Starting phenix.real_space_refine on Thu Sep 18 14:59:41 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8rt9_19483/09_2025/8rt9_19483.cif Found real_map, /net/cci-nas-00/data/ceres_data/8rt9_19483/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/8rt9_19483/09_2025/8rt9_19483.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8rt9_19483/09_2025/8rt9_19483.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8rt9_19483/09_2025/8rt9_19483.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8rt9_19483/09_2025/8rt9_19483.map" } resolution = 2.97 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.007 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: {'ARG:plan': 1, 'GLU:plan': 1, 'GLN:plan1': 5, '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: {'ARG:plan': 1, 'GLU:plan': 1, 'GLN:plan1': 3, '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: {'ARG:plan': 1, 'GLU:plan': 1, 'GLN:plan1': 3, '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: {'ARG:plan': 1, 'GLU:plan': 1, 'GLN:plan1': 3, '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: {'ARG:plan': 1, 'GLU:plan': 1, 'GLN:plan1': 3, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 24 Time building chain proxies: 4.99, per 1000 atoms: 0.28 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: 1.84 Conformation dependent library (CDL) restraints added in 848.1 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.47 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: 3.00 Time building geometry restraints manager: 2.36 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: 9.800 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.290 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 18.420 Find NCS groups from input model: 0.500 Set up NCS constraints: 0.040 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:7.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.290 ------------------------------------------------------------------------------- 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= 0.416 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.013 0.001 ARG C 210 TYR 0.018 0.002 TYR H 83 PHE 0.026 0.002 PHE F 213 TRP 0.010 0.001 TRP J 199 HIS 0.001 0.000 HIS G 193 Details of bonding type rmsd covalent geometry : bond 0.00728 (18106) covalent geometry : angle 0.79006 (24512) hydrogen bonds : bond 0.11053 ( 1597) hydrogen bonds : angle 4.83168 ( 4761) *********************** 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 : 0.726 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: 0.7155 time to fit residues: 483.4442 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 : 0.704 ------------------------------------------------------------------------------- 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 216 optimal weight: 0.5980 chunk 98 optimal weight: 0.9990 chunk 194 optimal weight: 0.9990 chunk 227 optimal weight: 0.6980 chunk 107 optimal weight: 0.6980 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 0.5980 chunk 103 optimal weight: 1.9990 chunk 200 optimal weight: 0.0020 overall best weight: 0.5188 ------------------------------------------------------------------------------- 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** C 154 GLN ** 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: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.080859 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.063337 restraints weight = 40076.527| |-----------------------------------------------------------------------------| r_work (start): 0.2897 rms_B_bonded: 2.63 r_work: 0.2750 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.2750 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2755 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2755 r_free = 0.2755 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 = 0.2755 r_free = 0.2755 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2755 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8623 moved from start: 0.2386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 18106 Z= 0.163 Angle : 0.573 10.710 24512 Z= 0.307 Chirality : 0.039 0.193 2874 Planarity : 0.004 0.054 3202 Dihedral : 5.156 140.005 2591 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 4.14 % Allowed : 14.50 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.07 (0.17), residues: 2375 helix: 2.85 (0.11), residues: 1890 sheet: None (None), residues: 0 loop : -1.55 (0.26), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 32 TYR 0.017 0.002 TYR F 83 PHE 0.030 0.001 PHE H 213 TRP 0.022 0.001 TRP H 189 HIS 0.001 0.000 HIS H 193 Details of bonding type rmsd covalent geometry : bond 0.00330 (18106) covalent geometry : angle 0.57258 (24512) hydrogen bonds : bond 0.05851 ( 1597) hydrogen bonds : angle 4.38070 ( 4761) *********************** 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 530 residues out of total 1840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 457 time to evaluate : 0.714 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: 0.9252 (m) cc_final: 0.8945 (m) REVERT: A 212 GLU cc_start: 0.9128 (OUTLIER) cc_final: 0.8887 (tp30) REVERT: B 38 GLN cc_start: 0.9436 (mm-40) cc_final: 0.9213 (mm-40) REVERT: B 81 GLU cc_start: 0.9141 (mm-30) cc_final: 0.8933 (mp0) REVERT: B 212 GLU cc_start: 0.9169 (OUTLIER) cc_final: 0.8912 (tm-30) REVERT: C 44 LYS cc_start: 0.9661 (tppp) cc_final: 0.9323 (tppp) REVERT: C 145 TYR cc_start: 0.9468 (t80) cc_final: 0.9112 (t80) REVERT: D 45 GLU cc_start: 0.9161 (pt0) cc_final: 0.8679 (pm20) REVERT: D 112 ASP cc_start: 0.9146 (m-30) cc_final: 0.8910 (m-30) REVERT: D 145 TYR cc_start: 0.9488 (t80) cc_final: 0.9260 (t80) REVERT: E 44 LYS cc_start: 0.9690 (tppp) cc_final: 0.9456 (tppp) REVERT: E 159 MET cc_start: 0.8922 (mtt) cc_final: 0.8558 (mtm) REVERT: F 4 GLU cc_start: 0.8801 (tp30) cc_final: 0.8591 (tp30) REVERT: F 23 ASP cc_start: 0.8522 (m-30) cc_final: 0.8312 (m-30) REVERT: F 63 PHE cc_start: 0.8959 (t80) cc_final: 0.8720 (t80) REVERT: F 132 GLU cc_start: 0.9026 (tt0) cc_final: 0.8613 (tt0) REVERT: F 201 GLN cc_start: 0.9307 (OUTLIER) cc_final: 0.8992 (tt0) REVERT: F 222 GLN cc_start: 0.8987 (tm-30) cc_final: 0.8735 (tm-30) REVERT: G 69 ARG cc_start: 0.8217 (ttt90) cc_final: 0.7993 (ttt180) REVERT: G 230 ASP cc_start: 0.9036 (t0) cc_final: 0.8526 (t0) REVERT: H 4 GLU cc_start: 0.9303 (mt-10) cc_final: 0.8994 (tp30) REVERT: H 23 ASP cc_start: 0.8782 (m-30) cc_final: 0.8575 (m-30) REVERT: H 230 ASP cc_start: 0.8948 (t0) cc_final: 0.8563 (t0) REVERT: I 4 GLU cc_start: 0.8697 (tp30) cc_final: 0.8450 (tp30) REVERT: I 129 GLU cc_start: 0.9175 (mt-10) cc_final: 0.8939 (mt-10) REVERT: I 189 TRP cc_start: 0.7913 (m100) cc_final: 0.7693 (m-10) REVERT: I 228 MET cc_start: 0.9473 (mmm) cc_final: 0.9252 (mmt) REVERT: I 230 ASP cc_start: 0.9104 (t0) cc_final: 0.8748 (t0) REVERT: J 4 GLU cc_start: 0.8709 (tp30) cc_final: 0.8421 (tp30) REVERT: J 222 GLN cc_start: 0.9004 (tm-30) cc_final: 0.8764 (tm-30) REVERT: J 230 ASP cc_start: 0.9197 (t0) cc_final: 0.8644 (t0) outliers start: 73 outliers final: 18 residues processed: 494 average time/residue: 0.6539 time to fit residues: 360.6007 Evaluate side-chains 402 residues out of total 1840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 381 time to evaluate : 0.723 ------------------------------------------------------------------------------- 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 F residue 260 LEU 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 115 LEU 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 68 LEU 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 38 optimal weight: 0.7980 chunk 92 optimal weight: 0.9990 chunk 137 optimal weight: 10.0000 chunk 187 optimal weight: 0.9980 chunk 141 optimal weight: 0.8980 chunk 186 optimal weight: 4.9990 chunk 75 optimal weight: 0.6980 chunk 99 optimal weight: 0.6980 chunk 183 optimal weight: 0.9980 chunk 160 optimal weight: 4.9990 chunk 117 optimal weight: 0.4980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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** ** B 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 107 ASN C 116 ASN ** D 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 53 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 118 GLN I 198 GLN I 259 GLN J 15 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 = 0.3227 r_free = 0.3227 target = 0.077972 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2866 r_free = 0.2866 target = 0.059676 restraints weight = 40615.995| |-----------------------------------------------------------------------------| r_work (start): 0.2844 rms_B_bonded: 2.64 r_work: 0.2697 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.2697 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2702 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2702 r_free = 0.2702 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 = 0.2702 r_free = 0.2702 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2702 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8602 moved from start: 0.2816 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= 0.164 Angle : 0.556 10.143 24512 Z= 0.289 Chirality : 0.038 0.188 2874 Planarity : 0.004 0.066 3202 Dihedral : 4.003 27.428 2585 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 4.31 % Allowed : 17.28 % Favored : 78.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.15 (0.17), residues: 2375 helix: 2.89 (0.11), residues: 1895 sheet: None (None), residues: 0 loop : -1.49 (0.26), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 32 TYR 0.017 0.001 TYR F 83 PHE 0.023 0.001 PHE H 213 TRP 0.027 0.001 TRP F 189 HIS 0.001 0.000 HIS H 193 Details of bonding type rmsd covalent geometry : bond 0.00347 (18106) covalent geometry : angle 0.55626 (24512) hydrogen bonds : bond 0.05512 ( 1597) hydrogen bonds : angle 4.25457 ( 4761) *********************** 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 496 residues out of total 1840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 420 time to evaluate : 0.722 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 125 SER cc_start: 0.9022 (m) cc_final: 0.8764 (m) REVERT: B 38 GLN cc_start: 0.9574 (mm-40) cc_final: 0.9332 (mm-40) REVERT: C 44 LYS cc_start: 0.9668 (tppp) cc_final: 0.9307 (tppp) REVERT: C 45 GLU cc_start: 0.9242 (pt0) cc_final: 0.8676 (pm20) REVERT: D 112 ASP cc_start: 0.9126 (m-30) cc_final: 0.8886 (m-30) REVERT: D 197 GLN cc_start: 0.9451 (OUTLIER) cc_final: 0.9107 (tt0) REVERT: E 44 LYS cc_start: 0.9643 (tppp) cc_final: 0.9382 (tppp) REVERT: F 4 GLU cc_start: 0.8871 (tp30) cc_final: 0.8614 (tp30) REVERT: F 23 ASP cc_start: 0.8553 (m-30) cc_final: 0.8315 (m-30) REVERT: F 62 GLU cc_start: 0.9001 (pp20) cc_final: 0.8774 (pp20) REVERT: F 65 ASN cc_start: 0.9092 (t0) cc_final: 0.8662 (p0) REVERT: F 132 GLU cc_start: 0.9058 (tt0) cc_final: 0.8650 (tt0) REVERT: F 157 LEU cc_start: 0.8822 (OUTLIER) cc_final: 0.8547 (tt) REVERT: F 230 ASP cc_start: 0.8918 (t0) cc_final: 0.8497 (t0) REVERT: G 230 ASP cc_start: 0.9049 (t0) cc_final: 0.8507 (t0) REVERT: H 23 ASP cc_start: 0.8789 (m-30) cc_final: 0.8516 (m-30) REVERT: H 87 ILE cc_start: 0.9079 (mm) cc_final: 0.8841 (mm) REVERT: H 230 ASP cc_start: 0.9018 (t0) cc_final: 0.8523 (t0) REVERT: I 4 GLU cc_start: 0.8732 (tp30) cc_final: 0.8489 (tp30) REVERT: I 23 ASP cc_start: 0.8696 (m-30) cc_final: 0.8398 (m-30) REVERT: I 129 GLU cc_start: 0.9184 (mt-10) cc_final: 0.8967 (mt-10) REVERT: I 189 TRP cc_start: 0.7807 (m100) cc_final: 0.7545 (m-10) REVERT: I 230 ASP cc_start: 0.9072 (t0) cc_final: 0.8565 (t0) REVERT: J 4 GLU cc_start: 0.8709 (tp30) cc_final: 0.8418 (tp30) REVERT: J 23 ASP cc_start: 0.8546 (m-30) cc_final: 0.8089 (m-30) REVERT: J 222 GLN cc_start: 0.9011 (tm-30) cc_final: 0.8797 (tm-30) REVERT: J 230 ASP cc_start: 0.9161 (t0) cc_final: 0.8600 (t0) outliers start: 76 outliers final: 28 residues processed: 460 average time/residue: 0.6628 time to fit residues: 339.5860 Evaluate side-chains 407 residues out of total 1840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 377 time to evaluate : 0.700 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 162 ILE Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain C residue 31 THR Chi-restraints excluded: chain C residue 34 LEU 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 157 LEU 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 68 LEU Chi-restraints excluded: chain G residue 97 GLU 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 84 optimal weight: 4.9990 chunk 191 optimal weight: 1.9990 chunk 171 optimal weight: 1.9990 chunk 166 optimal weight: 1.9990 chunk 149 optimal weight: 0.7980 chunk 165 optimal weight: 0.6980 chunk 157 optimal weight: 4.9990 chunk 217 optimal weight: 0.9980 chunk 180 optimal weight: 0.9990 chunk 187 optimal weight: 2.9990 chunk 91 optimal weight: 0.6980 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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 H 11 ASN H 118 GLN H 202 GLN H 237 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 = 0.3258 r_free = 0.3258 target = 0.079128 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2930 r_free = 0.2930 target = 0.061535 restraints weight = 40647.314| |-----------------------------------------------------------------------------| r_work (start): 0.2872 rms_B_bonded: 2.61 r_work: 0.2726 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.2726 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2731 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2731 r_free = 0.2731 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 = 0.2731 r_free = 0.2731 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2731 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8662 moved from start: 0.3066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 18106 Z= 0.171 Angle : 0.554 9.665 24512 Z= 0.288 Chirality : 0.038 0.184 2874 Planarity : 0.003 0.043 3202 Dihedral : 3.909 27.034 2585 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 3.40 % Allowed : 19.89 % Favored : 76.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.26 (0.17), residues: 2375 helix: 2.92 (0.11), residues: 1900 sheet: None (None), residues: 0 loop : -1.26 (0.27), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 32 TYR 0.018 0.002 TYR F 83 PHE 0.019 0.001 PHE H 213 TRP 0.023 0.001 TRP F 189 HIS 0.001 0.000 HIS H 193 Details of bonding type rmsd covalent geometry : bond 0.00371 (18106) covalent geometry : angle 0.55448 (24512) hydrogen bonds : bond 0.05406 ( 1597) hydrogen bonds : angle 4.23515 ( 4761) *********************** 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 452 residues out of total 1840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 392 time to evaluate : 0.783 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: 0.9269 (pt0) cc_final: 0.9012 (pm20) REVERT: A 125 SER cc_start: 0.9082 (m) cc_final: 0.8826 (m) REVERT: B 34 LEU cc_start: 0.9660 (mp) cc_final: 0.9340 (pt) REVERT: B 38 GLN cc_start: 0.9572 (mm-40) cc_final: 0.9275 (mm-40) REVERT: C 44 LYS cc_start: 0.9647 (tppp) cc_final: 0.9249 (tppp) REVERT: D 112 ASP cc_start: 0.9101 (m-30) cc_final: 0.8850 (m-30) REVERT: F 4 GLU cc_start: 0.8869 (tp30) cc_final: 0.8639 (tp30) REVERT: F 23 ASP cc_start: 0.8590 (m-30) cc_final: 0.8363 (m-30) REVERT: F 62 GLU cc_start: 0.8968 (pp20) cc_final: 0.8742 (pp20) REVERT: F 65 ASN cc_start: 0.9095 (t0) cc_final: 0.8661 (p0) REVERT: F 132 GLU cc_start: 0.9054 (tt0) cc_final: 0.8635 (tt0) REVERT: F 230 ASP cc_start: 0.8947 (t0) cc_final: 0.8525 (t0) REVERT: G 230 ASP cc_start: 0.9086 (t0) cc_final: 0.8546 (t0) REVERT: H 4 GLU cc_start: 0.9254 (mt-10) cc_final: 0.9048 (mm-30) REVERT: H 23 ASP cc_start: 0.8812 (m-30) cc_final: 0.8577 (m-30) REVERT: H 69 ARG cc_start: 0.8193 (OUTLIER) cc_final: 0.7961 (ttt180) REVERT: H 87 ILE cc_start: 0.9090 (mm) cc_final: 0.8818 (mm) REVERT: H 230 ASP cc_start: 0.9034 (t0) cc_final: 0.8547 (t0) REVERT: H 259 GLN cc_start: 0.8889 (OUTLIER) cc_final: 0.8683 (mp10) REVERT: H 263 ILE cc_start: 0.9494 (OUTLIER) cc_final: 0.9288 (mp) REVERT: I 4 GLU cc_start: 0.8749 (tp30) cc_final: 0.8498 (tp30) REVERT: I 23 ASP cc_start: 0.8754 (m-30) cc_final: 0.8417 (m-30) REVERT: I 230 ASP cc_start: 0.9123 (t0) cc_final: 0.8601 (t0) REVERT: J 4 GLU cc_start: 0.8736 (tp30) cc_final: 0.8450 (tp30) REVERT: J 11 ASN cc_start: 0.9073 (m-40) cc_final: 0.8816 (m-40) REVERT: J 62 GLU cc_start: 0.8911 (pp20) cc_final: 0.8596 (pp20) REVERT: J 222 GLN cc_start: 0.9061 (tm-30) cc_final: 0.8841 (tm-30) REVERT: J 230 ASP cc_start: 0.9155 (t0) cc_final: 0.8442 (t0) outliers start: 60 outliers final: 31 residues processed: 423 average time/residue: 0.6482 time to fit residues: 306.1593 Evaluate side-chains 408 residues out of total 1840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 374 time to evaluate : 0.757 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain B residue 31 THR 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 D residue 162 ILE 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 184 ILE 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 83 TYR Chi-restraints excluded: chain G residue 157 LEU Chi-restraints excluded: chain G residue 208 LEU Chi-restraints excluded: chain G residue 254 ILE 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 97 GLU 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 59 optimal weight: 0.8980 chunk 173 optimal weight: 0.0870 chunk 42 optimal weight: 0.9980 chunk 6 optimal weight: 0.7980 chunk 224 optimal weight: 0.9980 chunk 24 optimal weight: 2.9990 chunk 10 optimal weight: 0.9980 chunk 8 optimal weight: 0.8980 chunk 193 optimal weight: 1.9990 chunk 206 optimal weight: 0.8980 chunk 53 optimal weight: 1.9990 overall best weight: 0.7158 ------------------------------------------------------------------------------- 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 = 0.3263 r_free = 0.3263 target = 0.079375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2936 r_free = 0.2936 target = 0.061648 restraints weight = 40582.654| |-----------------------------------------------------------------------------| r_work (start): 0.2880 rms_B_bonded: 2.62 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: 0.8661 moved from start: 0.3240 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= 0.160 Angle : 0.546 9.961 24512 Z= 0.284 Chirality : 0.038 0.232 2874 Planarity : 0.003 0.040 3202 Dihedral : 3.856 26.037 2585 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 3.57 % Allowed : 20.85 % Favored : 75.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.30 (0.17), residues: 2375 helix: 2.97 (0.11), residues: 1895 sheet: None (None), residues: 0 loop : -1.33 (0.27), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 114 TYR 0.016 0.001 TYR F 83 PHE 0.019 0.001 PHE A 28 TRP 0.027 0.001 TRP F 189 HIS 0.001 0.000 HIS H 193 Details of bonding type rmsd covalent geometry : bond 0.00341 (18106) covalent geometry : angle 0.54628 (24512) hydrogen bonds : bond 0.05276 ( 1597) hydrogen bonds : angle 4.19983 ( 4761) *********************** 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 470 residues out of total 1840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 407 time to evaluate : 0.725 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: B 34 LEU cc_start: 0.9665 (mp) cc_final: 0.9328 (pt) REVERT: B 38 GLN cc_start: 0.9603 (mm-40) cc_final: 0.9290 (mm-40) REVERT: B 159 MET cc_start: 0.8553 (mtp) cc_final: 0.8297 (mtt) REVERT: B 223 GLN cc_start: 0.8657 (mm-40) cc_final: 0.8312 (mm110) REVERT: C 114 ARG cc_start: 0.8699 (mtp85) cc_final: 0.8440 (mmp80) REVERT: D 112 ASP cc_start: 0.9073 (m-30) cc_final: 0.8821 (m-30) REVERT: F 23 ASP cc_start: 0.8613 (m-30) cc_final: 0.8376 (m-30) REVERT: F 62 GLU cc_start: 0.8966 (pp20) cc_final: 0.8502 (pp20) REVERT: F 65 ASN cc_start: 0.9096 (t0) cc_final: 0.8632 (p0) REVERT: F 132 GLU cc_start: 0.9046 (tt0) cc_final: 0.8624 (tt0) REVERT: F 230 ASP cc_start: 0.8946 (t0) cc_final: 0.8558 (t0) REVERT: G 230 ASP cc_start: 0.9055 (t0) cc_final: 0.8525 (t0) REVERT: H 4 GLU cc_start: 0.9251 (mt-10) cc_final: 0.9047 (mm-30) REVERT: H 23 ASP cc_start: 0.8810 (m-30) cc_final: 0.8584 (m-30) REVERT: H 69 ARG cc_start: 0.8209 (OUTLIER) cc_final: 0.7978 (ttt180) REVERT: H 230 ASP cc_start: 0.9043 (t0) cc_final: 0.8533 (t0) REVERT: H 259 GLN cc_start: 0.8845 (mp10) cc_final: 0.8566 (mp10) REVERT: H 263 ILE cc_start: 0.9488 (OUTLIER) cc_final: 0.9285 (mp) REVERT: I 4 GLU cc_start: 0.8720 (tp30) cc_final: 0.8465 (tp30) REVERT: I 23 ASP cc_start: 0.8756 (m-30) cc_final: 0.8397 (m-30) REVERT: J 4 GLU cc_start: 0.8743 (tp30) cc_final: 0.8452 (tp30) REVERT: J 11 ASN cc_start: 0.9097 (m-40) cc_final: 0.8806 (m-40) REVERT: J 23 ASP cc_start: 0.8558 (m-30) cc_final: 0.8131 (m-30) REVERT: J 222 GLN cc_start: 0.9052 (tm-30) cc_final: 0.8779 (tm-30) REVERT: J 230 ASP cc_start: 0.9141 (t0) cc_final: 0.8433 (t0) outliers start: 63 outliers final: 30 residues processed: 442 average time/residue: 0.6177 time to fit residues: 305.9490 Evaluate side-chains 410 residues out of total 1840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 378 time to evaluate : 0.714 ------------------------------------------------------------------------------- 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 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 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 83 TYR Chi-restraints excluded: chain G residue 96 ASP Chi-restraints excluded: chain G residue 98 LEU Chi-restraints excluded: chain G residue 208 LEU Chi-restraints excluded: chain G residue 254 ILE 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 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 87 ILE 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: chunk 117 optimal weight: 1.9990 chunk 147 optimal weight: 0.9980 chunk 66 optimal weight: 1.9990 chunk 17 optimal weight: 0.5980 chunk 67 optimal weight: 0.7980 chunk 209 optimal weight: 0.8980 chunk 146 optimal weight: 0.9990 chunk 75 optimal weight: 2.9990 chunk 173 optimal weight: 0.6980 chunk 221 optimal weight: 0.9980 chunk 230 optimal weight: 0.5980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 I 11 ASN I 118 GLN I 198 GLN I 259 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.079299 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.061783 restraints weight = 40377.619| |-----------------------------------------------------------------------------| r_work (start): 0.2881 rms_B_bonded: 2.55 r_work: 0.2736 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.2736 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2742 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2742 r_free = 0.2742 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 = 0.2742 r_free = 0.2742 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2742 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8658 moved from start: 0.3363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 18106 Z= 0.161 Angle : 0.558 11.337 24512 Z= 0.289 Chirality : 0.038 0.300 2874 Planarity : 0.003 0.037 3202 Dihedral : 3.834 24.917 2585 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 3.85 % Allowed : 21.81 % Favored : 74.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.32 (0.17), residues: 2375 helix: 2.98 (0.11), residues: 1900 sheet: None (None), residues: 0 loop : -1.31 (0.28), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 232 TYR 0.015 0.001 TYR F 83 PHE 0.032 0.001 PHE H 213 TRP 0.032 0.001 TRP F 189 HIS 0.001 0.000 HIS J 193 Details of bonding type rmsd covalent geometry : bond 0.00345 (18106) covalent geometry : angle 0.55775 (24512) hydrogen bonds : bond 0.05250 ( 1597) hydrogen bonds : angle 4.19922 ( 4761) *********************** 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 459 residues out of total 1840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 391 time to evaluate : 0.730 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 GLU cc_start: 0.9283 (pt0) cc_final: 0.8836 (pm20) REVERT: B 159 MET cc_start: 0.8606 (mtp) cc_final: 0.8354 (mtm) REVERT: B 223 GLN cc_start: 0.8700 (mm-40) cc_final: 0.8341 (mm110) REVERT: C 44 LYS cc_start: 0.9636 (tppp) cc_final: 0.9280 (tppp) REVERT: C 159 MET cc_start: 0.8566 (OUTLIER) cc_final: 0.8151 (mtp) REVERT: D 45 GLU cc_start: 0.9201 (pt0) cc_final: 0.8683 (pm20) REVERT: D 112 ASP cc_start: 0.9077 (m-30) cc_final: 0.8825 (m-30) REVERT: D 197 GLN cc_start: 0.9449 (OUTLIER) cc_final: 0.8978 (tt0) REVERT: E 44 LYS cc_start: 0.9638 (tppp) cc_final: 0.9339 (tppp) REVERT: F 23 ASP cc_start: 0.8646 (m-30) cc_final: 0.8395 (m-30) REVERT: F 65 ASN cc_start: 0.9096 (t0) cc_final: 0.8628 (p0) REVERT: F 132 GLU cc_start: 0.9042 (tt0) cc_final: 0.8618 (tt0) REVERT: F 189 TRP cc_start: 0.8557 (m-90) cc_final: 0.8221 (m-10) REVERT: F 230 ASP cc_start: 0.8890 (t0) cc_final: 0.8489 (t0) REVERT: G 230 ASP cc_start: 0.9050 (t0) cc_final: 0.8527 (t0) REVERT: H 4 GLU cc_start: 0.9249 (mt-10) cc_final: 0.9044 (mm-30) REVERT: H 23 ASP cc_start: 0.8806 (m-30) cc_final: 0.8552 (m-30) REVERT: H 69 ARG cc_start: 0.8218 (OUTLIER) cc_final: 0.7978 (ttt180) REVERT: H 230 ASP cc_start: 0.9044 (t0) cc_final: 0.8538 (t0) REVERT: H 263 ILE cc_start: 0.9482 (OUTLIER) cc_final: 0.9277 (mp) REVERT: I 4 GLU cc_start: 0.8722 (tp30) cc_final: 0.8486 (tp30) REVERT: I 23 ASP cc_start: 0.8754 (m-30) cc_final: 0.8405 (m-30) REVERT: J 4 GLU cc_start: 0.8744 (tp30) cc_final: 0.8486 (tp30) REVERT: J 11 ASN cc_start: 0.9096 (m-40) cc_final: 0.8715 (m-40) REVERT: J 23 ASP cc_start: 0.8583 (m-30) cc_final: 0.8131 (m-30) REVERT: J 222 GLN cc_start: 0.9058 (tm-30) cc_final: 0.8796 (tm-30) REVERT: J 230 ASP cc_start: 0.9141 (t0) cc_final: 0.8415 (t0) outliers start: 68 outliers final: 35 residues processed: 432 average time/residue: 0.6331 time to fit residues: 305.9668 Evaluate side-chains 410 residues out of total 1840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 371 time to evaluate : 0.753 ------------------------------------------------------------------------------- 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 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 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 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 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 175 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: chunk 12 optimal weight: 0.5980 chunk 41 optimal weight: 3.9990 chunk 48 optimal weight: 1.9990 chunk 175 optimal weight: 1.9990 chunk 214 optimal weight: 5.9990 chunk 234 optimal weight: 2.9990 chunk 28 optimal weight: 0.8980 chunk 140 optimal weight: 0.9990 chunk 86 optimal weight: 0.9990 chunk 162 optimal weight: 0.0060 chunk 100 optimal weight: 0.0970 overall best weight: 0.5196 ------------------------------------------------------------------------------- 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 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: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.080126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.062478 restraints weight = 40598.102| |-----------------------------------------------------------------------------| r_work (start): 0.2897 rms_B_bonded: 2.60 r_work: 0.2753 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.2753 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2761 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2761 r_free = 0.2761 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 = 0.2761 r_free = 0.2761 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2761 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8650 moved from start: 0.3545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 18106 Z= 0.148 Angle : 0.555 10.490 24512 Z= 0.289 Chirality : 0.037 0.183 2874 Planarity : 0.003 0.031 3202 Dihedral : 3.805 23.994 2585 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 3.68 % Allowed : 22.15 % Favored : 74.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.33 (0.17), residues: 2375 helix: 2.97 (0.11), residues: 1900 sheet: None (None), residues: 0 loop : -1.27 (0.28), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 232 TYR 0.014 0.001 TYR F 227 PHE 0.030 0.002 PHE H 213 TRP 0.040 0.001 TRP I 189 HIS 0.001 0.000 HIS H 193 Details of bonding type rmsd covalent geometry : bond 0.00306 (18106) covalent geometry : angle 0.55486 (24512) hydrogen bonds : bond 0.05115 ( 1597) hydrogen bonds : angle 4.16215 ( 4761) *********************** 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 457 residues out of total 1840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 392 time to evaluate : 0.722 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: A 172 GLU cc_start: 0.9194 (mm-30) cc_final: 0.8601 (mm-30) REVERT: B 159 MET cc_start: 0.8549 (mtp) cc_final: 0.8292 (mtm) REVERT: B 223 GLN cc_start: 0.8719 (mm-40) cc_final: 0.8325 (mm110) REVERT: C 34 LEU cc_start: 0.9691 (mp) cc_final: 0.9468 (pt) REVERT: C 44 LYS cc_start: 0.9648 (tppp) cc_final: 0.9315 (tppp) REVERT: C 138 LYS cc_start: 0.9197 (OUTLIER) cc_final: 0.8796 (tttm) REVERT: D 112 ASP cc_start: 0.9082 (m-30) cc_final: 0.8845 (m-30) REVERT: D 197 GLN cc_start: 0.9449 (OUTLIER) cc_final: 0.8973 (tt0) REVERT: F 23 ASP cc_start: 0.8673 (m-30) cc_final: 0.8448 (m-30) REVERT: F 62 GLU cc_start: 0.8909 (pp20) cc_final: 0.8602 (pp20) REVERT: F 132 GLU cc_start: 0.9016 (tt0) cc_final: 0.8602 (tt0) REVERT: F 189 TRP cc_start: 0.8534 (m-90) cc_final: 0.8187 (m-10) REVERT: F 230 ASP cc_start: 0.8820 (t0) cc_final: 0.8424 (t0) REVERT: G 230 ASP cc_start: 0.8936 (t0) cc_final: 0.8448 (t0) REVERT: H 4 GLU cc_start: 0.9238 (mt-10) cc_final: 0.9034 (mm-30) REVERT: H 23 ASP cc_start: 0.8789 (m-30) cc_final: 0.8544 (m-30) REVERT: H 69 ARG cc_start: 0.8211 (OUTLIER) cc_final: 0.7955 (ttt180) REVERT: H 230 ASP cc_start: 0.9014 (t0) cc_final: 0.8554 (t0) REVERT: H 263 ILE cc_start: 0.9470 (OUTLIER) cc_final: 0.9268 (mp) REVERT: I 23 ASP cc_start: 0.8735 (m-30) cc_final: 0.8399 (m-30) REVERT: I 189 TRP cc_start: 0.8571 (m-90) cc_final: 0.8045 (m-10) REVERT: J 4 GLU cc_start: 0.8721 (tp30) cc_final: 0.8504 (tp30) REVERT: J 11 ASN cc_start: 0.9104 (m-40) cc_final: 0.8717 (m-40) REVERT: J 23 ASP cc_start: 0.8622 (m-30) cc_final: 0.8190 (m-30) REVERT: J 62 GLU cc_start: 0.8989 (pp20) cc_final: 0.8724 (pp20) REVERT: J 222 GLN cc_start: 0.9059 (tm-30) cc_final: 0.8607 (tm-30) REVERT: J 230 ASP cc_start: 0.9108 (t0) cc_final: 0.8483 (t0) outliers start: 65 outliers final: 33 residues processed: 428 average time/residue: 0.5537 time to fit residues: 266.5470 Evaluate side-chains 410 residues out of total 1840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 373 time to evaluate : 0.707 ------------------------------------------------------------------------------- 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 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 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 173 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 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 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 246 SER Chi-restraints excluded: chain J residue 64 LEU 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 195 optimal weight: 0.7980 chunk 190 optimal weight: 3.9990 chunk 114 optimal weight: 0.8980 chunk 207 optimal weight: 0.6980 chunk 86 optimal weight: 2.9990 chunk 166 optimal weight: 2.9990 chunk 91 optimal weight: 0.9990 chunk 83 optimal weight: 0.8980 chunk 116 optimal weight: 0.7980 chunk 71 optimal weight: 0.7980 chunk 90 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 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 = 0.3268 r_free = 0.3268 target = 0.079439 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2943 r_free = 0.2943 target = 0.061933 restraints weight = 40708.115| |-----------------------------------------------------------------------------| r_work (start): 0.2883 rms_B_bonded: 2.59 r_work: 0.2736 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.2736 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2742 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2742 r_free = 0.2742 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 = 0.2742 r_free = 0.2742 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2742 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8667 moved from start: 0.3608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 18106 Z= 0.165 Angle : 0.595 11.970 24512 Z= 0.304 Chirality : 0.038 0.236 2874 Planarity : 0.003 0.032 3202 Dihedral : 3.774 23.857 2585 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 3.12 % Allowed : 22.95 % Favored : 73.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.28 (0.17), residues: 2375 helix: 2.94 (0.11), residues: 1900 sheet: None (None), residues: 0 loop : -1.28 (0.28), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 232 TYR 0.017 0.001 TYR F 227 PHE 0.029 0.001 PHE H 213 TRP 0.035 0.001 TRP I 189 HIS 0.001 0.000 HIS J 193 Details of bonding type rmsd covalent geometry : bond 0.00357 (18106) covalent geometry : angle 0.59486 (24512) hydrogen bonds : bond 0.05188 ( 1597) hydrogen bonds : angle 4.19575 ( 4761) *********************** 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 434 residues out of total 1840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 379 time to evaluate : 0.753 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: 0.8633 (mtp) cc_final: 0.8402 (mtm) REVERT: C 34 LEU cc_start: 0.9701 (mp) cc_final: 0.9477 (pt) REVERT: C 44 LYS cc_start: 0.9623 (tppp) cc_final: 0.9283 (tppp) REVERT: C 45 GLU cc_start: 0.9245 (pt0) cc_final: 0.8740 (pm20) REVERT: C 138 LYS cc_start: 0.9210 (OUTLIER) cc_final: 0.8788 (tttm) REVERT: D 112 ASP cc_start: 0.9075 (m-30) cc_final: 0.8856 (m-30) REVERT: D 159 MET cc_start: 0.8438 (OUTLIER) cc_final: 0.8092 (mmm) REVERT: D 197 GLN cc_start: 0.9467 (OUTLIER) cc_final: 0.8980 (tt0) REVERT: F 23 ASP cc_start: 0.8690 (m-30) cc_final: 0.8470 (m-30) REVERT: F 62 GLU cc_start: 0.8889 (pp20) cc_final: 0.8485 (pp20) REVERT: F 65 ASN cc_start: 0.9073 (t0) cc_final: 0.8620 (p0) REVERT: F 132 GLU cc_start: 0.9024 (tt0) cc_final: 0.8623 (tt0) REVERT: F 189 TRP cc_start: 0.8489 (m-90) cc_final: 0.8132 (m-10) REVERT: F 230 ASP cc_start: 0.8830 (t0) cc_final: 0.8401 (t0) REVERT: G 230 ASP cc_start: 0.8926 (t0) cc_final: 0.8437 (t0) REVERT: H 4 GLU cc_start: 0.9228 (mt-10) cc_final: 0.8991 (mm-30) REVERT: H 23 ASP cc_start: 0.8825 (m-30) cc_final: 0.8570 (m-30) REVERT: H 69 ARG cc_start: 0.8218 (OUTLIER) cc_final: 0.7959 (ttt180) REVERT: H 142 LEU cc_start: 0.8603 (pt) cc_final: 0.7935 (tt) REVERT: H 230 ASP cc_start: 0.9062 (t0) cc_final: 0.8577 (t0) REVERT: I 4 GLU cc_start: 0.8772 (tp30) cc_final: 0.8566 (tp30) REVERT: I 23 ASP cc_start: 0.8706 (m-30) cc_final: 0.8379 (m-30) REVERT: I 132 GLU cc_start: 0.9036 (tt0) cc_final: 0.8794 (mt-10) REVERT: I 230 ASP cc_start: 0.8991 (t0) cc_final: 0.8345 (t0) REVERT: J 4 GLU cc_start: 0.8757 (tp30) cc_final: 0.8519 (tp30) REVERT: J 11 ASN cc_start: 0.9111 (m-40) cc_final: 0.8720 (m-40) REVERT: J 23 ASP cc_start: 0.8631 (m-30) cc_final: 0.8210 (m-30) REVERT: J 222 GLN cc_start: 0.9064 (tm-30) cc_final: 0.8581 (tm-30) REVERT: J 230 ASP cc_start: 0.9123 (t0) cc_final: 0.8462 (t0) outliers start: 55 outliers final: 35 residues processed: 412 average time/residue: 0.6200 time to fit residues: 286.2505 Evaluate side-chains 411 residues out of total 1840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 372 time to evaluate : 0.706 ------------------------------------------------------------------------------- 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 119 VAL Chi-restraints excluded: chain D residue 159 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 173 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 68 LEU 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 259 GLN 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 68 LEU 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 93 optimal weight: 0.6980 chunk 198 optimal weight: 3.9990 chunk 74 optimal weight: 1.9990 chunk 139 optimal weight: 2.9990 chunk 41 optimal weight: 2.9990 chunk 89 optimal weight: 2.9990 chunk 47 optimal weight: 3.9990 chunk 118 optimal weight: 0.9980 chunk 78 optimal weight: 1.9990 chunk 84 optimal weight: 0.8980 chunk 190 optimal weight: 0.7980 overall best weight: 1.0782 ------------------------------------------------------------------------------- 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 G 122 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: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.078271 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2916 r_free = 0.2916 target = 0.060700 restraints weight = 40618.640| |-----------------------------------------------------------------------------| r_work (start): 0.2877 rms_B_bonded: 2.62 r_work: 0.2744 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.2744 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2717 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2717 r_free = 0.2717 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 = 0.2717 r_free = 0.2717 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2717 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8753 moved from start: 0.3640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.103 18106 Z= 0.198 Angle : 0.617 10.302 24512 Z= 0.319 Chirality : 0.040 0.261 2874 Planarity : 0.003 0.036 3202 Dihedral : 3.821 24.956 2585 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 3.00 % Allowed : 23.23 % Favored : 73.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.14 (0.17), residues: 2375 helix: 2.81 (0.11), residues: 1915 sheet: None (None), residues: 0 loop : -1.32 (0.28), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 232 TYR 0.020 0.002 TYR F 227 PHE 0.028 0.002 PHE H 213 TRP 0.049 0.002 TRP I 189 HIS 0.001 0.000 HIS G 193 Details of bonding type rmsd covalent geometry : bond 0.00445 (18106) covalent geometry : angle 0.61747 (24512) hydrogen bonds : bond 0.05461 ( 1597) hydrogen bonds : angle 4.28633 ( 4761) *********************** 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 433 residues out of total 1840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 380 time to evaluate : 0.760 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: 0.8742 (mtp) cc_final: 0.8521 (mtm) REVERT: C 34 LEU cc_start: 0.9685 (mp) cc_final: 0.9459 (pt) REVERT: C 44 LYS cc_start: 0.9620 (tppp) cc_final: 0.9243 (tppp) REVERT: D 112 ASP cc_start: 0.9077 (m-30) cc_final: 0.8859 (m-30) REVERT: D 159 MET cc_start: 0.8578 (OUTLIER) cc_final: 0.8281 (mmm) REVERT: D 197 GLN cc_start: 0.9432 (OUTLIER) cc_final: 0.8937 (tt0) REVERT: E 44 LYS cc_start: 0.9647 (tppp) cc_final: 0.9350 (tppp) REVERT: F 20 TYR cc_start: 0.9097 (m-80) cc_final: 0.8892 (m-10) REVERT: F 23 ASP cc_start: 0.8682 (m-30) cc_final: 0.8466 (m-30) REVERT: F 62 GLU cc_start: 0.8902 (pp20) cc_final: 0.8505 (pp20) REVERT: F 65 ASN cc_start: 0.9088 (t0) cc_final: 0.8621 (p0) REVERT: F 132 GLU cc_start: 0.9018 (tt0) cc_final: 0.8622 (tt0) REVERT: F 189 TRP cc_start: 0.8614 (m-90) cc_final: 0.8256 (m-10) REVERT: F 230 ASP cc_start: 0.8925 (t0) cc_final: 0.8518 (t0) REVERT: G 230 ASP cc_start: 0.8992 (t0) cc_final: 0.8526 (t0) REVERT: H 4 GLU cc_start: 0.9178 (mt-10) cc_final: 0.8946 (mm-30) REVERT: H 23 ASP cc_start: 0.8733 (m-30) cc_final: 0.8415 (m-30) REVERT: H 69 ARG cc_start: 0.8322 (OUTLIER) cc_final: 0.8062 (ttt180) REVERT: H 142 LEU cc_start: 0.8579 (pt) cc_final: 0.7883 (tt) REVERT: H 230 ASP cc_start: 0.9095 (t0) cc_final: 0.8610 (t0) REVERT: I 4 GLU cc_start: 0.8791 (tp30) cc_final: 0.8584 (tp30) REVERT: I 23 ASP cc_start: 0.8758 (m-30) cc_final: 0.8424 (m-30) REVERT: I 189 TRP cc_start: 0.8435 (m-90) cc_final: 0.7855 (m-10) REVERT: I 230 ASP cc_start: 0.9061 (t0) cc_final: 0.8600 (t0) REVERT: J 4 GLU cc_start: 0.8732 (tp30) cc_final: 0.8457 (tp30) REVERT: J 11 ASN cc_start: 0.9137 (m-40) cc_final: 0.8742 (m-40) REVERT: J 20 TYR cc_start: 0.9067 (m-80) cc_final: 0.8746 (m-10) REVERT: J 23 ASP cc_start: 0.8629 (m-30) cc_final: 0.8395 (m-30) REVERT: J 222 GLN cc_start: 0.9073 (tm-30) cc_final: 0.8576 (tm-30) REVERT: J 230 ASP cc_start: 0.9148 (t0) cc_final: 0.8460 (t0) outliers start: 53 outliers final: 37 residues processed: 410 average time/residue: 0.6400 time to fit residues: 293.8082 Evaluate side-chains 406 residues out of total 1840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 366 time to evaluate : 0.702 ------------------------------------------------------------------------------- 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 162 ILE Chi-restraints excluded: chain D residue 119 VAL Chi-restraints excluded: chain D residue 159 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 173 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 68 LEU 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 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 62 GLU 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 175 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: chunk 112 optimal weight: 0.5980 chunk 133 optimal weight: 0.9990 chunk 61 optimal weight: 6.9990 chunk 102 optimal weight: 0.8980 chunk 151 optimal weight: 0.5980 chunk 142 optimal weight: 2.9990 chunk 63 optimal weight: 0.9980 chunk 163 optimal weight: 0.4980 chunk 230 optimal weight: 0.9990 chunk 73 optimal weight: 0.9990 chunk 25 optimal weight: 0.5980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 H 202 GLN I 11 ASN I 118 GLN I 198 GLN I 259 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 = 0.3248 r_free = 0.3248 target = 0.077950 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2888 r_free = 0.2888 target = 0.060057 restraints weight = 40587.910| |-----------------------------------------------------------------------------| r_work (start): 0.2882 rms_B_bonded: 2.76 r_work: 0.2744 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.2744 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2721 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2721 r_free = 0.2721 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 = 0.2721 r_free = 0.2721 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2721 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8680 moved from start: 0.3753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.086 18106 Z= 0.163 Angle : 0.625 10.271 24512 Z= 0.318 Chirality : 0.039 0.259 2874 Planarity : 0.003 0.036 3202 Dihedral : 3.836 25.377 2585 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 2.78 % Allowed : 23.74 % Favored : 73.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.13 (0.17), residues: 2375 helix: 2.84 (0.11), residues: 1905 sheet: None (None), residues: 0 loop : -1.39 (0.28), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 232 TYR 0.021 0.001 TYR F 227 PHE 0.017 0.001 PHE E 36 TRP 0.042 0.002 TRP I 189 HIS 0.001 0.000 HIS H 193 Details of bonding type rmsd covalent geometry : bond 0.00352 (18106) covalent geometry : angle 0.62520 (24512) hydrogen bonds : bond 0.05282 ( 1597) hydrogen bonds : angle 4.23720 ( 4761) ********************** 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 429 residues out of total 1840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 380 time to evaluate : 0.879 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: 0.8699 (mtp) cc_final: 0.8488 (mtm) REVERT: C 34 LEU cc_start: 0.9698 (mp) cc_final: 0.9486 (pt) REVERT: C 44 LYS cc_start: 0.9611 (tppp) cc_final: 0.9230 (tppp) REVERT: D 112 ASP cc_start: 0.9076 (m-30) cc_final: 0.8851 (m-30) REVERT: D 159 MET cc_start: 0.8458 (OUTLIER) cc_final: 0.8119 (mmm) REVERT: D 197 GLN cc_start: 0.9467 (OUTLIER) cc_final: 0.8987 (tt0) REVERT: E 44 LYS cc_start: 0.9646 (tppp) cc_final: 0.9357 (tppp) REVERT: F 23 ASP cc_start: 0.8720 (m-30) cc_final: 0.8481 (m-30) REVERT: F 62 GLU cc_start: 0.8868 (pp20) cc_final: 0.8475 (pp20) REVERT: F 65 ASN cc_start: 0.9063 (t0) cc_final: 0.8630 (p0) REVERT: F 132 GLU cc_start: 0.9044 (tt0) cc_final: 0.8690 (tt0) REVERT: F 189 TRP cc_start: 0.8525 (m-90) cc_final: 0.8168 (m-10) REVERT: F 230 ASP cc_start: 0.8843 (t0) cc_final: 0.8428 (t0) REVERT: G 230 ASP cc_start: 0.8917 (t0) cc_final: 0.8471 (t0) REVERT: H 4 GLU cc_start: 0.9203 (mt-10) cc_final: 0.8969 (mm-30) REVERT: H 23 ASP cc_start: 0.8773 (m-30) cc_final: 0.8352 (m-30) REVERT: H 69 ARG cc_start: 0.8245 (OUTLIER) cc_final: 0.7983 (ttt180) REVERT: H 142 LEU cc_start: 0.8625 (pt) cc_final: 0.7969 (tt) REVERT: H 179 LEU cc_start: 0.9011 (mm) cc_final: 0.8725 (mt) REVERT: H 230 ASP cc_start: 0.9073 (t0) cc_final: 0.8612 (t0) REVERT: I 4 GLU cc_start: 0.8803 (tp30) cc_final: 0.8582 (tp30) REVERT: I 23 ASP cc_start: 0.8739 (m-30) cc_final: 0.8401 (m-30) REVERT: I 132 GLU cc_start: 0.8972 (tt0) cc_final: 0.8758 (tt0) REVERT: I 230 ASP cc_start: 0.9022 (t0) cc_final: 0.8483 (t0) REVERT: J 4 GLU cc_start: 0.8768 (tp30) cc_final: 0.8485 (tp30) REVERT: J 11 ASN cc_start: 0.9090 (m-40) cc_final: 0.8684 (m-40) REVERT: J 20 TYR cc_start: 0.8997 (m-80) cc_final: 0.8743 (m-10) REVERT: J 23 ASP cc_start: 0.8609 (m-30) cc_final: 0.8355 (m-30) REVERT: J 222 GLN cc_start: 0.9047 (tm-30) cc_final: 0.8559 (tm-30) REVERT: J 230 ASP cc_start: 0.9116 (t0) cc_final: 0.8428 (t0) outliers start: 49 outliers final: 34 residues processed: 405 average time/residue: 0.6319 time to fit residues: 286.9853 Evaluate side-chains 410 residues out of total 1840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 373 time to evaluate : 0.775 ------------------------------------------------------------------------------- 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 162 ILE Chi-restraints excluded: chain D residue 119 VAL Chi-restraints excluded: chain D residue 159 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 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 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 175 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: chunk 153 optimal weight: 1.9990 chunk 194 optimal weight: 0.9980 chunk 111 optimal weight: 0.6980 chunk 159 optimal weight: 4.9990 chunk 77 optimal weight: 0.9990 chunk 37 optimal weight: 0.7980 chunk 128 optimal weight: 1.9990 chunk 35 optimal weight: 0.5980 chunk 223 optimal weight: 2.9990 chunk 72 optimal weight: 0.5980 chunk 180 optimal weight: 0.9980 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 15 GLN F 198 GLN G 11 ASN G 118 GLN G 122 GLN H 11 ASN H 259 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: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.079382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.061825 restraints weight = 41015.418| |-----------------------------------------------------------------------------| r_work (start): 0.2905 rms_B_bonded: 2.62 r_work: 0.2774 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.2774 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2748 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2748 r_free = 0.2748 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 = 0.2748 r_free = 0.2748 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2748 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8735 moved from start: 0.3813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.085 18106 Z= 0.168 Angle : 0.622 10.590 24512 Z= 0.317 Chirality : 0.039 0.256 2874 Planarity : 0.003 0.047 3202 Dihedral : 3.820 25.892 2585 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 2.72 % Allowed : 23.68 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.14 (0.17), residues: 2375 helix: 2.82 (0.11), residues: 1910 sheet: None (None), residues: 0 loop : -1.35 (0.28), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG G 232 TYR 0.019 0.001 TYR F 227 PHE 0.028 0.002 PHE A 28 TRP 0.046 0.002 TRP I 189 HIS 0.001 0.000 HIS J 193 Details of bonding type rmsd covalent geometry : bond 0.00367 (18106) covalent geometry : angle 0.62214 (24512) hydrogen bonds : bond 0.05241 ( 1597) hydrogen bonds : angle 4.23137 ( 4761) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7262.30 seconds wall clock time: 124 minutes 22.63 seconds (7462.63 seconds total)