: "G" Number of atoms: 1977 Number of conformers: 1 Conformer: "A" Number of residues, atoms: 272, 1977 Classifications: {'peptide': 272} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 8, 'TRANS': 263} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 29 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 1, 'ARG:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 24 Chain: "H" Number of atoms: 1977 Number of conformers: 1 Conformer: "A" Number of residues, atoms: 272, 1977 Classifications: {'peptide': 272} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 8, 'TRANS': 263} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 29 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 1, 'ARG:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 24 Chain: "I" Number of atoms: 1977 Number of conformers: 1 Conformer: "A" Number of residues, atoms: 272, 1977 Classifications: {'peptide': 272} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 8, 'TRANS': 263} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 29 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 1, 'ARG:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 24 Chain: "J" Number of atoms: 1977 Number of conformers: 1 Conformer: "A" Number of residues, atoms: 272, 1977 Classifications: {'peptide': 272} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 8, 'TRANS': 263} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 29 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 1, 'ARG:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 24 Time building chain proxies: 12.92, per 1000 atoms: 0.72 Number of scatterers: 17866 At special positions: 0 Unit cell: (109.901, 107.767, 234.74, 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 3374 8.00 N 3083 7.00 C 11349 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.69 Conformation dependent library (CDL) restraints added in 2.3 seconds 4750 Ramachandran restraints generated. 2375 Oldfield, 0 Emsley, 2375 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4310 Finding SS restraints... Secondary structure from input PDB file: 74 helices and 0 sheets defined 83.9% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.33 Creating SS restraints... Processing helix chain 'A' and resid 29 through 65 removed outlier: 3.635A pdb=" N ALA A 33 " --> pdb=" O ASP A 29 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N LEU A 34 " --> pdb=" O GLY A 30 " (cutoff:3.500A) Processing helix chain 'A' and resid 78 through 83 removed outlier: 3.505A pdb=" N GLU A 81 " --> pdb=" O GLN A 78 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEU A 83 " --> pdb=" O ARG A 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 89 through 93 removed outlier: 3.748A pdb=" N SER A 93 " --> pdb=" O VAL A 90 " (cutoff:3.500A) Processing helix chain 'A' and resid 99 through 113 removed outlier: 3.783A pdb=" N GLY A 104 " --> pdb=" O SER A 100 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N SER A 105 " --> pdb=" O GLY A 101 " (cutoff:3.500A) Processing helix chain 'A' and resid 118 through 163 Processing helix chain 'A' and resid 167 through 219 removed outlier: 3.529A pdb=" N ILE A 171 " --> pdb=" O ASP A 167 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 65 removed outlier: 3.636A pdb=" N ALA B 33 " --> pdb=" O ASP B 29 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N LEU B 34 " --> pdb=" O GLY B 30 " (cutoff:3.500A) Processing helix chain 'B' and resid 78 through 83 removed outlier: 3.504A pdb=" N GLU B 81 " --> pdb=" O GLN B 78 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LEU B 83 " --> pdb=" O ARG B 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 89 through 93 removed outlier: 3.747A pdb=" N SER B 93 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing helix chain 'B' and resid 99 through 113 removed outlier: 3.783A pdb=" N GLY B 104 " --> pdb=" O SER B 100 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N SER B 105 " --> pdb=" O GLY B 101 " (cutoff:3.500A) Processing helix chain 'B' and resid 118 through 165 removed outlier: 3.511A pdb=" N SER B 163 " --> pdb=" O MET B 159 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ARG B 164 " --> pdb=" O ASP B 160 " (cutoff:3.500A) Processing helix chain 'B' and resid 167 through 219 removed outlier: 3.528A pdb=" N ILE B 171 " --> pdb=" O ASP B 167 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 65 removed outlier: 3.635A pdb=" N ALA C 33 " --> pdb=" O ASP C 29 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N LEU C 34 " --> pdb=" O GLY C 30 " (cutoff:3.500A) Processing helix chain 'C' and resid 78 through 83 removed outlier: 3.504A pdb=" N GLU C 81 " --> pdb=" O GLN C 78 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LEU C 83 " --> pdb=" O ARG C 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 89 through 93 removed outlier: 3.747A pdb=" N SER C 93 " --> pdb=" O VAL C 90 " (cutoff:3.500A) Processing helix chain 'C' and resid 99 through 113 removed outlier: 4.015A pdb=" N GLY C 104 " --> pdb=" O SER C 100 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N SER C 105 " --> pdb=" O GLY C 101 " (cutoff:3.500A) Processing helix chain 'C' and resid 118 through 163 removed outlier: 3.601A pdb=" N SER C 163 " --> pdb=" O MET C 159 " (cutoff:3.500A) Processing helix chain 'C' and resid 167 through 219 removed outlier: 3.528A pdb=" N ILE C 171 " --> pdb=" O ASP C 167 " (cutoff:3.500A) Processing helix chain 'D' and resid 29 through 65 removed outlier: 3.634A pdb=" N ALA D 33 " --> pdb=" O ASP D 29 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N LEU D 34 " --> pdb=" O GLY D 30 " (cutoff:3.500A) Processing helix chain 'D' and resid 78 through 83 removed outlier: 3.504A pdb=" N GLU D 81 " --> pdb=" O GLN D 78 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEU D 83 " --> pdb=" O ARG D 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 89 through 93 removed outlier: 3.747A pdb=" N SER D 93 " --> pdb=" O VAL D 90 " (cutoff:3.500A) Processing helix chain 'D' and resid 99 through 113 removed outlier: 3.533A pdb=" N GLY D 104 " --> pdb=" O SER D 100 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N SER D 105 " --> pdb=" O GLY D 101 " (cutoff:3.500A) Processing helix chain 'D' and resid 118 through 164 removed outlier: 3.689A pdb=" N SER D 163 " --> pdb=" O MET D 159 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N ARG D 164 " --> pdb=" O ASP D 160 " (cutoff:3.500A) Processing helix chain 'D' and resid 167 through 219 removed outlier: 3.528A pdb=" N ILE D 171 " --> pdb=" O ASP D 167 " (cutoff:3.500A) Processing helix chain 'E' and resid 29 through 65 removed outlier: 3.635A pdb=" N ALA E 33 " --> pdb=" O ASP E 29 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N LEU E 34 " --> pdb=" O GLY E 30 " (cutoff:3.500A) Processing helix chain 'E' and resid 78 through 83 removed outlier: 3.505A pdb=" N GLU E 81 " --> pdb=" O GLN E 78 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LEU E 83 " --> pdb=" O ARG E 80 " (cutoff:3.500A) Processing helix chain 'E' and resid 89 through 93 removed outlier: 3.747A pdb=" N SER E 93 " --> pdb=" O VAL E 90 " (cutoff:3.500A) Processing helix chain 'E' and resid 99 through 113 removed outlier: 3.500A pdb=" N GLY E 104 " --> pdb=" O SER E 100 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N SER E 105 " --> pdb=" O GLY E 101 " (cutoff:3.500A) Processing helix chain 'E' and resid 118 through 163 removed outlier: 3.716A pdb=" N SER E 163 " --> pdb=" O MET E 159 " (cutoff:3.500A) Processing helix chain 'E' and resid 167 through 219 removed outlier: 3.529A pdb=" N ILE E 171 " --> pdb=" O ASP E 167 " (cutoff:3.500A) Processing helix chain 'F' and resid 5 through 22 Processing helix chain 'F' and resid 22 through 53 Proline residue: F 34 - end of helix Processing helix chain 'F' and resid 61 through 80 Processing helix chain 'F' and resid 82 through 101 removed outlier: 3.734A pdb=" N GLU F 86 " --> pdb=" O LEU F 82 " (cutoff:3.500A) Proline residue: F 95 - end of helix removed outlier: 3.948A pdb=" N SER F 100 " --> pdb=" O ASP F 96 " (cutoff:3.500A) Processing helix chain 'F' and resid 111 through 137 Processing helix chain 'F' and resid 141 through 185 Proline residue: F 181 - end of helix Processing helix chain 'F' and resid 186 through 188 No H-bonds generated for 'chain 'F' and resid 186 through 188' Processing helix chain 'F' and resid 189 through 191 No H-bonds generated for 'chain 'F' and resid 189 through 191' Processing helix chain 'F' and resid 192 through 231 removed outlier: 3.805A pdb=" N PHE F 196 " --> pdb=" O ATHR F 192 " (cutoff:3.500A) Processing helix chain 'F' and resid 238 through 271 removed outlier: 3.582A pdb=" N LEU F 260 " --> pdb=" O LEU F 256 " (cutoff:3.500A) Proline residue: F 261 - end of helix Processing helix chain 'G' and resid 5 through 20 Processing helix chain 'G' and resid 20 through 53 removed outlier: 3.512A pdb=" N SER G 25 " --> pdb=" O VAL G 21 " (cutoff:3.500A) Proline residue: G 34 - end of helix Processing helix chain 'G' and resid 61 through 79 Processing helix chain 'G' and resid 82 through 101 removed outlier: 3.794A pdb=" N GLU G 86 " --> pdb=" O LEU G 82 " (cutoff:3.500A) Proline residue: G 95 - end of helix removed outlier: 4.084A pdb=" N SER G 100 " --> pdb=" O ASP G 96 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ALA G 101 " --> pdb=" O GLU G 97 " (cutoff:3.500A) Processing helix chain 'G' and resid 111 through 137 Processing helix chain 'G' and resid 141 through 185 Proline residue: G 181 - end of helix Processing helix chain 'G' and resid 186 through 188 No H-bonds generated for 'chain 'G' and resid 186 through 188' Processing helix chain 'G' and resid 192 through 231 removed outlier: 3.793A pdb=" N PHE G 196 " --> pdb=" O ATHR G 192 " (cutoff:3.500A) Processing helix chain 'G' and resid 238 through 271 removed outlier: 3.589A pdb=" N LEU G 260 " --> pdb=" O LEU G 256 " (cutoff:3.500A) Proline residue: G 261 - end of helix Processing helix chain 'H' and resid 5 through 53 removed outlier: 4.556A pdb=" N ASP H 23 " --> pdb=" O THR H 19 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ILE H 24 " --> pdb=" O TYR H 20 " (cutoff:3.500A) Proline residue: H 34 - end of helix Processing helix chain 'H' and resid 61 through 80 Processing helix chain 'H' and resid 82 through 101 removed outlier: 3.994A pdb=" N GLU H 86 " --> pdb=" O LEU H 82 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N VAL H 94 " --> pdb=" O ALA H 90 " (cutoff:3.500A) Proline residue: H 95 - end of helix removed outlier: 4.029A pdb=" N SER H 100 " --> pdb=" O ASP H 96 " (cutoff:3.500A) Processing helix chain 'H' and resid 111 through 137 Processing helix chain 'H' and resid 141 through 185 Proline residue: H 181 - end of helix Processing helix chain 'H' and resid 186 through 188 No H-bonds generated for 'chain 'H' and resid 186 through 188' Processing helix chain 'H' and resid 189 through 191 No H-bonds generated for 'chain 'H' and resid 189 through 191' Processing helix chain 'H' and resid 192 through 231 removed outlier: 3.811A pdb=" N PHE H 196 " --> pdb=" O ATHR H 192 " (cutoff:3.500A) Processing helix chain 'H' and resid 238 through 271 Proline residue: H 261 - end of helix Processing helix chain 'I' and resid 5 through 53 removed outlier: 3.806A pdb=" N THR I 22 " --> pdb=" O ALA I 18 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N ASP I 23 " --> pdb=" O THR I 19 " (cutoff:3.500A) Proline residue: I 34 - end of helix Processing helix chain 'I' and resid 61 through 79 Processing helix chain 'I' and resid 82 through 101 removed outlier: 4.014A pdb=" N GLU I 86 " --> pdb=" O LEU I 82 " (cutoff:3.500A) Proline residue: I 95 - end of helix removed outlier: 3.936A pdb=" N SER I 100 " --> pdb=" O ASP I 96 " (cutoff:3.500A) Processing helix chain 'I' and resid 111 through 137 Processing helix chain 'I' and resid 141 through 186 Proline residue: I 181 - end of helix Processing helix chain 'I' and resid 187 through 191 removed outlier: 5.275A pdb=" N GLN I 190 " --> pdb=" O LEU I 187 " (cutoff:3.500A) Proline residue: I 191 - end of helix No H-bonds generated for 'chain 'I' and resid 187 through 191' Processing helix chain 'I' and resid 192 through 230 removed outlier: 3.950A pdb=" N PHE I 196 " --> pdb=" O ATHR I 192 " (cutoff:3.500A) Processing helix chain 'I' and resid 238 through 271 Proline residue: I 261 - end of helix Processing helix chain 'J' and resid 5 through 21 Processing helix chain 'J' and resid 21 through 53 Proline residue: J 34 - end of helix Processing helix chain 'J' and resid 61 through 80 Processing helix chain 'J' and resid 82 through 101 removed outlier: 4.036A pdb=" N GLU J 86 " --> pdb=" O LEU J 82 " (cutoff:3.500A) Proline residue: J 95 - end of helix removed outlier: 3.991A pdb=" N SER J 100 " --> pdb=" O ASP J 96 " (cutoff:3.500A) Processing helix chain 'J' and resid 111 through 137 Processing helix chain 'J' and resid 141 through 186 Proline residue: J 181 - end of helix Processing helix chain 'J' and resid 192 through 230 removed outlier: 3.975A pdb=" N PHE J 196 " --> pdb=" O ATHR J 192 " (cutoff:3.500A) Processing helix chain 'J' and resid 238 through 271 Proline residue: J 261 - end of helix 1597 hydrogen bonds defined for protein. 4761 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: 5.47 Time building geometry restraints manager: 5.40 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: 4797 1.33 - 1.45: 3041 1.45 - 1.57: 10153 1.57 - 1.69: 0 1.69 - 1.81: 115 Bond restraints: 18106 Sorted by residual: bond pdb=" N PRO H 95 " pdb=" CD PRO H 95 " ideal model delta sigma weight residual 1.473 1.395 0.078 1.40e-02 5.10e+03 3.07e+01 bond pdb=" N THR H 33 " pdb=" CA THR H 33 " ideal model delta sigma weight residual 1.459 1.498 -0.038 1.04e-02 9.25e+03 1.37e+01 bond pdb=" N ILE B 102 " pdb=" CA ILE B 102 " ideal model delta sigma weight residual 1.460 1.496 -0.036 1.21e-02 6.83e+03 9.09e+00 bond pdb=" N THR A 165 " pdb=" CA THR A 165 " ideal model delta sigma weight residual 1.456 1.493 -0.037 1.23e-02 6.61e+03 9.09e+00 bond pdb=" N SER H 100 " pdb=" CA SER H 100 " ideal model delta sigma weight residual 1.458 1.485 -0.027 9.00e-03 1.23e+04 9.05e+00 ... (remaining 18101 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.54: 22951 1.54 - 3.09: 1347 3.09 - 4.63: 160 4.63 - 6.17: 46 6.17 - 7.71: 8 Bond angle restraints: 24512 Sorted by residual: angle pdb=" CA GLY B 71 " pdb=" C GLY B 71 " pdb=" O GLY B 71 " ideal model delta sigma weight residual 122.29 117.07 5.22 8.10e-01 1.52e+00 4.15e+01 angle pdb=" N GLY J 80 " pdb=" CA GLY J 80 " pdb=" C GLY J 80 " ideal model delta sigma weight residual 114.40 108.24 6.16 1.11e+00 8.12e-01 3.08e+01 angle pdb=" N GLY B 71 " pdb=" CA GLY B 71 " pdb=" C GLY B 71 " ideal model delta sigma weight residual 112.68 106.32 6.36 1.26e+00 6.30e-01 2.55e+01 angle pdb=" C THR I 19 " pdb=" N TYR I 20 " pdb=" CA TYR I 20 " ideal model delta sigma weight residual 121.71 114.87 6.84 1.39e+00 5.18e-01 2.42e+01 angle pdb=" N LEU H 102 " pdb=" CA LEU H 102 " pdb=" C LEU H 102 " ideal model delta sigma weight residual 114.12 107.30 6.82 1.39e+00 5.18e-01 2.41e+01 ... (remaining 24507 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.70: 9984 17.70 - 35.41: 660 35.41 - 53.11: 107 53.11 - 70.81: 31 70.81 - 88.52: 13 Dihedral angle restraints: 10795 sinusoidal: 4040 harmonic: 6755 Sorted by residual: dihedral pdb=" CA GLY D 71 " pdb=" C GLY D 71 " pdb=" N ASP D 72 " pdb=" CA ASP D 72 " ideal model delta harmonic sigma weight residual 180.00 -143.85 -36.15 0 5.00e+00 4.00e-02 5.23e+01 dihedral pdb=" CA GLY E 71 " pdb=" C GLY E 71 " pdb=" N ASP E 72 " pdb=" CA ASP E 72 " ideal model delta harmonic sigma weight residual -180.00 -143.89 -36.11 0 5.00e+00 4.00e-02 5.21e+01 dihedral pdb=" CA GLY A 71 " pdb=" C GLY A 71 " pdb=" N ASP A 72 " pdb=" CA ASP A 72 " ideal model delta harmonic sigma weight residual -180.00 -143.91 -36.09 0 5.00e+00 4.00e-02 5.21e+01 ... (remaining 10792 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.104: 2703 0.104 - 0.209: 162 0.209 - 0.313: 7 0.313 - 0.417: 1 0.417 - 0.521: 1 Chirality restraints: 2874 Sorted by residual: chirality pdb=" CA THR H 33 " pdb=" N THR H 33 " pdb=" C THR H 33 " pdb=" CB THR H 33 " both_signs ideal model delta sigma weight residual False 2.53 2.00 0.52 2.00e-01 2.50e+01 6.80e+00 chirality pdb=" CA LEU H 82 " pdb=" N LEU H 82 " pdb=" C LEU H 82 " pdb=" CB LEU H 82 " both_signs ideal model delta sigma weight residual False 2.51 2.83 -0.32 2.00e-01 2.50e+01 2.62e+00 chirality pdb=" CA LEU J 82 " pdb=" N LEU J 82 " pdb=" C LEU J 82 " pdb=" CB LEU J 82 " both_signs ideal model delta sigma weight residual False 2.51 2.80 -0.29 2.00e-01 2.50e+01 2.17e+00 ... (remaining 2871 not shown) Planarity restraints: 3202 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG B 68 " 0.012 2.00e-02 2.50e+03 2.34e-02 5.49e+00 pdb=" C ARG B 68 " -0.041 2.00e-02 2.50e+03 pdb=" O ARG B 68 " 0.015 2.00e-02 2.50e+03 pdb=" N GLY B 69 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA H 18 " 0.011 2.00e-02 2.50e+03 2.24e-02 5.00e+00 pdb=" C ALA H 18 " -0.039 2.00e-02 2.50e+03 pdb=" O ALA H 18 " 0.015 2.00e-02 2.50e+03 pdb=" N THR H 19 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA G 18 " 0.011 2.00e-02 2.50e+03 2.18e-02 4.77e+00 pdb=" C ALA G 18 " -0.038 2.00e-02 2.50e+03 pdb=" O ALA G 18 " 0.014 2.00e-02 2.50e+03 pdb=" N THR G 19 " 0.013 2.00e-02 2.50e+03 ... (remaining 3199 not shown) Histogram of nonbonded interaction distances: 2.37 - 2.88: 6669 2.88 - 3.38: 19560 3.38 - 3.89: 31039 3.89 - 4.39: 35013 4.39 - 4.90: 57982 Nonbonded interactions: 150263 Sorted by model distance: nonbonded pdb=" O ILE J 243 " pdb=" OG SER J 246 " model vdw 2.370 3.040 nonbonded pdb=" O GLU D 81 " pdb=" OH TYR D 99 " model vdw 2.390 3.040 nonbonded pdb=" O PRO F 34 " pdb=" OG SER F 37 " model vdw 2.394 3.040 nonbonded pdb=" OG SER A 220 " pdb=" OE1 GLU J 132 " model vdw 2.417 3.040 nonbonded pdb=" O ASN G 89 " pdb=" OG1 THR G 93 " model vdw 2.420 3.040 ... (remaining 150258 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 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' } ncs_group { reference = chain 'F' selection = (chain 'G' and (resid 2 through 116 or (resid 117 and (name N or name CA or name \ C or name O or name CB )) or resid 118 or (resid 119 through 122 and (name N or \ name CA or name C or name O or name CB )) or resid 123 through 154 or (resid 15 \ 5 and (name N or name CA or name C or name O or name CB )) or resid 156 through \ 273)) selection = (chain 'H' and (resid 2 through 116 or (resid 117 and (name N or name CA or name \ C or name O or name CB )) or resid 118 or (resid 119 through 122 and (name N or \ name CA or name C or name O or name CB )) or resid 123 through 154 or (resid 15 \ 5 and (name N or name CA or name C or name O or name CB )) or resid 156 through \ 273)) selection = (chain 'I' and (resid 2 through 116 or (resid 117 and (name N or name CA or name \ C or name O or name CB )) or resid 118 or (resid 119 through 122 and (name N or \ name CA or name C or name O or name CB )) or resid 123 through 154 or (resid 15 \ 5 and (name N or name CA or name C or name O or name CB )) or resid 156 through \ 273)) selection = (chain 'J' and (resid 2 through 116 or (resid 117 and (name N or name CA or name \ C or name O or name CB )) or resid 118 or (resid 119 through 122 and (name N or \ name CA or name C or name O or name CB )) or resid 123 through 154 or (resid 15 \ 5 and (name N or name CA or name C or name O or name CB )) or resid 156 through \ 273)) } 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: 16.300 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: 0.000 Extract box with map and model: 0.000 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 41.520 Find NCS groups from input model: 0.670 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 70.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8276 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 : 0.007 0.078 18106 Z= 0.472 Angle : 0.790 7.714 24512 Z= 0.543 Chirality : 0.053 0.521 2874 Planarity : 0.004 0.046 3202 Dihedral : 12.660 88.516 6485 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.55 (0.17), residues: 2375 helix: 2.52 (0.11), residues: 1905 sheet: None (None), residues: 0 loop : -2.06 (0.24), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP J 199 HIS 0.001 0.000 HIS G 193 PHE 0.026 0.002 PHE F 213 TYR 0.018 0.002 TYR H 83 ARG 0.013 0.001 ARG C 210 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4750 Ramachandran restraints generated. 2375 Oldfield, 0 Emsley, 2375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4750 Ramachandran restraints generated. 2375 Oldfield, 0 Emsley, 2375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 611 residues out of total 1840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 611 time to evaluate : 1.877 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 145 TYR cc_start: 0.9055 (t80) cc_final: 0.8759 (t80) REVERT: H 129 GLU cc_start: 0.7808 (mt-10) cc_final: 0.7582 (mt-10) REVERT: H 221 MET cc_start: 0.8281 (tpt) cc_final: 0.8019 (tpt) REVERT: J 230 ASP cc_start: 0.7794 (t0) cc_final: 0.7539 (t0) outliers start: 0 outliers final: 2 residues processed: 611 average time/residue: 1.4180 time to fit residues: 960.3082 Evaluate side-chains 374 residues out of total 1840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 372 time to evaluate : 2.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 62 GLU Chi-restraints excluded: chain C residue 81 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: chunk 198 optimal weight: 0.8980 chunk 178 optimal weight: 0.9990 chunk 98 optimal weight: 0.9990 chunk 60 optimal weight: 20.0000 chunk 120 optimal weight: 0.5980 chunk 95 optimal weight: 1.9990 chunk 184 optimal weight: 2.9990 chunk 71 optimal weight: 0.7980 chunk 112 optimal weight: 1.9990 chunk 137 optimal weight: 0.0970 chunk 213 optimal weight: 10.0000 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 11 ASN F 118 GLN G 11 ASN G 201 GLN H 11 ASN H 118 GLN H 198 GLN H 202 GLN H 237 GLN I 11 ASN I 15 GLN I 118 GLN I 198 GLN J 11 ASN J 118 GLN J 201 GLN J 202 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.080285 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.062849 restraints weight = 40220.214| |-----------------------------------------------------------------------------| r_work (start): 0.2885 rms_B_bonded: 2.56 r_work: 0.2740 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.2740 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2747 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2747 r_free = 0.2747 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2747 r_free = 0.2747 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2747 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8632 moved from start: 0.2388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 18106 Z= 0.239 Angle : 0.577 10.627 24512 Z= 0.309 Chirality : 0.039 0.208 2874 Planarity : 0.004 0.055 3202 Dihedral : 5.155 139.611 2591 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 9.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 4.25 % Allowed : 14.39 % Favored : 81.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: 3.06 (0.17), residues: 2375 helix: 2.84 (0.11), residues: 1890 sheet: None (None), residues: 0 loop : -1.56 (0.26), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP H 189 HIS 0.001 0.000 HIS G 193 PHE 0.030 0.001 PHE H 213 TYR 0.017 0.002 TYR F 83 ARG 0.007 0.001 ARG E 32 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4750 Ramachandran restraints generated. 2375 Oldfield, 0 Emsley, 2375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4750 Ramachandran restraints generated. 2375 Oldfield, 0 Emsley, 2375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 520 residues out of total 1840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 445 time to evaluate : 2.018 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 GLU cc_start: 0.9221 (pt0) cc_final: 0.8993 (pm20) REVERT: A 125 SER cc_start: 0.9260 (m) cc_final: 0.8959 (m) REVERT: A 212 GLU cc_start: 0.9116 (OUTLIER) cc_final: 0.8902 (tp30) REVERT: B 34 LEU cc_start: 0.9665 (mp) cc_final: 0.9462 (mm) REVERT: B 38 GLN cc_start: 0.9412 (mm-40) cc_final: 0.9165 (mm-40) REVERT: B 212 GLU cc_start: 0.9169 (OUTLIER) cc_final: 0.8910 (tm-30) REVERT: C 44 LYS cc_start: 0.9663 (tppp) cc_final: 0.9327 (tppp) REVERT: D 45 GLU cc_start: 0.9164 (pt0) cc_final: 0.8667 (pm20) REVERT: D 112 ASP cc_start: 0.9147 (m-30) cc_final: 0.8910 (m-30) REVERT: E 44 LYS cc_start: 0.9687 (tppp) cc_final: 0.9451 (tppp) REVERT: F 4 GLU cc_start: 0.8813 (tp30) cc_final: 0.8608 (tp30) REVERT: F 23 ASP cc_start: 0.8537 (m-30) cc_final: 0.8330 (m-30) REVERT: F 63 PHE cc_start: 0.8968 (t80) cc_final: 0.8693 (t80) REVERT: F 132 GLU cc_start: 0.9036 (tt0) cc_final: 0.8609 (tt0) REVERT: F 201 GLN cc_start: 0.9298 (OUTLIER) cc_final: 0.8985 (tt0) REVERT: F 222 GLN cc_start: 0.9014 (tm-30) cc_final: 0.8762 (tm-30) REVERT: F 232 ARG cc_start: 0.9146 (mtm110) cc_final: 0.8917 (mtm-85) REVERT: G 69 ARG cc_start: 0.8232 (ttt90) cc_final: 0.8012 (ttt180) REVERT: G 133 GLU cc_start: 0.9233 (mm-30) cc_final: 0.9019 (mm-30) REVERT: H 4 GLU cc_start: 0.9323 (mt-10) cc_final: 0.9008 (tp30) REVERT: H 23 ASP cc_start: 0.8780 (m-30) cc_final: 0.8544 (m-30) REVERT: H 230 ASP cc_start: 0.8929 (t0) cc_final: 0.8518 (t0) REVERT: I 4 GLU cc_start: 0.8692 (tp30) cc_final: 0.8441 (tp30) REVERT: I 129 GLU cc_start: 0.9179 (mt-10) cc_final: 0.8942 (mt-10) REVERT: I 189 TRP cc_start: 0.7929 (m100) cc_final: 0.7702 (m-10) REVERT: I 228 MET cc_start: 0.9479 (mmm) cc_final: 0.9233 (mmt) REVERT: I 230 ASP cc_start: 0.9116 (t0) cc_final: 0.8773 (t0) REVERT: J 4 GLU cc_start: 0.8689 (tp30) cc_final: 0.8383 (tp30) REVERT: J 222 GLN cc_start: 0.9010 (tm-30) cc_final: 0.8769 (tm-30) REVERT: J 230 ASP cc_start: 0.9209 (t0) cc_final: 0.8659 (t0) outliers start: 75 outliers final: 18 residues processed: 486 average time/residue: 1.2969 time to fit residues: 705.0934 Evaluate side-chains 396 residues out of total 1840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 375 time to evaluate : 2.062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 212 GLU Chi-restraints excluded: chain B residue 212 GLU Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain E residue 118 SER Chi-restraints excluded: chain F residue 50 LEU Chi-restraints excluded: chain F residue 67 CYS Chi-restraints excluded: chain F residue 201 GLN Chi-restraints excluded: chain F residue 208 LEU Chi-restraints excluded: chain F residue 246 SER Chi-restraints excluded: chain G residue 67 CYS Chi-restraints excluded: chain H residue 67 CYS Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain H residue 138 SER Chi-restraints excluded: chain H residue 246 SER Chi-restraints excluded: chain I residue 33 THR Chi-restraints excluded: chain I residue 64 LEU Chi-restraints excluded: chain I residue 67 CYS Chi-restraints excluded: chain I residue 68 LEU Chi-restraints excluded: chain I residue 138 SER Chi-restraints excluded: chain I residue 246 SER Chi-restraints excluded: chain J residue 64 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: chunk 89 optimal weight: 1.9990 chunk 151 optimal weight: 1.9990 chunk 143 optimal weight: 0.9990 chunk 24 optimal weight: 0.9990 chunk 23 optimal weight: 0.7980 chunk 216 optimal weight: 3.9990 chunk 200 optimal weight: 0.1980 chunk 60 optimal weight: 0.6980 chunk 167 optimal weight: 0.7980 chunk 109 optimal weight: 1.9990 chunk 30 optimal weight: 0.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 107 ASN C 116 ASN ** C 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 11 ASN F 15 GLN F 118 GLN F 198 GLN G 11 ASN G 118 GLN H 11 ASN H 118 GLN H 202 GLN H 237 GLN I 11 ASN I 15 GLN I 118 GLN I 198 GLN I 259 GLN J 118 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.077847 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2864 r_free = 0.2864 target = 0.059588 restraints weight = 40174.418| |-----------------------------------------------------------------------------| r_work (start): 0.2847 rms_B_bonded: 2.62 r_work: 0.2701 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.2701 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2701 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2701 r_free = 0.2701 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2701 r_free = 0.2701 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2701 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8592 moved from start: 0.2818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 18106 Z= 0.223 Angle : 0.555 9.750 24512 Z= 0.289 Chirality : 0.038 0.189 2874 Planarity : 0.004 0.068 3202 Dihedral : 4.006 27.351 2585 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 4.19 % Allowed : 17.51 % Favored : 78.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.14 (0.17), residues: 2375 helix: 2.89 (0.11), residues: 1895 sheet: None (None), residues: 0 loop : -1.50 (0.26), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP F 189 HIS 0.001 0.000 HIS H 193 PHE 0.023 0.001 PHE H 213 TYR 0.018 0.002 TYR F 83 ARG 0.007 0.001 ARG A 32 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4750 Ramachandran restraints generated. 2375 Oldfield, 0 Emsley, 2375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4750 Ramachandran restraints generated. 2375 Oldfield, 0 Emsley, 2375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 497 residues out of total 1840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 423 time to evaluate : 2.139 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 125 SER cc_start: 0.9006 (m) cc_final: 0.8747 (m) REVERT: B 34 LEU cc_start: 0.9684 (mp) cc_final: 0.9329 (pt) REVERT: B 38 GLN cc_start: 0.9576 (mm-40) cc_final: 0.9308 (mm-40) REVERT: B 212 GLU cc_start: 0.9157 (OUTLIER) cc_final: 0.8913 (tp30) REVERT: C 32 ARG cc_start: 0.8636 (OUTLIER) cc_final: 0.8312 (ttp80) REVERT: C 44 LYS cc_start: 0.9666 (tppp) cc_final: 0.9298 (tppp) REVERT: D 112 ASP cc_start: 0.9121 (m-30) cc_final: 0.8878 (m-30) REVERT: D 197 GLN cc_start: 0.9454 (OUTLIER) cc_final: 0.9108 (tt0) REVERT: E 44 LYS cc_start: 0.9639 (tppp) cc_final: 0.9373 (tppp) REVERT: F 4 GLU cc_start: 0.8872 (tp30) cc_final: 0.8612 (tp30) REVERT: F 23 ASP cc_start: 0.8554 (m-30) cc_final: 0.8315 (m-30) REVERT: F 62 GLU cc_start: 0.9009 (pp20) cc_final: 0.8779 (pp20) REVERT: F 65 ASN cc_start: 0.9089 (t0) cc_final: 0.8661 (p0) REVERT: F 132 GLU cc_start: 0.9050 (tt0) cc_final: 0.8632 (tt0) REVERT: F 157 LEU cc_start: 0.8824 (OUTLIER) cc_final: 0.8526 (tt) REVERT: F 230 ASP cc_start: 0.8884 (t0) cc_final: 0.8446 (t0) REVERT: G 230 ASP cc_start: 0.8956 (t0) cc_final: 0.8501 (t0) REVERT: H 23 ASP cc_start: 0.8783 (m-30) cc_final: 0.8556 (m-30) REVERT: H 87 ILE cc_start: 0.9076 (mm) cc_final: 0.8836 (mm) REVERT: H 230 ASP cc_start: 0.9008 (t0) cc_final: 0.8519 (t0) REVERT: I 4 GLU cc_start: 0.8727 (tp30) cc_final: 0.8424 (tp30) REVERT: I 23 ASP cc_start: 0.8700 (m-30) cc_final: 0.8403 (m-30) REVERT: I 189 TRP cc_start: 0.7818 (m100) cc_final: 0.7546 (m-10) REVERT: I 230 ASP cc_start: 0.9065 (t0) cc_final: 0.8561 (t0) REVERT: J 4 GLU cc_start: 0.8730 (tp30) cc_final: 0.8434 (tp30) REVERT: J 62 GLU cc_start: 0.8956 (pp20) cc_final: 0.8595 (pp20) REVERT: J 230 ASP cc_start: 0.9159 (t0) cc_final: 0.8627 (t0) outliers start: 74 outliers final: 27 residues processed: 461 average time/residue: 1.3021 time to fit residues: 673.6183 Evaluate side-chains 411 residues out of total 1840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 380 time to evaluate : 2.027 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain B residue 162 ILE Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 212 GLU Chi-restraints excluded: chain C residue 31 THR Chi-restraints excluded: chain C residue 32 ARG Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain D residue 197 GLN Chi-restraints excluded: chain F residue 50 LEU Chi-restraints excluded: chain F residue 64 LEU Chi-restraints excluded: chain F residue 67 CYS Chi-restraints excluded: chain F residue 157 LEU Chi-restraints excluded: chain F residue 208 LEU Chi-restraints excluded: chain F residue 246 SER Chi-restraints excluded: chain G residue 67 CYS Chi-restraints excluded: chain G residue 68 LEU Chi-restraints excluded: chain G residue 97 GLU Chi-restraints excluded: chain G residue 157 LEU Chi-restraints excluded: chain G residue 258 MET Chi-restraints excluded: chain H residue 33 THR Chi-restraints excluded: chain H residue 67 CYS Chi-restraints excluded: chain H residue 115 LEU Chi-restraints excluded: chain H residue 138 SER Chi-restraints excluded: chain H residue 237 GLN Chi-restraints excluded: chain H residue 246 SER Chi-restraints excluded: chain I residue 64 LEU Chi-restraints excluded: chain I residue 67 CYS Chi-restraints excluded: chain I residue 246 SER Chi-restraints excluded: chain J residue 64 LEU Chi-restraints excluded: chain J residue 67 CYS Chi-restraints excluded: chain J residue 68 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: chunk 17 optimal weight: 0.6980 chunk 156 optimal weight: 3.9990 chunk 54 optimal weight: 2.9990 chunk 38 optimal weight: 0.6980 chunk 206 optimal weight: 1.9990 chunk 9 optimal weight: 0.9980 chunk 7 optimal weight: 5.9990 chunk 189 optimal weight: 1.9990 chunk 228 optimal weight: 0.9980 chunk 78 optimal weight: 0.5980 chunk 63 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 107 ASN C 116 ASN ** C 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 11 ASN G 11 ASN G 118 GLN H 11 ASN H 118 GLN H 202 GLN H 259 GLN I 11 ASN I 118 GLN I 198 GLN J 11 ASN J 118 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.079426 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2936 r_free = 0.2936 target = 0.061785 restraints weight = 40391.364| |-----------------------------------------------------------------------------| r_work (start): 0.2879 rms_B_bonded: 2.61 r_work: 0.2732 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.2732 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2737 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2737 r_free = 0.2737 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2737 r_free = 0.2737 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2737 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8657 moved from start: 0.3087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 18106 Z= 0.228 Angle : 0.547 9.601 24512 Z= 0.285 Chirality : 0.038 0.183 2874 Planarity : 0.003 0.045 3202 Dihedral : 3.911 26.709 2585 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 3.46 % Allowed : 20.17 % Favored : 76.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.28 (0.17), residues: 2375 helix: 2.93 (0.11), residues: 1905 sheet: None (None), residues: 0 loop : -1.29 (0.27), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP F 189 HIS 0.001 0.000 HIS H 193 PHE 0.020 0.001 PHE H 213 TYR 0.016 0.001 TYR F 83 ARG 0.006 0.000 ARG A 32 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4750 Ramachandran restraints generated. 2375 Oldfield, 0 Emsley, 2375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4750 Ramachandran restraints generated. 2375 Oldfield, 0 Emsley, 2375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 467 residues out of total 1840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 406 time to evaluate : 2.235 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 GLU cc_start: 0.9277 (pt0) cc_final: 0.9019 (pm20) REVERT: B 34 LEU cc_start: 0.9662 (mp) cc_final: 0.9312 (pt) REVERT: B 38 GLN cc_start: 0.9579 (mm-40) cc_final: 0.9280 (mm-40) REVERT: C 44 LYS cc_start: 0.9648 (tppp) cc_final: 0.9244 (tppp) REVERT: D 112 ASP cc_start: 0.9088 (m-30) cc_final: 0.8833 (m-30) REVERT: E 44 LYS cc_start: 0.9634 (tppp) cc_final: 0.9351 (tppp) REVERT: F 4 GLU cc_start: 0.8864 (tp30) cc_final: 0.8630 (tp30) REVERT: F 23 ASP cc_start: 0.8586 (m-30) cc_final: 0.8358 (m-30) REVERT: F 62 GLU cc_start: 0.8988 (pp20) cc_final: 0.8749 (pp20) REVERT: F 65 ASN cc_start: 0.9089 (t0) cc_final: 0.8656 (p0) REVERT: F 132 GLU cc_start: 0.9051 (tt0) cc_final: 0.8634 (tt0) REVERT: F 230 ASP cc_start: 0.8911 (t0) cc_final: 0.8509 (t0) REVERT: G 133 GLU cc_start: 0.9258 (mm-30) cc_final: 0.9055 (mm-30) REVERT: G 230 ASP cc_start: 0.9017 (t0) cc_final: 0.8578 (t0) REVERT: H 4 GLU cc_start: 0.9242 (mt-10) cc_final: 0.9037 (mm-30) REVERT: H 23 ASP cc_start: 0.8807 (m-30) cc_final: 0.8574 (m-30) REVERT: H 69 ARG cc_start: 0.8198 (OUTLIER) cc_final: 0.7959 (ttt180) REVERT: H 87 ILE cc_start: 0.9082 (mm) cc_final: 0.8806 (mm) REVERT: H 230 ASP cc_start: 0.9028 (t0) cc_final: 0.8527 (t0) REVERT: H 259 GLN cc_start: 0.8877 (OUTLIER) cc_final: 0.8673 (mp10) REVERT: H 263 ILE cc_start: 0.9495 (OUTLIER) cc_final: 0.9289 (mp) REVERT: I 4 GLU cc_start: 0.8702 (tp30) cc_final: 0.8449 (tp30) REVERT: I 23 ASP cc_start: 0.8753 (m-30) cc_final: 0.8413 (m-30) REVERT: I 230 ASP cc_start: 0.9114 (t0) cc_final: 0.8564 (t0) REVERT: J 4 GLU cc_start: 0.8739 (tp30) cc_final: 0.8444 (tp30) REVERT: J 11 ASN cc_start: 0.9070 (m-40) cc_final: 0.8812 (m-40) REVERT: J 23 ASP cc_start: 0.8567 (m-30) cc_final: 0.8125 (m-30) REVERT: J 62 GLU cc_start: 0.8912 (pp20) cc_final: 0.8643 (pp20) REVERT: J 230 ASP cc_start: 0.9150 (t0) cc_final: 0.8438 (t0) REVERT: J 259 GLN cc_start: 0.9053 (OUTLIER) cc_final: 0.8845 (mp10) outliers start: 61 outliers final: 24 residues processed: 439 average time/residue: 1.2268 time to fit residues: 605.1887 Evaluate side-chains 401 residues out of total 1840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 373 time to evaluate : 1.956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 162 ILE Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain E residue 118 SER Chi-restraints excluded: chain F residue 50 LEU Chi-restraints excluded: chain F residue 64 LEU Chi-restraints excluded: chain F residue 67 CYS Chi-restraints excluded: chain F residue 208 LEU Chi-restraints excluded: chain F residue 246 SER Chi-restraints excluded: chain G residue 67 CYS Chi-restraints excluded: chain G residue 157 LEU Chi-restraints excluded: chain G residue 208 LEU Chi-restraints excluded: chain G residue 258 MET Chi-restraints excluded: chain H residue 33 THR Chi-restraints excluded: chain H residue 67 CYS Chi-restraints excluded: chain H residue 69 ARG Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain H residue 194 ARG Chi-restraints excluded: chain H residue 259 GLN Chi-restraints excluded: chain H residue 263 ILE Chi-restraints excluded: chain I residue 64 LEU Chi-restraints excluded: chain I residue 67 CYS Chi-restraints excluded: chain I residue 246 SER Chi-restraints excluded: chain J residue 64 LEU Chi-restraints excluded: chain J residue 67 CYS Chi-restraints excluded: chain J residue 68 LEU Chi-restraints excluded: chain J residue 259 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: chunk 179 optimal weight: 1.9990 chunk 83 optimal weight: 1.9990 chunk 197 optimal weight: 0.8980 chunk 11 optimal weight: 0.9990 chunk 170 optimal weight: 0.9980 chunk 224 optimal weight: 0.8980 chunk 160 optimal weight: 2.9990 chunk 141 optimal weight: 1.9990 chunk 10 optimal weight: 0.9980 chunk 90 optimal weight: 0.3980 chunk 114 optimal weight: 0.9980 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 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 107 ASN C 116 ASN ** C 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 11 ASN F 15 GLN G 11 ASN H 11 ASN H 118 GLN I 11 ASN I 118 GLN I 198 GLN I 259 GLN J 15 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.078973 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2930 r_free = 0.2930 target = 0.061298 restraints weight = 40909.338| |-----------------------------------------------------------------------------| r_work (start): 0.2869 rms_B_bonded: 2.61 r_work: 0.2720 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.2720 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2728 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2728 r_free = 0.2728 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2728 r_free = 0.2728 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2728 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8667 moved from start: 0.3255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 18106 Z= 0.240 Angle : 0.555 11.147 24512 Z= 0.288 Chirality : 0.038 0.271 2874 Planarity : 0.003 0.041 3202 Dihedral : 3.851 26.069 2585 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 3.85 % Allowed : 20.74 % Favored : 75.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.30 (0.17), residues: 2375 helix: 2.91 (0.11), residues: 1910 sheet: None (None), residues: 0 loop : -1.18 (0.28), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP F 189 HIS 0.001 0.000 HIS H 193 PHE 0.023 0.001 PHE B 36 TYR 0.016 0.001 TYR F 83 ARG 0.010 0.000 ARG C 32 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4750 Ramachandran restraints generated. 2375 Oldfield, 0 Emsley, 2375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4750 Ramachandran restraints generated. 2375 Oldfield, 0 Emsley, 2375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 466 residues out of total 1840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 398 time to evaluate : 2.059 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 34 LEU cc_start: 0.9659 (mp) cc_final: 0.9319 (pt) REVERT: B 38 GLN cc_start: 0.9605 (mm-40) cc_final: 0.9257 (mm-40) REVERT: B 223 GLN cc_start: 0.8670 (mm-40) cc_final: 0.8330 (mm110) REVERT: D 112 ASP cc_start: 0.9079 (m-30) cc_final: 0.8825 (m-30) REVERT: D 197 GLN cc_start: 0.9459 (OUTLIER) cc_final: 0.9001 (tt0) REVERT: F 23 ASP cc_start: 0.8624 (m-30) cc_final: 0.8380 (m-30) REVERT: F 65 ASN cc_start: 0.9098 (t0) cc_final: 0.8631 (p0) REVERT: F 132 GLU cc_start: 0.9049 (tt0) cc_final: 0.8636 (tt0) REVERT: F 230 ASP cc_start: 0.8930 (t0) cc_final: 0.8522 (t0) REVERT: G 230 ASP cc_start: 0.8974 (t0) cc_final: 0.8532 (t0) REVERT: H 4 GLU cc_start: 0.9250 (mt-10) cc_final: 0.9044 (mm-30) REVERT: H 23 ASP cc_start: 0.8813 (m-30) cc_final: 0.8586 (m-30) REVERT: H 69 ARG cc_start: 0.8235 (OUTLIER) cc_final: 0.8008 (ttt180) REVERT: H 230 ASP cc_start: 0.9055 (t0) cc_final: 0.8544 (t0) REVERT: H 263 ILE cc_start: 0.9491 (OUTLIER) cc_final: 0.9289 (mp) REVERT: I 4 GLU cc_start: 0.8740 (tp30) cc_final: 0.8508 (tp30) REVERT: I 23 ASP cc_start: 0.8763 (m-30) cc_final: 0.8387 (m-30) REVERT: J 4 GLU cc_start: 0.8770 (tp30) cc_final: 0.8472 (tp30) REVERT: J 11 ASN cc_start: 0.9099 (m-40) cc_final: 0.8807 (m-40) REVERT: J 23 ASP cc_start: 0.8586 (m-30) cc_final: 0.8137 (m-30) REVERT: J 230 ASP cc_start: 0.9152 (t0) cc_final: 0.8446 (t0) outliers start: 68 outliers final: 31 residues processed: 434 average time/residue: 1.2687 time to fit residues: 619.6758 Evaluate side-chains 407 residues out of total 1840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 373 time to evaluate : 2.019 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 SER Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 95 ASN Chi-restraints excluded: chain B residue 162 ILE Chi-restraints excluded: chain D residue 162 ILE Chi-restraints excluded: chain D residue 197 GLN Chi-restraints excluded: chain E residue 118 SER Chi-restraints excluded: chain F residue 50 LEU Chi-restraints excluded: chain F residue 64 LEU Chi-restraints excluded: chain F residue 67 CYS Chi-restraints excluded: chain F residue 208 LEU Chi-restraints excluded: chain F residue 246 SER Chi-restraints excluded: chain G residue 67 CYS Chi-restraints excluded: chain G residue 98 LEU Chi-restraints excluded: chain G residue 157 LEU Chi-restraints excluded: chain G residue 208 LEU Chi-restraints excluded: chain H residue 33 THR Chi-restraints excluded: chain H residue 67 CYS Chi-restraints excluded: chain H residue 69 ARG Chi-restraints excluded: chain H residue 83 TYR Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain H residue 194 ARG Chi-restraints excluded: chain H residue 237 GLN Chi-restraints excluded: chain H residue 263 ILE Chi-restraints excluded: chain I residue 15 GLN Chi-restraints excluded: chain I residue 64 LEU Chi-restraints excluded: chain I residue 67 CYS Chi-restraints excluded: chain I residue 68 LEU Chi-restraints excluded: chain I residue 246 SER Chi-restraints excluded: chain J residue 64 LEU Chi-restraints excluded: chain J residue 67 CYS Chi-restraints excluded: chain J residue 68 LEU Chi-restraints excluded: chain J residue 97 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: chunk 29 optimal weight: 3.9990 chunk 231 optimal weight: 3.9990 chunk 104 optimal weight: 2.9990 chunk 35 optimal weight: 0.9990 chunk 38 optimal weight: 0.5980 chunk 155 optimal weight: 1.9990 chunk 88 optimal weight: 0.6980 chunk 187 optimal weight: 0.9980 chunk 122 optimal weight: 0.9980 chunk 62 optimal weight: 0.6980 chunk 171 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 107 ASN C 116 ASN ** C 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 187 ASN F 198 GLN G 11 ASN H 11 ASN H 15 GLN H 259 GLN I 11 ASN I 118 GLN I 198 GLN I 259 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.078961 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2933 r_free = 0.2933 target = 0.061365 restraints weight = 40748.281| |-----------------------------------------------------------------------------| r_work (start): 0.2872 rms_B_bonded: 2.57 r_work: 0.2727 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.2727 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2728 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2728 r_free = 0.2728 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2728 r_free = 0.2728 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2728 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8668 moved from start: 0.3398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 18106 Z= 0.237 Angle : 0.561 11.422 24512 Z= 0.293 Chirality : 0.038 0.293 2874 Planarity : 0.003 0.039 3202 Dihedral : 3.829 24.892 2585 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 4.02 % Allowed : 21.36 % Favored : 74.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.29 (0.17), residues: 2375 helix: 2.90 (0.11), residues: 1915 sheet: None (None), residues: 0 loop : -1.18 (0.28), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP F 189 HIS 0.001 0.000 HIS J 193 PHE 0.030 0.001 PHE H 213 TYR 0.025 0.002 TYR H 83 ARG 0.004 0.000 ARG C 32 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4750 Ramachandran restraints generated. 2375 Oldfield, 0 Emsley, 2375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4750 Ramachandran restraints generated. 2375 Oldfield, 0 Emsley, 2375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 458 residues out of total 1840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 387 time to evaluate : 1.872 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 159 MET cc_start: 0.8841 (OUTLIER) cc_final: 0.7909 (mmt) REVERT: B 159 MET cc_start: 0.8616 (mtp) cc_final: 0.8403 (mtm) REVERT: C 44 LYS cc_start: 0.9635 (tppp) cc_final: 0.9271 (tppp) REVERT: C 159 MET cc_start: 0.8591 (OUTLIER) cc_final: 0.8175 (mtp) REVERT: D 112 ASP cc_start: 0.9081 (m-30) cc_final: 0.8845 (m-30) REVERT: E 44 LYS cc_start: 0.9635 (tppp) cc_final: 0.9334 (tppp) REVERT: F 23 ASP cc_start: 0.8669 (m-30) cc_final: 0.8449 (m-30) REVERT: F 62 GLU cc_start: 0.8987 (pp20) cc_final: 0.8542 (pp20) REVERT: F 132 GLU cc_start: 0.9045 (tt0) cc_final: 0.8628 (tt0) REVERT: F 230 ASP cc_start: 0.8926 (t0) cc_final: 0.8521 (t0) REVERT: G 230 ASP cc_start: 0.8953 (t0) cc_final: 0.8454 (t0) REVERT: H 4 GLU cc_start: 0.9244 (mt-10) cc_final: 0.9036 (mm-30) REVERT: H 23 ASP cc_start: 0.8823 (m-30) cc_final: 0.8589 (m-30) REVERT: H 69 ARG cc_start: 0.8238 (OUTLIER) cc_final: 0.7997 (ttt180) REVERT: H 230 ASP cc_start: 0.9059 (t0) cc_final: 0.8524 (t0) REVERT: H 263 ILE cc_start: 0.9488 (OUTLIER) cc_final: 0.9282 (mp) REVERT: I 23 ASP cc_start: 0.8759 (m-30) cc_final: 0.8416 (m-30) REVERT: J 4 GLU cc_start: 0.8750 (tp30) cc_final: 0.8482 (tp30) REVERT: J 11 ASN cc_start: 0.9099 (m-40) cc_final: 0.8717 (m-40) REVERT: J 23 ASP cc_start: 0.8632 (m-30) cc_final: 0.8194 (m-30) REVERT: J 62 GLU cc_start: 0.8893 (pp20) cc_final: 0.8617 (pp20) REVERT: J 230 ASP cc_start: 0.9135 (t0) cc_final: 0.8423 (t0) outliers start: 71 outliers final: 38 residues processed: 424 average time/residue: 1.2367 time to fit residues: 589.7803 Evaluate side-chains 404 residues out of total 1840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 362 time to evaluate : 2.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 SER Chi-restraints excluded: chain A residue 159 MET Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain B residue 28 PHE Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 95 ASN Chi-restraints excluded: chain B residue 162 ILE Chi-restraints excluded: chain C residue 159 MET Chi-restraints excluded: chain C residue 162 ILE Chi-restraints excluded: chain D residue 162 ILE Chi-restraints excluded: chain E residue 118 SER Chi-restraints excluded: chain E residue 227 THR Chi-restraints excluded: chain F residue 50 LEU Chi-restraints excluded: chain F residue 64 LEU Chi-restraints excluded: chain F residue 67 CYS Chi-restraints excluded: chain F residue 184 ILE Chi-restraints excluded: chain F residue 194 ARG Chi-restraints excluded: chain F residue 208 LEU Chi-restraints excluded: chain F residue 260 LEU Chi-restraints excluded: chain G residue 67 CYS Chi-restraints excluded: chain G residue 98 LEU Chi-restraints excluded: chain G residue 157 LEU Chi-restraints excluded: chain G residue 182 LEU Chi-restraints excluded: chain G residue 208 LEU Chi-restraints excluded: chain H residue 33 THR Chi-restraints excluded: chain H residue 67 CYS Chi-restraints excluded: chain H residue 69 ARG Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain H residue 194 ARG Chi-restraints excluded: chain H residue 213 PHE Chi-restraints excluded: chain H residue 237 GLN Chi-restraints excluded: chain H residue 263 ILE Chi-restraints excluded: chain I residue 15 GLN Chi-restraints excluded: chain I residue 64 LEU Chi-restraints excluded: chain I residue 67 CYS Chi-restraints excluded: chain I residue 68 LEU Chi-restraints excluded: chain I residue 246 SER Chi-restraints excluded: chain J residue 64 LEU Chi-restraints excluded: chain J residue 67 CYS Chi-restraints excluded: chain J residue 68 LEU Chi-restraints excluded: chain J residue 97 GLU Chi-restraints excluded: chain J residue 175 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: chunk 5 optimal weight: 1.9990 chunk 64 optimal weight: 4.9990 chunk 166 optimal weight: 2.9990 chunk 180 optimal weight: 0.7980 chunk 139 optimal weight: 2.9990 chunk 25 optimal weight: 0.9980 chunk 150 optimal weight: 1.9990 chunk 212 optimal weight: 1.9990 chunk 63 optimal weight: 0.7980 chunk 184 optimal weight: 0.9980 chunk 79 optimal weight: 2.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 107 ASN C 116 ASN ** C 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 187 ASN ** E 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 15 GLN F 198 GLN G 11 ASN G 118 GLN H 11 ASN I 11 ASN I 118 GLN I 198 GLN I 259 GLN J 118 GLN J 259 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.077466 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2874 r_free = 0.2874 target = 0.059827 restraints weight = 40582.064| |-----------------------------------------------------------------------------| r_work (start): 0.2847 rms_B_bonded: 2.65 r_work: 0.2709 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.2709 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2687 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2687 r_free = 0.2687 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2687 r_free = 0.2687 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2687 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8698 moved from start: 0.3470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 18106 Z= 0.289 Angle : 0.586 9.813 24512 Z= 0.307 Chirality : 0.039 0.181 2874 Planarity : 0.003 0.035 3202 Dihedral : 3.812 25.482 2585 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 4.02 % Allowed : 21.47 % Favored : 74.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.23 (0.17), residues: 2375 helix: 2.85 (0.11), residues: 1920 sheet: None (None), residues: 0 loop : -1.25 (0.28), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP I 189 HIS 0.001 0.000 HIS G 193 PHE 0.030 0.002 PHE H 213 TYR 0.018 0.002 TYR F 227 ARG 0.002 0.000 ARG G 232 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4750 Ramachandran restraints generated. 2375 Oldfield, 0 Emsley, 2375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4750 Ramachandran restraints generated. 2375 Oldfield, 0 Emsley, 2375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 440 residues out of total 1840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 369 time to evaluate : 1.972 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 159 MET cc_start: 0.8889 (OUTLIER) cc_final: 0.8063 (mmt) REVERT: B 159 MET cc_start: 0.8705 (mtp) cc_final: 0.8499 (mtm) REVERT: B 223 GLN cc_start: 0.8746 (mm-40) cc_final: 0.8408 (mm110) REVERT: C 44 LYS cc_start: 0.9653 (tppp) cc_final: 0.9328 (tppp) REVERT: C 159 MET cc_start: 0.8669 (OUTLIER) cc_final: 0.8294 (mtp) REVERT: D 45 GLU cc_start: 0.9209 (pt0) cc_final: 0.8687 (pm20) REVERT: D 112 ASP cc_start: 0.9099 (m-30) cc_final: 0.8868 (m-30) REVERT: D 197 GLN cc_start: 0.9463 (OUTLIER) cc_final: 0.8983 (tt0) REVERT: F 23 ASP cc_start: 0.8711 (m-30) cc_final: 0.8467 (m-30) REVERT: F 62 GLU cc_start: 0.8883 (pp20) cc_final: 0.8518 (pp20) REVERT: F 65 ASN cc_start: 0.9087 (t0) cc_final: 0.8624 (p0) REVERT: F 132 GLU cc_start: 0.9043 (tt0) cc_final: 0.8644 (tt0) REVERT: F 189 TRP cc_start: 0.8670 (m-90) cc_final: 0.8231 (m-10) REVERT: F 230 ASP cc_start: 0.8939 (t0) cc_final: 0.8557 (t0) REVERT: G 132 GLU cc_start: 0.8900 (mt-10) cc_final: 0.8666 (mt-10) REVERT: G 230 ASP cc_start: 0.8926 (t0) cc_final: 0.8470 (t0) REVERT: H 4 GLU cc_start: 0.9258 (mt-10) cc_final: 0.8961 (tp30) REVERT: H 23 ASP cc_start: 0.8834 (m-30) cc_final: 0.8590 (m-30) REVERT: H 69 ARG cc_start: 0.8261 (OUTLIER) cc_final: 0.8038 (ttt180) REVERT: H 230 ASP cc_start: 0.9065 (t0) cc_final: 0.8524 (t0) REVERT: H 263 ILE cc_start: 0.9508 (OUTLIER) cc_final: 0.9301 (mp) REVERT: I 23 ASP cc_start: 0.8739 (m-30) cc_final: 0.8388 (m-30) REVERT: I 132 GLU cc_start: 0.9035 (tt0) cc_final: 0.8792 (tt0) REVERT: I 230 ASP cc_start: 0.9065 (t0) cc_final: 0.8602 (t0) REVERT: J 4 GLU cc_start: 0.8761 (tp30) cc_final: 0.8458 (tp30) REVERT: J 11 ASN cc_start: 0.9090 (m-40) cc_final: 0.8702 (m-40) REVERT: J 23 ASP cc_start: 0.8639 (m-30) cc_final: 0.8207 (m-30) REVERT: J 230 ASP cc_start: 0.9141 (t0) cc_final: 0.8355 (t0) outliers start: 71 outliers final: 40 residues processed: 409 average time/residue: 1.2191 time to fit residues: 560.4944 Evaluate side-chains 403 residues out of total 1840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 358 time to evaluate : 1.985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 SER Chi-restraints excluded: chain A residue 159 MET Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 162 ILE Chi-restraints excluded: chain C residue 159 MET Chi-restraints excluded: chain C residue 162 ILE Chi-restraints excluded: chain D residue 162 ILE Chi-restraints excluded: chain D residue 197 GLN Chi-restraints excluded: chain E residue 118 SER Chi-restraints excluded: chain E residue 218 LEU Chi-restraints excluded: chain E residue 227 THR Chi-restraints excluded: chain F residue 50 LEU Chi-restraints excluded: chain F residue 64 LEU Chi-restraints excluded: chain F residue 67 CYS Chi-restraints excluded: chain F residue 184 ILE Chi-restraints excluded: chain F residue 194 ARG Chi-restraints excluded: chain F residue 208 LEU Chi-restraints excluded: chain F residue 246 SER Chi-restraints excluded: chain F residue 260 LEU Chi-restraints excluded: chain G residue 67 CYS Chi-restraints excluded: chain G residue 68 LEU Chi-restraints excluded: chain G residue 83 TYR Chi-restraints excluded: chain G residue 98 LEU Chi-restraints excluded: chain G residue 182 LEU Chi-restraints excluded: chain G residue 208 LEU Chi-restraints excluded: chain H residue 33 THR Chi-restraints excluded: chain H residue 67 CYS Chi-restraints excluded: chain H residue 69 ARG Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain H residue 194 ARG Chi-restraints excluded: chain H residue 237 GLN Chi-restraints excluded: chain H residue 259 GLN Chi-restraints excluded: chain H residue 263 ILE Chi-restraints excluded: chain I residue 15 GLN Chi-restraints excluded: chain I residue 64 LEU Chi-restraints excluded: chain I residue 67 CYS Chi-restraints excluded: chain I residue 68 LEU Chi-restraints excluded: chain I residue 185 LEU Chi-restraints excluded: chain I residue 246 SER Chi-restraints excluded: chain J residue 64 LEU Chi-restraints excluded: chain J residue 67 CYS Chi-restraints excluded: chain J residue 68 LEU Chi-restraints excluded: chain J residue 97 GLU Chi-restraints excluded: chain J residue 175 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: chunk 63 optimal weight: 0.5980 chunk 95 optimal weight: 0.9990 chunk 121 optimal weight: 0.7980 chunk 102 optimal weight: 0.7980 chunk 181 optimal weight: 0.0670 chunk 70 optimal weight: 0.5980 chunk 54 optimal weight: 1.9990 chunk 150 optimal weight: 0.8980 chunk 67 optimal weight: 0.0270 chunk 143 optimal weight: 0.9990 chunk 101 optimal weight: 0.7980 overall best weight: 0.4176 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 107 ASN C 116 ASN ** C 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 198 GLN G 11 ASN G 118 GLN I 11 ASN I 118 GLN I 198 GLN I 259 GLN J 118 GLN J 259 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.078392 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2898 r_free = 0.2898 target = 0.060524 restraints weight = 40743.117| |-----------------------------------------------------------------------------| r_work (start): 0.2889 rms_B_bonded: 2.72 r_work: 0.2752 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.2752 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2733 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2733 r_free = 0.2733 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2733 r_free = 0.2733 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2733 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8664 moved from start: 0.3613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 18106 Z= 0.194 Angle : 0.577 10.677 24512 Z= 0.298 Chirality : 0.038 0.252 2874 Planarity : 0.003 0.035 3202 Dihedral : 3.805 24.054 2585 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 3.34 % Allowed : 22.55 % Favored : 74.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.28 (0.17), residues: 2375 helix: 2.94 (0.11), residues: 1900 sheet: None (None), residues: 0 loop : -1.31 (0.28), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP I 189 HIS 0.001 0.000 HIS H 193 PHE 0.027 0.001 PHE H 213 TYR 0.018 0.001 TYR F 83 ARG 0.003 0.000 ARG C 111 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4750 Ramachandran restraints generated. 2375 Oldfield, 0 Emsley, 2375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4750 Ramachandran restraints generated. 2375 Oldfield, 0 Emsley, 2375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 452 residues out of total 1840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 393 time to evaluate : 2.107 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 159 MET cc_start: 0.8598 (mtp) cc_final: 0.8378 (mtm) REVERT: B 215 MET cc_start: 0.9104 (mmt) cc_final: 0.8893 (mmp) REVERT: B 223 GLN cc_start: 0.8731 (mm-40) cc_final: 0.8375 (mm110) REVERT: C 44 LYS cc_start: 0.9626 (tppp) cc_final: 0.9287 (tppp) REVERT: C 138 LYS cc_start: 0.9216 (OUTLIER) cc_final: 0.8800 (tttm) REVERT: D 45 GLU cc_start: 0.9212 (pt0) cc_final: 0.8682 (pm20) REVERT: D 112 ASP cc_start: 0.9077 (m-30) cc_final: 0.8838 (m-30) REVERT: D 197 GLN cc_start: 0.9445 (OUTLIER) cc_final: 0.8949 (tt0) REVERT: E 44 LYS cc_start: 0.9636 (tppp) cc_final: 0.9341 (tppp) REVERT: F 23 ASP cc_start: 0.8699 (m-30) cc_final: 0.8478 (m-30) REVERT: F 62 GLU cc_start: 0.8872 (pp20) cc_final: 0.8524 (pp20) REVERT: F 65 ASN cc_start: 0.9075 (t0) cc_final: 0.8615 (p0) REVERT: F 132 GLU cc_start: 0.9024 (tt0) cc_final: 0.8659 (tt0) REVERT: F 230 ASP cc_start: 0.8837 (t0) cc_final: 0.8437 (t0) REVERT: G 230 ASP cc_start: 0.8873 (t0) cc_final: 0.8399 (t0) REVERT: H 4 GLU cc_start: 0.9246 (mt-10) cc_final: 0.9010 (mm-30) REVERT: H 23 ASP cc_start: 0.8820 (m-30) cc_final: 0.8587 (m-30) REVERT: H 69 ARG cc_start: 0.8217 (OUTLIER) cc_final: 0.7960 (ttt180) REVERT: H 230 ASP cc_start: 0.9011 (t0) cc_final: 0.8518 (t0) REVERT: H 263 ILE cc_start: 0.9472 (OUTLIER) cc_final: 0.9270 (mp) REVERT: I 23 ASP cc_start: 0.8740 (m-30) cc_final: 0.8398 (m-30) REVERT: I 132 GLU cc_start: 0.9018 (tt0) cc_final: 0.8762 (tt0) REVERT: J 4 GLU cc_start: 0.8763 (tp30) cc_final: 0.8513 (tp30) REVERT: J 11 ASN cc_start: 0.9099 (m-40) cc_final: 0.8712 (m-40) REVERT: J 23 ASP cc_start: 0.8637 (m-30) cc_final: 0.8199 (m-30) REVERT: J 230 ASP cc_start: 0.9105 (t0) cc_final: 0.8407 (t0) outliers start: 59 outliers final: 34 residues processed: 424 average time/residue: 1.2219 time to fit residues: 584.4205 Evaluate side-chains 408 residues out of total 1840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 370 time to evaluate : 2.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 SER Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 162 ILE Chi-restraints excluded: chain C residue 138 LYS Chi-restraints excluded: chain D residue 162 ILE Chi-restraints excluded: chain D residue 197 GLN Chi-restraints excluded: chain E residue 118 SER Chi-restraints excluded: chain E residue 227 THR Chi-restraints excluded: chain F residue 67 CYS Chi-restraints excluded: chain F residue 68 LEU Chi-restraints excluded: chain F residue 98 LEU Chi-restraints excluded: chain F residue 173 LEU Chi-restraints excluded: chain F residue 182 LEU Chi-restraints excluded: chain F residue 184 ILE Chi-restraints excluded: chain F residue 208 LEU Chi-restraints excluded: chain F residue 213 PHE Chi-restraints excluded: chain F residue 260 LEU Chi-restraints excluded: chain G residue 67 CYS Chi-restraints excluded: chain G residue 98 LEU Chi-restraints excluded: chain G residue 208 LEU Chi-restraints excluded: chain H residue 33 THR Chi-restraints excluded: chain H residue 67 CYS Chi-restraints excluded: chain H residue 69 ARG Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain H residue 194 ARG Chi-restraints excluded: chain H residue 259 GLN Chi-restraints excluded: chain H residue 263 ILE Chi-restraints excluded: chain I residue 15 GLN Chi-restraints excluded: chain I residue 64 LEU Chi-restraints excluded: chain I residue 67 CYS Chi-restraints excluded: chain I residue 185 LEU Chi-restraints excluded: chain I residue 246 SER Chi-restraints excluded: chain J residue 64 LEU Chi-restraints excluded: chain J residue 68 LEU Chi-restraints excluded: chain J residue 70 ILE Chi-restraints excluded: chain J residue 97 GLU Chi-restraints excluded: chain J residue 175 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: chunk 26 optimal weight: 0.4980 chunk 104 optimal weight: 3.9990 chunk 186 optimal weight: 7.9990 chunk 155 optimal weight: 2.9990 chunk 132 optimal weight: 7.9990 chunk 210 optimal weight: 1.9990 chunk 2 optimal weight: 0.6980 chunk 51 optimal weight: 1.9990 chunk 231 optimal weight: 0.0040 chunk 22 optimal weight: 1.9990 chunk 185 optimal weight: 3.9990 overall best weight: 1.0396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 107 ASN C 116 ASN ** C 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 15 GLN F 198 GLN G 11 ASN G 118 GLN G 122 GLN H 11 ASN I 11 ASN I 118 GLN I 198 GLN I 259 GLN J 259 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.077661 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2881 r_free = 0.2881 target = 0.059995 restraints weight = 40627.814| |-----------------------------------------------------------------------------| r_work (start): 0.2854 rms_B_bonded: 2.67 r_work: 0.2717 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.2717 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2695 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2695 r_free = 0.2695 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2695 r_free = 0.2695 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2695 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8696 moved from start: 0.3651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 18106 Z= 0.281 Angle : 0.618 9.825 24512 Z= 0.318 Chirality : 0.039 0.248 2874 Planarity : 0.003 0.036 3202 Dihedral : 3.821 25.121 2585 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 2.78 % Allowed : 23.57 % Favored : 73.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.19 (0.17), residues: 2375 helix: 2.85 (0.11), residues: 1905 sheet: None (None), residues: 0 loop : -1.24 (0.27), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP I 189 HIS 0.000 0.000 HIS G 193 PHE 0.031 0.002 PHE B 36 TYR 0.020 0.002 TYR F 227 ARG 0.004 0.000 ARG G 232 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4750 Ramachandran restraints generated. 2375 Oldfield, 0 Emsley, 2375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4750 Ramachandran restraints generated. 2375 Oldfield, 0 Emsley, 2375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 420 residues out of total 1840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 371 time to evaluate : 1.964 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 159 MET cc_start: 0.8706 (mtp) cc_final: 0.8486 (mtm) REVERT: C 34 LEU cc_start: 0.9705 (mp) cc_final: 0.9488 (pt) REVERT: C 44 LYS cc_start: 0.9661 (tppp) cc_final: 0.9311 (tppp) REVERT: D 112 ASP cc_start: 0.9086 (m-30) cc_final: 0.8696 (m-30) REVERT: D 197 GLN cc_start: 0.9471 (OUTLIER) cc_final: 0.8984 (tt0) REVERT: E 44 LYS cc_start: 0.9638 (tppp) cc_final: 0.9337 (tppp) REVERT: F 23 ASP cc_start: 0.8712 (m-30) cc_final: 0.8487 (m-30) REVERT: F 62 GLU cc_start: 0.8921 (pp20) cc_final: 0.8552 (pp20) REVERT: F 65 ASN cc_start: 0.9082 (t0) cc_final: 0.8620 (p0) REVERT: F 132 GLU cc_start: 0.9053 (tt0) cc_final: 0.8640 (tt0) REVERT: F 230 ASP cc_start: 0.8923 (t0) cc_final: 0.8494 (t0) REVERT: G 132 GLU cc_start: 0.8960 (mt-10) cc_final: 0.8733 (mt-10) REVERT: G 230 ASP cc_start: 0.8897 (t0) cc_final: 0.8458 (t0) REVERT: H 4 GLU cc_start: 0.9246 (mt-10) cc_final: 0.8998 (mm-30) REVERT: H 23 ASP cc_start: 0.8743 (m-30) cc_final: 0.8414 (m-30) REVERT: H 69 ARG cc_start: 0.8263 (OUTLIER) cc_final: 0.8000 (ttt180) REVERT: H 230 ASP cc_start: 0.9065 (t0) cc_final: 0.8579 (t0) REVERT: H 263 ILE cc_start: 0.9490 (OUTLIER) cc_final: 0.9281 (mp) REVERT: I 23 ASP cc_start: 0.8742 (m-30) cc_final: 0.8399 (m-30) REVERT: I 132 GLU cc_start: 0.9042 (tt0) cc_final: 0.8735 (tt0) REVERT: I 230 ASP cc_start: 0.9049 (t0) cc_final: 0.8617 (t0) REVERT: J 4 GLU cc_start: 0.8746 (tp30) cc_final: 0.8473 (tp30) REVERT: J 11 ASN cc_start: 0.9092 (m-40) cc_final: 0.8816 (m-40) REVERT: J 20 TYR cc_start: 0.9021 (m-80) cc_final: 0.8737 (m-10) REVERT: J 23 ASP cc_start: 0.8649 (m-30) cc_final: 0.8388 (m-30) REVERT: J 230 ASP cc_start: 0.9126 (t0) cc_final: 0.8412 (t0) outliers start: 49 outliers final: 39 residues processed: 401 average time/residue: 1.2564 time to fit residues: 564.4494 Evaluate side-chains 405 residues out of total 1840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 363 time to evaluate : 1.877 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 SER Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 162 ILE Chi-restraints excluded: chain B residue 227 THR Chi-restraints excluded: chain C residue 162 ILE Chi-restraints excluded: chain C residue 215 MET Chi-restraints excluded: chain D residue 162 ILE Chi-restraints excluded: chain D residue 197 GLN Chi-restraints excluded: chain E residue 118 SER Chi-restraints excluded: chain E residue 218 LEU Chi-restraints excluded: chain E residue 227 THR Chi-restraints excluded: chain F residue 50 LEU Chi-restraints excluded: chain F residue 64 LEU Chi-restraints excluded: chain F residue 67 CYS Chi-restraints excluded: chain F residue 68 LEU Chi-restraints excluded: chain F residue 98 LEU Chi-restraints excluded: chain F residue 173 LEU Chi-restraints excluded: chain F residue 182 LEU Chi-restraints excluded: chain F residue 184 ILE Chi-restraints excluded: chain F residue 208 LEU Chi-restraints excluded: chain F residue 213 PHE Chi-restraints excluded: chain G residue 67 CYS Chi-restraints excluded: chain G residue 98 LEU Chi-restraints excluded: chain G residue 157 LEU Chi-restraints excluded: chain G residue 208 LEU Chi-restraints excluded: chain H residue 33 THR Chi-restraints excluded: chain H residue 67 CYS Chi-restraints excluded: chain H residue 69 ARG Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain H residue 194 ARG Chi-restraints excluded: chain H residue 259 GLN Chi-restraints excluded: chain H residue 263 ILE Chi-restraints excluded: chain I residue 15 GLN Chi-restraints excluded: chain I residue 64 LEU Chi-restraints excluded: chain I residue 67 CYS Chi-restraints excluded: chain I residue 185 LEU Chi-restraints excluded: chain I residue 246 SER Chi-restraints excluded: chain J residue 64 LEU Chi-restraints excluded: chain J residue 68 LEU Chi-restraints excluded: chain J residue 70 ILE Chi-restraints excluded: chain J residue 175 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: chunk 221 optimal weight: 0.6980 chunk 103 optimal weight: 0.8980 chunk 139 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 63 optimal weight: 0.5980 chunk 113 optimal weight: 1.9990 chunk 173 optimal weight: 0.0070 chunk 98 optimal weight: 0.6980 chunk 126 optimal weight: 0.6980 chunk 27 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 overall best weight: 0.5398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 107 ASN C 116 ASN ** C 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 198 GLN G 11 ASN G 118 GLN I 11 ASN I 118 GLN I 198 GLN I 259 GLN J 259 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.078360 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2901 r_free = 0.2901 target = 0.060407 restraints weight = 40664.071| |-----------------------------------------------------------------------------| r_work (start): 0.2891 rms_B_bonded: 2.75 r_work: 0.2755 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.2755 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2734 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2734 r_free = 0.2734 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2734 r_free = 0.2734 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2734 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8672 moved from start: 0.3804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.114 18106 Z= 0.214 Angle : 0.611 11.432 24512 Z= 0.312 Chirality : 0.039 0.323 2874 Planarity : 0.003 0.034 3202 Dihedral : 3.815 25.138 2585 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 2.49 % Allowed : 23.91 % Favored : 73.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.19 (0.17), residues: 2375 helix: 2.89 (0.11), residues: 1900 sheet: None (None), residues: 0 loop : -1.35 (0.28), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP I 189 HIS 0.001 0.000 HIS H 193 PHE 0.032 0.001 PHE B 36 TYR 0.020 0.001 TYR F 227 ARG 0.007 0.000 ARG F 232 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4750 Ramachandran restraints generated. 2375 Oldfield, 0 Emsley, 2375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4750 Ramachandran restraints generated. 2375 Oldfield, 0 Emsley, 2375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 426 residues out of total 1840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 382 time to evaluate : 2.162 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 159 MET cc_start: 0.8585 (mtp) cc_final: 0.8357 (mtm) REVERT: C 34 LEU cc_start: 0.9689 (mp) cc_final: 0.9479 (pt) REVERT: C 44 LYS cc_start: 0.9621 (tppp) cc_final: 0.9249 (tppp) REVERT: C 215 MET cc_start: 0.9184 (OUTLIER) cc_final: 0.8936 (mmm) REVERT: D 112 ASP cc_start: 0.9068 (m-30) cc_final: 0.8836 (m-30) REVERT: D 197 GLN cc_start: 0.9450 (OUTLIER) cc_final: 0.8968 (tt0) REVERT: E 44 LYS cc_start: 0.9647 (tppp) cc_final: 0.9356 (tppp) REVERT: F 23 ASP cc_start: 0.8665 (m-30) cc_final: 0.8406 (m-30) REVERT: F 62 GLU cc_start: 0.8904 (pp20) cc_final: 0.8530 (pp20) REVERT: F 65 ASN cc_start: 0.9068 (t0) cc_final: 0.8604 (p0) REVERT: F 132 GLU cc_start: 0.9019 (tt0) cc_final: 0.8655 (tt0) REVERT: F 230 ASP cc_start: 0.8836 (t0) cc_final: 0.8436 (t0) REVERT: G 132 GLU cc_start: 0.8917 (mt-10) cc_final: 0.8691 (mt-10) REVERT: G 133 GLU cc_start: 0.9366 (mm-30) cc_final: 0.9155 (mm-30) REVERT: G 230 ASP cc_start: 0.8837 (t0) cc_final: 0.8444 (t0) REVERT: H 4 GLU cc_start: 0.9208 (mt-10) cc_final: 0.8978 (mm-30) REVERT: H 23 ASP cc_start: 0.8770 (m-30) cc_final: 0.8425 (m-30) REVERT: H 69 ARG cc_start: 0.8256 (OUTLIER) cc_final: 0.8011 (ttt180) REVERT: H 179 LEU cc_start: 0.9019 (mm) cc_final: 0.8728 (mt) REVERT: H 230 ASP cc_start: 0.9026 (t0) cc_final: 0.8549 (t0) REVERT: I 23 ASP cc_start: 0.8751 (m-30) cc_final: 0.8412 (m-30) REVERT: I 132 GLU cc_start: 0.9032 (tt0) cc_final: 0.8760 (tt0) REVERT: I 230 ASP cc_start: 0.9042 (t0) cc_final: 0.8413 (t0) REVERT: J 4 GLU cc_start: 0.8736 (tp30) cc_final: 0.8372 (tp30) REVERT: J 11 ASN cc_start: 0.9083 (m-40) cc_final: 0.8809 (m-40) REVERT: J 23 ASP cc_start: 0.8641 (m-30) cc_final: 0.8380 (m-30) REVERT: J 230 ASP cc_start: 0.9105 (t0) cc_final: 0.8442 (t0) outliers start: 44 outliers final: 29 residues processed: 405 average time/residue: 1.2562 time to fit residues: 573.3448 Evaluate side-chains 403 residues out of total 1840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 371 time to evaluate : 2.064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 SER Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 162 ILE Chi-restraints excluded: chain C residue 215 MET Chi-restraints excluded: chain D residue 162 ILE Chi-restraints excluded: chain D residue 197 GLN Chi-restraints excluded: chain E residue 118 SER Chi-restraints excluded: chain E residue 227 THR Chi-restraints excluded: chain F residue 50 LEU Chi-restraints excluded: chain F residue 67 CYS Chi-restraints excluded: chain F residue 98 LEU Chi-restraints excluded: chain F residue 173 LEU Chi-restraints excluded: chain F residue 182 LEU Chi-restraints excluded: chain F residue 184 ILE Chi-restraints excluded: chain F residue 208 LEU Chi-restraints excluded: chain F residue 213 PHE Chi-restraints excluded: chain G residue 67 CYS Chi-restraints excluded: chain G residue 98 LEU Chi-restraints excluded: chain G residue 157 LEU Chi-restraints excluded: chain G residue 208 LEU Chi-restraints excluded: chain H residue 33 THR Chi-restraints excluded: chain H residue 67 CYS Chi-restraints excluded: chain H residue 69 ARG Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain H residue 259 GLN Chi-restraints excluded: chain I residue 15 GLN Chi-restraints excluded: chain I residue 67 CYS Chi-restraints excluded: chain I residue 185 LEU Chi-restraints excluded: chain I residue 246 SER Chi-restraints excluded: chain J residue 64 LEU Chi-restraints excluded: chain J residue 175 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: chunk 137 optimal weight: 8.9990 chunk 157 optimal weight: 0.8980 chunk 183 optimal weight: 0.5980 chunk 16 optimal weight: 0.9990 chunk 174 optimal weight: 0.8980 chunk 100 optimal weight: 0.6980 chunk 231 optimal weight: 0.0570 chunk 46 optimal weight: 0.9980 chunk 133 optimal weight: 0.0020 chunk 164 optimal weight: 0.0970 chunk 60 optimal weight: 0.0980 overall best weight: 0.1704 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 107 ASN C 116 ASN ** C 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 198 GLN G 11 ASN G 118 GLN G 122 GLN H 11 ASN I 11 ASN I 118 GLN I 198 GLN J 118 GLN J 259 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.082693 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.065168 restraints weight = 40304.230| |-----------------------------------------------------------------------------| r_work (start): 0.2981 rms_B_bonded: 2.64 r_work: 0.2857 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.2857 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2827 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2827 r_free = 0.2827 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2827 r_free = 0.2827 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2827 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8667 moved from start: 0.4083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.082 18106 Z= 0.185 Angle : 0.614 12.035 24512 Z= 0.309 Chirality : 0.038 0.266 2874 Planarity : 0.003 0.050 3202 Dihedral : 3.760 26.357 2585 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 2.04 % Allowed : 24.82 % Favored : 73.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.23 (0.17), residues: 2375 helix: 2.91 (0.11), residues: 1900 sheet: None (None), residues: 0 loop : -1.31 (0.28), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.001 TRP I 189 HIS 0.001 0.000 HIS H 193 PHE 0.030 0.002 PHE B 36 TYR 0.018 0.001 TYR F 227 ARG 0.013 0.000 ARG F 232 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13626.48 seconds wall clock time: 240 minutes 57.43 seconds (14457.43 seconds total)