Starting phenix.real_space_refine on Sat Aug 23 06:05:53 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8q86_18248/08_2025/8q86_18248.cif Found real_map, /net/cci-nas-00/data/ceres_data/8q86_18248/08_2025/8q86_18248.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.69 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8q86_18248/08_2025/8q86_18248.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8q86_18248/08_2025/8q86_18248.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8q86_18248/08_2025/8q86_18248.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8q86_18248/08_2025/8q86_18248.map" } resolution = 3.69 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= 0.002 sd= 0.028 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 25 5.16 5 C 6557 2.51 5 N 1708 2.21 5 O 2061 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 10351 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 167 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 167 Classifications: {'peptide': 21} Link IDs: {'PTRANS': 1, 'TRANS': 19} Chain breaks: 4 Chain: "B" Number of atoms: 463 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 463 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 2, 'TRANS': 51} Chain breaks: 7 Chain: "C" Number of atoms: 1330 Number of conformers: 1 Conformer: "" Number of residues, atoms: 163, 1330 Classifications: {'peptide': 163} Link IDs: {'PTRANS': 2, 'TRANS': 160} Chain breaks: 5 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Chain: "D" Number of atoms: 1701 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 1701 Classifications: {'peptide': 207} Link IDs: {'PTRANS': 3, 'TRANS': 203} Chain breaks: 3 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Chain: "E" Number of atoms: 1797 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1797 Classifications: {'peptide': 219} Link IDs: {'PTRANS': 4, 'TRANS': 214} Chain breaks: 1 Chain: "F" Number of atoms: 1797 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1797 Classifications: {'peptide': 219} Link IDs: {'PTRANS': 4, 'TRANS': 214} Chain breaks: 1 Chain: "G" Number of atoms: 1635 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 1635 Classifications: {'peptide': 199} Link IDs: {'PTRANS': 3, 'TRANS': 195} Chain breaks: 5 Chain: "H" Number of atoms: 1401 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1401 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 2, 'TRANS': 169} Chain breaks: 8 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Classifications: {'water': 9} Link IDs: {None: 8} Chain: "C" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 10 Classifications: {'water': 10} Link IDs: {None: 9} Chain: "D" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 15 Classifications: {'water': 15} Link IDs: {None: 14} Chain: "E" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "G" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Classifications: {'water': 8} Link IDs: {None: 7} Chain: "H" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 11 Classifications: {'water': 11} Link IDs: {None: 10} Time building chain proxies: 3.07, per 1000 atoms: 0.30 Number of scatterers: 10351 At special positions: 0 Unit cell: (182.77, 73.854, 102.948, 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 25 16.00 O 2061 8.00 N 1708 7.00 C 6557 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: 0.90 Conformation dependent library (CDL) restraints added in 371.9 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2454 Finding SS restraints... Secondary structure from input PDB file: 56 helices and 20 sheets defined 45.1% alpha, 21.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.39 Creating SS restraints... Processing helix chain 'B' and resid 162 through 166 Processing helix chain 'B' and resid 169 through 177 removed outlier: 3.814A pdb=" N SER B 177 " --> pdb=" O ASN B 173 " (cutoff:3.500A) Processing helix chain 'C' and resid 6 through 14 WARNING: missing atoms! Processing helix chain 'C' and resid 16 through 25 Processing helix chain 'C' and resid 27 through 35 Processing helix chain 'C' and resid 44 through 55 Processing helix chain 'C' and resid 57 through 62 removed outlier: 4.020A pdb=" N PHE C 61 " --> pdb=" O SER C 57 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N PHE C 62 " --> pdb=" O PRO C 58 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 57 through 62' Processing helix chain 'C' and resid 150 through 160 removed outlier: 3.725A pdb=" N LEU C 160 " --> pdb=" O TYR C 156 " (cutoff:3.500A) Processing helix chain 'C' and resid 161 through 185 removed outlier: 4.033A pdb=" N GLU C 182 " --> pdb=" O GLY C 178 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N ILE C 183 " --> pdb=" O TYR C 179 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N ILE C 184 " --> pdb=" O VAL C 180 " (cutoff:3.500A) Processing helix chain 'C' and resid 207 through 212 removed outlier: 3.946A pdb=" N GLN C 211 " --> pdb=" O LYS C 207 " (cutoff:3.500A) Processing helix chain 'D' and resid 5 through 14 removed outlier: 4.200A pdb=" N LEU D 9 " --> pdb=" O ARG D 5 " (cutoff:3.500A) Processing helix chain 'D' and resid 16 through 24 removed outlier: 3.743A pdb=" N LYS D 22 " --> pdb=" O SER D 18 " (cutoff:3.500A) Processing helix chain 'D' and resid 27 through 34 Processing helix chain 'D' and resid 44 through 54 Processing helix chain 'D' and resid 57 through 61 Processing helix chain 'D' and resid 151 through 159 Processing helix chain 'D' and resid 161 through 187 removed outlier: 3.617A pdb=" N LYS D 186 " --> pdb=" O GLU D 182 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N ASN D 187 " --> pdb=" O ILE D 183 " (cutoff:3.500A) Processing helix chain 'D' and resid 204 through 212 Processing helix chain 'E' and resid 6 through 14 Processing helix chain 'E' and resid 16 through 24 Processing helix chain 'E' and resid 27 through 36 removed outlier: 3.718A pdb=" N GLN E 36 " --> pdb=" O THR E 32 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 55 Processing helix chain 'E' and resid 57 through 61 removed outlier: 3.744A pdb=" N PHE E 61 " --> pdb=" O SER E 57 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 57 through 61' Processing helix chain 'E' and resid 87 through 91 Processing helix chain 'E' and resid 93 through 97 removed outlier: 3.535A pdb=" N ALA E 97 " --> pdb=" O ASN E 93 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 93 through 97' Processing helix chain 'E' and resid 150 through 158 removed outlier: 3.709A pdb=" N LYS E 154 " --> pdb=" O ASN E 150 " (cutoff:3.500A) Processing helix chain 'E' and resid 161 through 188 Processing helix chain 'E' and resid 204 through 212 Processing helix chain 'F' and resid 5 through 14 Processing helix chain 'F' and resid 16 through 24 Processing helix chain 'F' and resid 27 through 36 removed outlier: 3.737A pdb=" N GLN F 36 " --> pdb=" O THR F 32 " (cutoff:3.500A) Processing helix chain 'F' and resid 44 through 55 Processing helix chain 'F' and resid 57 through 61 removed outlier: 3.730A pdb=" N PHE F 61 " --> pdb=" O SER F 57 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 57 through 61' Processing helix chain 'F' and resid 93 through 98 removed outlier: 3.753A pdb=" N ALA F 97 " --> pdb=" O ASN F 93 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N PHE F 98 " --> pdb=" O ILE F 94 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 93 through 98' Processing helix chain 'F' and resid 147 through 149 No H-bonds generated for 'chain 'F' and resid 147 through 149' Processing helix chain 'F' and resid 150 through 158 removed outlier: 3.775A pdb=" N LYS F 154 " --> pdb=" O ASN F 150 " (cutoff:3.500A) Processing helix chain 'F' and resid 161 through 188 Processing helix chain 'F' and resid 204 through 212 Processing helix chain 'G' and resid 5 through 14 Processing helix chain 'G' and resid 16 through 24 removed outlier: 3.940A pdb=" N LYS G 22 " --> pdb=" O SER G 18 " (cutoff:3.500A) Processing helix chain 'G' and resid 27 through 35 Processing helix chain 'G' and resid 44 through 54 Processing helix chain 'G' and resid 57 through 61 Processing helix chain 'G' and resid 93 through 97 removed outlier: 3.638A pdb=" N ALA G 97 " --> pdb=" O ASN G 93 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 93 through 97' Processing helix chain 'G' and resid 151 through 160 removed outlier: 3.697A pdb=" N SER G 159 " --> pdb=" O LYS G 155 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LEU G 160 " --> pdb=" O TYR G 156 " (cutoff:3.500A) Processing helix chain 'G' and resid 161 through 186 Processing helix chain 'G' and resid 204 through 210 Processing helix chain 'H' and resid 5 through 14 WARNING: missing atoms! Processing helix chain 'H' and resid 16 through 25 removed outlier: 3.506A pdb=" N LYS H 22 " --> pdb=" O SER H 18 " (cutoff:3.500A) Processing helix chain 'H' and resid 27 through 35 Processing helix chain 'H' and resid 44 through 54 Processing helix chain 'H' and resid 57 through 61 removed outlier: 3.706A pdb=" N PHE H 61 " --> pdb=" O SER H 57 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 57 through 61' Processing helix chain 'H' and resid 93 through 98 removed outlier: 4.042A pdb=" N PHE H 98 " --> pdb=" O ILE H 94 " (cutoff:3.500A) Processing helix chain 'H' and resid 154 through 160 removed outlier: 3.719A pdb=" N LEU H 160 " --> pdb=" O TYR H 156 " (cutoff:3.500A) Processing helix chain 'H' and resid 161 through 181 Processing helix chain 'H' and resid 183 through 185 No H-bonds generated for 'chain 'H' and resid 183 through 185' Processing sheet with id=AA1, first strand: chain 'C' and resid 41 through 43 removed outlier: 3.869A pdb=" N ILE D 42 " --> pdb=" O ILE C 42 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 71 through 72 Processing sheet with id=AA3, first strand: chain 'C' and resid 125 through 126 removed outlier: 4.226A pdb=" N SER C 126 " --> pdb=" O THR C 143 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N THR C 143 " --> pdb=" O SER C 126 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 139 through 141 removed outlier: 6.269A pdb=" N PHE C 140 " --> pdb=" O ARG C 215 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'D' and resid 68 through 73 removed outlier: 3.783A pdb=" N SER D 99 " --> pdb=" O ASN D 82 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N LYS D 80 " --> pdb=" O GLU D 101 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N PHE D 103 " --> pdb=" O ASN D 78 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N ASN D 78 " --> pdb=" O PHE D 103 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 68 through 73 removed outlier: 12.583A pdb=" N SER D 99 " --> pdb=" O GLU D 131 " (cutoff:3.500A) removed outlier: 13.213A pdb=" N GLU D 131 " --> pdb=" O SER D 99 " (cutoff:3.500A) removed outlier: 10.475A pdb=" N GLU D 101 " --> pdb=" O GLU D 129 " (cutoff:3.500A) removed outlier: 8.583A pdb=" N GLU D 129 " --> pdb=" O GLU D 101 " (cutoff:3.500A) removed outlier: 5.980A pdb=" N PHE D 103 " --> pdb=" O TYR D 127 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N PHE D 105 " --> pdb=" O VAL D 125 " (cutoff:3.500A) removed outlier: 7.171A pdb=" N ILE D 141 " --> pdb=" O LYS D 128 " (cutoff:3.500A) removed outlier: 5.173A pdb=" N THR D 130 " --> pdb=" O ARG D 139 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N ARG D 139 " --> pdb=" O THR D 130 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N PHE D 140 " --> pdb=" O ARG D 215 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 2 through 4 removed outlier: 3.637A pdb=" N ARG E 3 " --> pdb=" O GLU E 63 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N GLU E 63 " --> pdb=" O ARG E 3 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'E' and resid 41 through 43 Processing sheet with id=AA9, first strand: chain 'E' and resid 71 through 73 removed outlier: 5.558A pdb=" N ILE E 100 " --> pdb=" O ASN E 82 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N ASN E 82 " --> pdb=" O ILE E 100 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ASN E 102 " --> pdb=" O LYS E 80 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 71 through 73 removed outlier: 12.809A pdb=" N SER E 99 " --> pdb=" O GLU E 131 " (cutoff:3.500A) removed outlier: 12.689A pdb=" N GLU E 131 " --> pdb=" O SER E 99 " (cutoff:3.500A) removed outlier: 10.554A pdb=" N GLU E 101 " --> pdb=" O GLU E 129 " (cutoff:3.500A) removed outlier: 8.296A pdb=" N GLU E 129 " --> pdb=" O GLU E 101 " (cutoff:3.500A) removed outlier: 5.711A pdb=" N PHE E 103 " --> pdb=" O TYR E 127 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N PHE E 105 " --> pdb=" O VAL E 125 " (cutoff:3.500A) removed outlier: 7.180A pdb=" N ILE E 141 " --> pdb=" O LYS E 128 " (cutoff:3.500A) removed outlier: 5.702A pdb=" N THR E 130 " --> pdb=" O ARG E 139 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N ARG E 139 " --> pdb=" O THR E 130 " (cutoff:3.500A) removed outlier: 5.499A pdb=" N LYS E 132 " --> pdb=" O GLN E 137 " (cutoff:3.500A) removed outlier: 7.696A pdb=" N GLN E 137 " --> pdb=" O LYS E 132 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N ASP E 213 " --> pdb=" O HIS E 138 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N PHE E 140 " --> pdb=" O ASP E 213 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 2 through 4 Processing sheet with id=AB3, first strand: chain 'F' and resid 68 through 73 removed outlier: 6.791A pdb=" N LYS F 80 " --> pdb=" O GLU F 101 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N PHE F 103 " --> pdb=" O ASN F 78 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N ASN F 78 " --> pdb=" O PHE F 103 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 68 through 73 removed outlier: 9.911A pdb=" N GLU F 101 " --> pdb=" O GLU F 129 " (cutoff:3.500A) removed outlier: 8.203A pdb=" N GLU F 129 " --> pdb=" O GLU F 101 " (cutoff:3.500A) removed outlier: 5.912A pdb=" N PHE F 103 " --> pdb=" O TYR F 127 " (cutoff:3.500A) removed outlier: 5.990A pdb=" N TYR F 127 " --> pdb=" O THR F 143 " (cutoff:3.500A) removed outlier: 6.013A pdb=" N THR F 143 " --> pdb=" O TYR F 127 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N GLU F 129 " --> pdb=" O ILE F 141 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'G' and resid 2 through 4 Processing sheet with id=AB6, first strand: chain 'G' and resid 41 through 43 Processing sheet with id=AB7, first strand: chain 'G' and resid 71 through 73 removed outlier: 6.873A pdb=" N LYS G 80 " --> pdb=" O GLU G 101 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N PHE G 103 " --> pdb=" O ASN G 78 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N ASN G 78 " --> pdb=" O PHE G 103 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'G' and resid 71 through 73 removed outlier: 9.687A pdb=" N GLU G 101 " --> pdb=" O GLU G 129 " (cutoff:3.500A) removed outlier: 7.915A pdb=" N GLU G 129 " --> pdb=" O GLU G 101 " (cutoff:3.500A) removed outlier: 5.993A pdb=" N PHE G 103 " --> pdb=" O TYR G 127 " (cutoff:3.500A) removed outlier: 7.323A pdb=" N ILE G 141 " --> pdb=" O LYS G 128 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ARG G 215 " --> pdb=" O PHE G 140 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'H' and resid 2 through 4 Processing sheet with id=AC1, first strand: chain 'H' and resid 70 through 72 removed outlier: 3.785A pdb=" N ASP H 70 " --> pdb=" O ASP H 110 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'H' and resid 129 through 131 removed outlier: 6.088A pdb=" N PHE H 140 " --> pdb=" O ARG H 215 " (cutoff:3.500A) 423 hydrogen bonds defined for protein. 1218 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.42 Time building geometry restraints manager: 1.21 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: 2163 1.33 - 1.45: 2252 1.45 - 1.57: 5968 1.57 - 1.69: 0 1.69 - 1.82: 43 Bond restraints: 10426 Sorted by residual: bond pdb=" N ILE B 81 " pdb=" CA ILE B 81 " ideal model delta sigma weight residual 1.457 1.495 -0.038 1.11e-02 8.12e+03 1.17e+01 bond pdb=" N VAL D 125 " pdb=" CA VAL D 125 " ideal model delta sigma weight residual 1.456 1.495 -0.039 1.15e-02 7.56e+03 1.16e+01 bond pdb=" N ILE C 2 " pdb=" CA ILE C 2 " ideal model delta sigma weight residual 1.456 1.494 -0.038 1.14e-02 7.69e+03 1.11e+01 bond pdb=" N ILE D 94 " pdb=" CA ILE D 94 " ideal model delta sigma weight residual 1.459 1.500 -0.041 1.25e-02 6.40e+03 1.10e+01 bond pdb=" N ILE G 56 " pdb=" CA ILE G 56 " ideal model delta sigma weight residual 1.456 1.494 -0.037 1.14e-02 7.69e+03 1.07e+01 ... (remaining 10421 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.65: 13139 2.65 - 5.29: 806 5.29 - 7.94: 10 7.94 - 10.58: 0 10.58 - 13.23: 1 Bond angle restraints: 13956 Sorted by residual: angle pdb=" N LEU E 6 " pdb=" CA LEU E 6 " pdb=" C LEU E 6 " ideal model delta sigma weight residual 113.55 100.32 13.23 1.26e+00 6.30e-01 1.10e+02 angle pdb=" N PHE D 61 " pdb=" CA PHE D 61 " pdb=" C PHE D 61 " ideal model delta sigma weight residual 112.92 107.23 5.69 1.23e+00 6.61e-01 2.14e+01 angle pdb=" N ARG E 5 " pdb=" CA ARG E 5 " pdb=" C ARG E 5 " ideal model delta sigma weight residual 109.39 102.19 7.20 1.59e+00 3.96e-01 2.05e+01 angle pdb=" N ILE E 133 " pdb=" CA ILE E 133 " pdb=" C ILE E 133 " ideal model delta sigma weight residual 110.74 106.72 4.02 9.10e-01 1.21e+00 1.95e+01 angle pdb=" N ASN E 135 " pdb=" CA ASN E 135 " pdb=" C ASN E 135 " ideal model delta sigma weight residual 113.19 108.10 5.09 1.19e+00 7.06e-01 1.83e+01 ... (remaining 13951 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.11: 5842 17.11 - 34.22: 439 34.22 - 51.32: 90 51.32 - 68.43: 14 68.43 - 85.54: 11 Dihedral angle restraints: 6396 sinusoidal: 2694 harmonic: 3702 Sorted by residual: dihedral pdb=" C ASP C 48 " pdb=" N ASP C 48 " pdb=" CA ASP C 48 " pdb=" CB ASP C 48 " ideal model delta harmonic sigma weight residual -122.60 -131.89 9.29 0 2.50e+00 1.60e-01 1.38e+01 dihedral pdb=" C ASP H 48 " pdb=" N ASP H 48 " pdb=" CA ASP H 48 " pdb=" CB ASP H 48 " ideal model delta harmonic sigma weight residual -122.60 -131.27 8.67 0 2.50e+00 1.60e-01 1.20e+01 dihedral pdb=" C ASP D 38 " pdb=" N ASP D 38 " pdb=" CA ASP D 38 " pdb=" CB ASP D 38 " ideal model delta harmonic sigma weight residual -122.60 -131.08 8.48 0 2.50e+00 1.60e-01 1.15e+01 ... (remaining 6393 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 810 0.067 - 0.133: 503 0.133 - 0.200: 240 0.200 - 0.267: 35 0.267 - 0.333: 2 Chirality restraints: 1590 Sorted by residual: chirality pdb=" CA ARG E 5 " pdb=" N ARG E 5 " pdb=" C ARG E 5 " pdb=" CB ARG E 5 " both_signs ideal model delta sigma weight residual False 2.51 2.84 -0.33 2.00e-01 2.50e+01 2.78e+00 chirality pdb=" CA ASP C 48 " pdb=" N ASP C 48 " pdb=" C ASP C 48 " pdb=" CB ASP C 48 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.85e+00 chirality pdb=" CA ILE E 26 " pdb=" N ILE E 26 " pdb=" C ILE E 26 " pdb=" CB ILE E 26 " both_signs ideal model delta sigma weight residual False 2.43 2.69 -0.25 2.00e-01 2.50e+01 1.60e+00 ... (remaining 1587 not shown) Planarity restraints: 1769 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA MET G 34 " -0.020 2.00e-02 2.50e+03 4.04e-02 1.63e+01 pdb=" C MET G 34 " 0.070 2.00e-02 2.50e+03 pdb=" O MET G 34 " -0.026 2.00e-02 2.50e+03 pdb=" N ALA G 35 " -0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG D 19 " 0.275 9.50e-02 1.11e+02 1.23e-01 9.33e+00 pdb=" NE ARG D 19 " -0.017 2.00e-02 2.50e+03 pdb=" CZ ARG D 19 " -0.000 2.00e-02 2.50e+03 pdb=" NH1 ARG D 19 " -0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG D 19 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 43 " 0.242 9.50e-02 1.11e+02 1.08e-01 7.21e+00 pdb=" NE ARG C 43 " -0.015 2.00e-02 2.50e+03 pdb=" CZ ARG C 43 " -0.001 2.00e-02 2.50e+03 pdb=" NH1 ARG C 43 " -0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG C 43 " 0.008 2.00e-02 2.50e+03 ... (remaining 1766 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 1105 2.76 - 3.29: 9942 3.29 - 3.83: 14270 3.83 - 4.36: 18222 4.36 - 4.90: 29206 Nonbonded interactions: 72745 Sorted by model distance: nonbonded pdb=" NZ LYS D 22 " pdb=" O HOH D 301 " model vdw 2.220 3.120 nonbonded pdb=" OG SER C 126 " pdb=" O HOH C 301 " model vdw 2.245 3.040 nonbonded pdb=" NH2 ARG H 19 " pdb=" O HOH H 301 " model vdw 2.292 3.120 nonbonded pdb=" ND2 ASN C 37 " pdb=" O HOH C 302 " model vdw 2.323 3.120 nonbonded pdb=" OD2 ASP G 104 " pdb=" O HOH G 301 " model vdw 2.326 3.040 ... (remaining 72740 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 'C' and (resid 1 through 6 or (resid 7 and (name N or name CA or name C o \ r name CB or name OG )) or resid 8 through 73 or resid 75 or resid 106 through 1 \ 21 or resid 126 through 146 or resid 149 through 151 or resid 153 through 181 or \ resid 183 through 185 or resid 209 through 218)) selection = (chain 'H' and (resid 1 through 2 or (resid 3 and (name N or name CA or name C o \ r name CB or name CG or name CD or name NE or name CZ or name NH1 or name NH2)) \ or resid 4 through 7 or (resid 8 and (name N or name CA or name C or name CB or \ name CG or name CD or name OE1 or name OE2)) or resid 9 through 73 or resid 101 \ or resid 106 through 121 or resid 126 through 130 or resid 136 through 146 or re \ sid 149 through 218)) } ncs_group { reference = (chain 'D' and (resid 1 through 86 or resid 92 through 130 or resid 139 through \ 148 or resid 150 through 189 or resid 191 through 223)) selection = (chain 'E' and (resid 1 or (resid 2 and (name N or name CA or name C or name CB \ or name CG1 or name CG2 or name CD1)) or (resid 3 and (name N or name CA or name \ C or name CB or name CG or name CD or name NE or name CZ or name NH1 or name NH \ 2)) or resid 4 through 86 or resid 92 through 130 or resid 139 through 148 or re \ sid 150 through 189 or resid 191 through 193 or resid 203 through 223)) selection = (chain 'F' and (resid 1 or (resid 2 and (name N or name CA or name C or name CB \ or name CG1 or name CG2 or name CD1)) or (resid 3 and (name N or name CA or name \ C or name CB or name CG or name CD or name NE or name CZ or name NH1 or name NH \ 2)) or resid 4 through 86 or resid 92 through 130 or resid 139 through 148 or re \ sid 150 through 189 or resid 191 through 193 or resid 203 through 223)) selection = (chain 'G' and (resid 1 or (resid 2 and (name N or name CA or name C or name CB \ or name CG1 or name CG2 or name CD1)) or (resid 3 and (name N or name CA or name \ C or name CB or name CG or name CD or name NE or name CZ or name NH1 or name NH \ 2)) or resid 4 through 223)) } 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 group one per residue 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: 2.310 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.210 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 11.390 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7791 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 : 0.010 0.047 10426 Z= 0.783 Angle : 1.289 13.231 13956 Z= 0.985 Chirality : 0.093 0.333 1590 Planarity : 0.008 0.123 1769 Dihedral : 12.953 85.541 3942 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 0.08 % Allowed : 8.27 % Favored : 91.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.91 (0.24), residues: 1170 helix: 0.83 (0.24), residues: 488 sheet: -1.28 (0.33), residues: 250 loop : -1.80 (0.23), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 28 TYR 0.019 0.001 TYR F 79 PHE 0.016 0.002 PHE E 221 HIS 0.004 0.001 HIS E 64 Details of bonding type rmsd covalent geometry : bond 0.01037 (10426) covalent geometry : angle 1.28929 (13956) hydrogen bonds : bond 0.22654 ( 407) hydrogen bonds : angle 7.40874 ( 1218) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 362 residues out of total 1185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 361 time to evaluate : 0.470 Fit side-chains TARDY: cannot create tardy model for: "GLU C 8 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ARG D 3 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash REVERT: C 34 MET cc_start: 0.9127 (ttm) cc_final: 0.8919 (ttm) REVERT: C 65 ASN cc_start: 0.8203 (t0) cc_final: 0.7643 (m-40) REVERT: C 108 LEU cc_start: 0.7045 (tp) cc_final: 0.6785 (tp) REVERT: C 183 ILE cc_start: 0.6524 (mm) cc_final: 0.5924 (pt) REVERT: D 85 PHE cc_start: 0.6985 (m-10) cc_final: 0.6572 (m-10) REVERT: D 169 PHE cc_start: 0.8355 (t80) cc_final: 0.7842 (t80) REVERT: D 183 ILE cc_start: 0.8738 (tp) cc_final: 0.8524 (tt) REVERT: E 169 PHE cc_start: 0.8217 (t80) cc_final: 0.8012 (t80) REVERT: E 174 GLN cc_start: 0.8541 (tm-30) cc_final: 0.8178 (tm-30) REVERT: E 182 GLU cc_start: 0.7785 (tp30) cc_final: 0.7395 (tp30) REVERT: F 174 GLN cc_start: 0.8494 (tm-30) cc_final: 0.7947 (tm-30) REVERT: G 79 TYR cc_start: 0.7940 (p90) cc_final: 0.7681 (p90) REVERT: G 211 GLN cc_start: 0.8238 (tt0) cc_final: 0.8026 (tt0) outliers start: 1 outliers final: 0 residues processed: 361 average time/residue: 0.1200 time to fit residues: 58.5582 Evaluate side-chains 219 residues out of total 1185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 219 time to evaluate : 0.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 108 optimal weight: 0.5980 chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 0.9980 chunk 113 optimal weight: 7.9990 chunk 53 optimal weight: 0.8980 chunk 5 optimal weight: 5.9990 chunk 33 optimal weight: 0.7980 chunk 65 optimal weight: 0.9980 chunk 62 optimal weight: 20.0000 chunk 51 optimal weight: 5.9990 chunk 117 optimal weight: 10.0000 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 64 HIS C 150 ASN C 206 HIS D 37 ASN D 55 HIS ** D 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 138 HIS E 37 ASN G 150 ASN H 117 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4152 r_free = 0.4152 target = 0.179984 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.144563 restraints weight = 15128.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.144884 restraints weight = 10524.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.145666 restraints weight = 9835.729| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.146375 restraints weight = 6157.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.147032 restraints weight = 5463.754| |-----------------------------------------------------------------------------| r_work (final): 0.3733 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7856 moved from start: 0.2918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 10426 Z= 0.114 Angle : 0.505 8.339 13956 Z= 0.275 Chirality : 0.038 0.174 1590 Planarity : 0.003 0.035 1769 Dihedral : 3.674 14.799 1303 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.03 % Favored : 98.97 % Rotamer: Outliers : 1.69 % Allowed : 14.43 % Favored : 83.88 % 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: 0.14 (0.24), residues: 1170 helix: 1.91 (0.24), residues: 499 sheet: -0.95 (0.34), residues: 253 loop : -1.46 (0.24), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 215 TYR 0.017 0.001 TYR D 127 PHE 0.012 0.001 PHE G 105 HIS 0.005 0.001 HIS H 96 Details of bonding type rmsd covalent geometry : bond 0.00254 (10426) covalent geometry : angle 0.50470 (13956) hydrogen bonds : bond 0.03768 ( 407) hydrogen bonds : angle 4.52599 ( 1218) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 1185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 228 time to evaluate : 0.539 Fit side-chains TARDY: cannot create tardy model for: "GLU C 8 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ARG D 3 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash REVERT: A 19 ARG cc_start: 0.6955 (tpt90) cc_final: 0.6069 (tpt90) REVERT: C 65 ASN cc_start: 0.8178 (t0) cc_final: 0.7896 (m-40) REVERT: D 86 GLU cc_start: 0.6623 (tp30) cc_final: 0.6152 (pp20) REVERT: D 183 ILE cc_start: 0.8814 (tp) cc_final: 0.8547 (tt) REVERT: E 4 ASN cc_start: 0.8840 (p0) cc_final: 0.8382 (p0) REVERT: E 169 PHE cc_start: 0.7911 (t80) cc_final: 0.7653 (t80) REVERT: E 174 GLN cc_start: 0.8428 (tm-30) cc_final: 0.8057 (tm-30) REVERT: E 182 GLU cc_start: 0.8150 (tp30) cc_final: 0.7850 (tp30) REVERT: F 117 GLN cc_start: 0.8620 (pp30) cc_final: 0.8283 (pm20) REVERT: F 174 GLN cc_start: 0.8462 (tm-30) cc_final: 0.7864 (tm-30) REVERT: G 32 THR cc_start: 0.9050 (t) cc_final: 0.8846 (t) REVERT: G 211 GLN cc_start: 0.8346 (tt0) cc_final: 0.8115 (tt0) REVERT: G 215 ARG cc_start: 0.8156 (ttm110) cc_final: 0.7860 (ttm110) REVERT: H 4 ASN cc_start: 0.8914 (OUTLIER) cc_final: 0.8668 (p0) REVERT: H 169 PHE cc_start: 0.6231 (m-80) cc_final: 0.5818 (m-80) outliers start: 20 outliers final: 10 residues processed: 239 average time/residue: 0.1099 time to fit residues: 36.8252 Evaluate side-chains 205 residues out of total 1185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 194 time to evaluate : 0.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 140 PHE Chi-restraints excluded: chain D residue 55 HIS Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain D residue 177 SER Chi-restraints excluded: chain D residue 220 ILE Chi-restraints excluded: chain F residue 83 ASP Chi-restraints excluded: chain F residue 166 ASN Chi-restraints excluded: chain G residue 94 ILE Chi-restraints excluded: chain G residue 114 ASP Chi-restraints excluded: chain G residue 168 LEU Chi-restraints excluded: chain H residue 4 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 62 optimal weight: 7.9990 chunk 67 optimal weight: 0.0570 chunk 78 optimal weight: 8.9990 chunk 77 optimal weight: 1.9990 chunk 11 optimal weight: 3.9990 chunk 55 optimal weight: 2.9990 chunk 72 optimal weight: 3.9990 chunk 65 optimal weight: 0.9990 chunk 29 optimal weight: 0.9980 chunk 91 optimal weight: 0.0470 chunk 42 optimal weight: 9.9990 overall best weight: 0.8200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 115 ASN D 117 GLN ** D 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 115 ASN F 115 ASN G 55 HIS G 117 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.170290 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.136601 restraints weight = 15252.093| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.135409 restraints weight = 10712.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.136550 restraints weight = 10457.095| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.137534 restraints weight = 6882.186| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.138021 restraints weight = 6122.219| |-----------------------------------------------------------------------------| r_work (final): 0.3610 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7823 moved from start: 0.3406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 10426 Z= 0.098 Angle : 0.445 5.694 13956 Z= 0.242 Chirality : 0.037 0.135 1590 Planarity : 0.003 0.025 1769 Dihedral : 3.494 12.926 1303 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 1.69 % Allowed : 16.03 % Favored : 82.28 % 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: 0.40 (0.25), residues: 1170 helix: 2.17 (0.24), residues: 502 sheet: -0.87 (0.34), residues: 247 loop : -1.39 (0.24), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 215 TYR 0.017 0.001 TYR G 53 PHE 0.012 0.001 PHE G 105 HIS 0.019 0.001 HIS D 55 Details of bonding type rmsd covalent geometry : bond 0.00221 (10426) covalent geometry : angle 0.44471 (13956) hydrogen bonds : bond 0.03130 ( 407) hydrogen bonds : angle 4.06130 ( 1218) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 207 time to evaluate : 0.448 Fit side-chains TARDY: cannot create tardy model for: "GLU C 8 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ARG D 3 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash REVERT: A 19 ARG cc_start: 0.6914 (tpt90) cc_final: 0.6025 (tpt90) REVERT: C 4 ASN cc_start: 0.8168 (m-40) cc_final: 0.7859 (m-40) REVERT: C 65 ASN cc_start: 0.8188 (t0) cc_final: 0.7881 (m-40) REVERT: C 175 LYS cc_start: 0.8634 (mttt) cc_final: 0.8414 (mttm) REVERT: D 183 ILE cc_start: 0.8781 (tp) cc_final: 0.8462 (tt) REVERT: E 169 PHE cc_start: 0.7948 (t80) cc_final: 0.7711 (t80) REVERT: E 174 GLN cc_start: 0.8428 (tm-30) cc_final: 0.8015 (tm-30) REVERT: E 182 GLU cc_start: 0.8228 (tp30) cc_final: 0.7944 (tp30) REVERT: F 117 GLN cc_start: 0.8650 (pp30) cc_final: 0.8253 (pm20) REVERT: F 137 GLN cc_start: 0.6263 (mm-40) cc_final: 0.6044 (mm-40) REVERT: F 169 PHE cc_start: 0.8034 (t80) cc_final: 0.7825 (t80) REVERT: F 174 GLN cc_start: 0.8436 (tm-30) cc_final: 0.8010 (tm-30) outliers start: 20 outliers final: 14 residues processed: 222 average time/residue: 0.1135 time to fit residues: 35.1542 Evaluate side-chains 202 residues out of total 1185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 188 time to evaluate : 0.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 144 ILE Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain D residue 114 ASP Chi-restraints excluded: chain D residue 147 GLU Chi-restraints excluded: chain D residue 177 SER Chi-restraints excluded: chain F residue 166 ASN Chi-restraints excluded: chain G residue 55 HIS Chi-restraints excluded: chain G residue 94 ILE Chi-restraints excluded: chain G residue 106 GLU Chi-restraints excluded: chain G residue 114 ASP Chi-restraints excluded: chain G residue 168 LEU Chi-restraints excluded: chain G residue 191 ILE Chi-restraints excluded: chain G residue 214 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 35 optimal weight: 7.9990 chunk 48 optimal weight: 6.9990 chunk 59 optimal weight: 3.9990 chunk 31 optimal weight: 8.9990 chunk 115 optimal weight: 20.0000 chunk 60 optimal weight: 3.9990 chunk 76 optimal weight: 1.9990 chunk 113 optimal weight: 9.9990 chunk 36 optimal weight: 4.9990 chunk 68 optimal weight: 0.6980 chunk 94 optimal weight: 0.2980 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 55 HIS D 93 ASN E 115 ASN ** F 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 4 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4103 r_free = 0.4103 target = 0.175576 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.140897 restraints weight = 15067.940| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.139582 restraints weight = 11603.680| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.141090 restraints weight = 10142.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.142004 restraints weight = 6584.017| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.142512 restraints weight = 5957.121| |-----------------------------------------------------------------------------| r_work (final): 0.3662 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7973 moved from start: 0.3793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 10426 Z= 0.159 Angle : 0.497 6.645 13956 Z= 0.266 Chirality : 0.038 0.140 1590 Planarity : 0.003 0.026 1769 Dihedral : 3.759 13.821 1303 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 2.11 % Allowed : 17.97 % Favored : 79.92 % 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: 0.39 (0.25), residues: 1170 helix: 2.07 (0.24), residues: 501 sheet: -0.70 (0.34), residues: 266 loop : -1.40 (0.25), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 116 TYR 0.022 0.002 TYR G 53 PHE 0.016 0.001 PHE E 105 HIS 0.023 0.002 HIS G 55 Details of bonding type rmsd covalent geometry : bond 0.00387 (10426) covalent geometry : angle 0.49696 (13956) hydrogen bonds : bond 0.04148 ( 407) hydrogen bonds : angle 4.12909 ( 1218) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 194 time to evaluate : 0.441 Fit side-chains TARDY: cannot create tardy model for: "GLU C 8 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ARG D 3 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash REVERT: A 19 ARG cc_start: 0.7015 (tpt90) cc_final: 0.6197 (tpt90) REVERT: C 2 ILE cc_start: 0.8722 (tp) cc_final: 0.8494 (tt) REVERT: C 65 ASN cc_start: 0.8231 (t0) cc_final: 0.7720 (m-40) REVERT: D 169 PHE cc_start: 0.8295 (t80) cc_final: 0.7828 (t80) REVERT: D 183 ILE cc_start: 0.8894 (tp) cc_final: 0.8566 (tt) REVERT: D 208 GLU cc_start: 0.7548 (tp30) cc_final: 0.7230 (tp30) REVERT: E 169 PHE cc_start: 0.8109 (t80) cc_final: 0.7791 (t80) REVERT: E 174 GLN cc_start: 0.8470 (tm-30) cc_final: 0.8099 (tm-30) REVERT: E 182 GLU cc_start: 0.8147 (tp30) cc_final: 0.7895 (tp30) REVERT: F 117 GLN cc_start: 0.8659 (pp30) cc_final: 0.8198 (pm20) REVERT: F 174 GLN cc_start: 0.8568 (tm-30) cc_final: 0.8129 (tm-30) REVERT: G 174 GLN cc_start: 0.8754 (tm-30) cc_final: 0.8482 (tm-30) REVERT: H 73 PHE cc_start: 0.7049 (m-80) cc_final: 0.6434 (m-10) outliers start: 25 outliers final: 18 residues processed: 214 average time/residue: 0.1084 time to fit residues: 32.8540 Evaluate side-chains 197 residues out of total 1185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 179 time to evaluate : 0.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain D residue 55 HIS Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain D residue 114 ASP Chi-restraints excluded: chain D residue 147 GLU Chi-restraints excluded: chain D residue 177 SER Chi-restraints excluded: chain D residue 180 VAL Chi-restraints excluded: chain D residue 184 ILE Chi-restraints excluded: chain D residue 185 VAL Chi-restraints excluded: chain D residue 214 SER Chi-restraints excluded: chain D residue 220 ILE Chi-restraints excluded: chain E residue 180 VAL Chi-restraints excluded: chain F residue 166 ASN Chi-restraints excluded: chain G residue 94 ILE Chi-restraints excluded: chain G residue 114 ASP Chi-restraints excluded: chain G residue 177 SER Chi-restraints excluded: chain G residue 191 ILE Chi-restraints excluded: chain G residue 214 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 13 optimal weight: 5.9990 chunk 70 optimal weight: 0.5980 chunk 89 optimal weight: 0.8980 chunk 119 optimal weight: 8.9990 chunk 20 optimal weight: 6.9990 chunk 75 optimal weight: 6.9990 chunk 55 optimal weight: 6.9990 chunk 9 optimal weight: 3.9990 chunk 76 optimal weight: 0.9980 chunk 79 optimal weight: 0.7980 chunk 19 optimal weight: 2.9990 overall best weight: 1.2582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 146 ASN ** D 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 115 ASN E 115 ASN F 115 ASN G 55 HIS H 146 ASN ** H 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.177649 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.142752 restraints weight = 14939.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.142988 restraints weight = 10599.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.143912 restraints weight = 9920.061| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.144501 restraints weight = 6221.071| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.145229 restraints weight = 5588.063| |-----------------------------------------------------------------------------| r_work (final): 0.3699 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7919 moved from start: 0.4030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10426 Z= 0.109 Angle : 0.449 7.551 13956 Z= 0.241 Chirality : 0.037 0.136 1590 Planarity : 0.002 0.026 1769 Dihedral : 3.564 12.946 1303 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 2.11 % Allowed : 18.90 % Favored : 78.99 % 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: 0.54 (0.25), residues: 1170 helix: 2.20 (0.25), residues: 497 sheet: -0.61 (0.34), residues: 266 loop : -1.30 (0.25), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 116 TYR 0.014 0.001 TYR D 127 PHE 0.013 0.001 PHE G 105 HIS 0.013 0.001 HIS D 55 Details of bonding type rmsd covalent geometry : bond 0.00261 (10426) covalent geometry : angle 0.44874 (13956) hydrogen bonds : bond 0.03261 ( 407) hydrogen bonds : angle 3.91393 ( 1218) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 192 time to evaluate : 0.471 Fit side-chains TARDY: cannot create tardy model for: "GLU C 8 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ARG D 3 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash REVERT: A 19 ARG cc_start: 0.7030 (tpt90) cc_final: 0.6238 (tpt90) REVERT: C 65 ASN cc_start: 0.8264 (t0) cc_final: 0.7730 (m-40) REVERT: D 169 PHE cc_start: 0.8223 (t80) cc_final: 0.7759 (t80) REVERT: E 137 GLN cc_start: 0.6476 (mm110) cc_final: 0.6275 (mm110) REVERT: E 169 PHE cc_start: 0.8011 (t80) cc_final: 0.7679 (t80) REVERT: E 174 GLN cc_start: 0.8393 (tm-30) cc_final: 0.8070 (tm-30) REVERT: E 182 GLU cc_start: 0.8175 (tp30) cc_final: 0.7873 (tp30) REVERT: F 117 GLN cc_start: 0.8723 (pp30) cc_final: 0.8282 (pm20) REVERT: F 169 PHE cc_start: 0.7998 (t80) cc_final: 0.7617 (t80) REVERT: F 174 GLN cc_start: 0.8595 (tm-30) cc_final: 0.7988 (tm-30) REVERT: G 174 GLN cc_start: 0.8795 (tm-30) cc_final: 0.8535 (tm-30) REVERT: H 60 GLU cc_start: 0.8566 (mp0) cc_final: 0.8301 (mp0) REVERT: H 112 GLU cc_start: 0.7545 (mt-10) cc_final: 0.7079 (mp0) outliers start: 25 outliers final: 20 residues processed: 212 average time/residue: 0.1079 time to fit residues: 32.2025 Evaluate side-chains 198 residues out of total 1185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 178 time to evaluate : 0.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain D residue 114 ASP Chi-restraints excluded: chain D residue 147 GLU Chi-restraints excluded: chain D residue 177 SER Chi-restraints excluded: chain D residue 180 VAL Chi-restraints excluded: chain D residue 184 ILE Chi-restraints excluded: chain D residue 185 VAL Chi-restraints excluded: chain D residue 220 ILE Chi-restraints excluded: chain E residue 177 SER Chi-restraints excluded: chain E residue 180 VAL Chi-restraints excluded: chain F residue 111 VAL Chi-restraints excluded: chain F residue 166 ASN Chi-restraints excluded: chain F residue 177 SER Chi-restraints excluded: chain G residue 55 HIS Chi-restraints excluded: chain G residue 94 ILE Chi-restraints excluded: chain G residue 114 ASP Chi-restraints excluded: chain G residue 177 SER Chi-restraints excluded: chain G residue 191 ILE Chi-restraints excluded: chain G residue 214 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 87 optimal weight: 9.9990 chunk 0 optimal weight: 20.0000 chunk 75 optimal weight: 0.7980 chunk 46 optimal weight: 3.9990 chunk 37 optimal weight: 5.9990 chunk 31 optimal weight: 8.9990 chunk 93 optimal weight: 3.9990 chunk 83 optimal weight: 10.0000 chunk 88 optimal weight: 2.9990 chunk 2 optimal weight: 4.9990 chunk 74 optimal weight: 0.8980 overall best weight: 2.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 55 HIS D 93 ASN E 115 ASN F 115 ASN ** H 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.163392 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.129853 restraints weight = 15545.190| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.128245 restraints weight = 11141.969| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.129398 restraints weight = 11219.018| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.130407 restraints weight = 7358.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.130855 restraints weight = 6493.076| |-----------------------------------------------------------------------------| r_work (final): 0.3503 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7973 moved from start: 0.4239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 10426 Z= 0.179 Angle : 0.517 7.163 13956 Z= 0.274 Chirality : 0.038 0.140 1590 Planarity : 0.003 0.031 1769 Dihedral : 3.843 18.150 1303 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 2.62 % Allowed : 19.32 % Favored : 78.06 % 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: 0.42 (0.25), residues: 1170 helix: 2.09 (0.25), residues: 496 sheet: -0.62 (0.35), residues: 266 loop : -1.38 (0.25), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 13 TYR 0.015 0.002 TYR D 127 PHE 0.015 0.001 PHE E 105 HIS 0.014 0.001 HIS G 55 Details of bonding type rmsd covalent geometry : bond 0.00439 (10426) covalent geometry : angle 0.51685 (13956) hydrogen bonds : bond 0.04194 ( 407) hydrogen bonds : angle 4.10992 ( 1218) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 179 time to evaluate : 0.463 Fit side-chains TARDY: cannot create tardy model for: "GLU C 8 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ARG D 3 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash REVERT: A 19 ARG cc_start: 0.6976 (tpt90) cc_final: 0.6139 (tpt90) REVERT: C 57 SER cc_start: 0.8870 (OUTLIER) cc_final: 0.8556 (t) REVERT: C 65 ASN cc_start: 0.8299 (t0) cc_final: 0.7760 (m-40) REVERT: D 93 ASN cc_start: 0.8001 (OUTLIER) cc_final: 0.7567 (t0) REVERT: D 169 PHE cc_start: 0.8370 (t80) cc_final: 0.7870 (t80) REVERT: D 208 GLU cc_start: 0.7502 (tp30) cc_final: 0.7179 (tp30) REVERT: E 45 ASP cc_start: 0.8627 (m-30) cc_final: 0.8379 (m-30) REVERT: E 137 GLN cc_start: 0.6761 (mm110) cc_final: 0.6520 (mm110) REVERT: E 169 PHE cc_start: 0.8187 (t80) cc_final: 0.7840 (t80) REVERT: E 174 GLN cc_start: 0.8525 (tm-30) cc_final: 0.8000 (tm-30) REVERT: E 182 GLU cc_start: 0.8227 (tp30) cc_final: 0.7905 (tp30) REVERT: F 117 GLN cc_start: 0.8732 (pp30) cc_final: 0.8127 (pm20) REVERT: F 169 PHE cc_start: 0.8135 (t80) cc_final: 0.7720 (t80) REVERT: F 174 GLN cc_start: 0.8635 (tm-30) cc_final: 0.8041 (tm-30) REVERT: G 117 GLN cc_start: 0.8558 (pt0) cc_final: 0.8302 (pp30) REVERT: G 174 GLN cc_start: 0.8920 (tm-30) cc_final: 0.8685 (tm-30) REVERT: H 169 PHE cc_start: 0.6438 (m-80) cc_final: 0.5693 (m-80) outliers start: 31 outliers final: 22 residues processed: 202 average time/residue: 0.1064 time to fit residues: 30.3951 Evaluate side-chains 194 residues out of total 1185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 170 time to evaluate : 0.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain C residue 57 SER Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain D residue 55 HIS Chi-restraints excluded: chain D residue 93 ASN Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain D residue 114 ASP Chi-restraints excluded: chain D residue 147 GLU Chi-restraints excluded: chain D residue 177 SER Chi-restraints excluded: chain D residue 180 VAL Chi-restraints excluded: chain D residue 184 ILE Chi-restraints excluded: chain D residue 185 VAL Chi-restraints excluded: chain D residue 220 ILE Chi-restraints excluded: chain E residue 177 SER Chi-restraints excluded: chain E residue 180 VAL Chi-restraints excluded: chain F residue 111 VAL Chi-restraints excluded: chain F residue 177 SER Chi-restraints excluded: chain F residue 209 ILE Chi-restraints excluded: chain G residue 94 ILE Chi-restraints excluded: chain G residue 114 ASP Chi-restraints excluded: chain G residue 177 SER Chi-restraints excluded: chain G residue 188 ILE Chi-restraints excluded: chain G residue 191 ILE Chi-restraints excluded: chain G residue 214 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 72 optimal weight: 0.6980 chunk 45 optimal weight: 2.9990 chunk 30 optimal weight: 0.8980 chunk 62 optimal weight: 20.0000 chunk 53 optimal weight: 0.8980 chunk 85 optimal weight: 4.9990 chunk 2 optimal weight: 0.5980 chunk 0 optimal weight: 20.0000 chunk 33 optimal weight: 1.9990 chunk 82 optimal weight: 1.9990 chunk 28 optimal weight: 6.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 166 ASN D 55 HIS D 93 ASN D 138 HIS E 166 ASN G 55 HIS G 173 ASN ** H 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.172731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.138342 restraints weight = 15717.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.138076 restraints weight = 10864.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.139055 restraints weight = 10611.427| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.139846 restraints weight = 6646.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.141098 restraints weight = 5881.864| |-----------------------------------------------------------------------------| r_work (final): 0.3634 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7936 moved from start: 0.4390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 10426 Z= 0.099 Angle : 0.441 6.851 13956 Z= 0.238 Chirality : 0.036 0.134 1590 Planarity : 0.002 0.026 1769 Dihedral : 3.578 16.768 1303 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 2.11 % Allowed : 20.51 % Favored : 77.38 % 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: 0.54 (0.25), residues: 1170 helix: 2.19 (0.25), residues: 497 sheet: -0.49 (0.34), residues: 261 loop : -1.36 (0.25), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 13 TYR 0.013 0.001 TYR D 127 PHE 0.012 0.001 PHE G 105 HIS 0.016 0.001 HIS D 55 Details of bonding type rmsd covalent geometry : bond 0.00232 (10426) covalent geometry : angle 0.44060 (13956) hydrogen bonds : bond 0.03051 ( 407) hydrogen bonds : angle 3.86464 ( 1218) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 186 time to evaluate : 0.433 Fit side-chains TARDY: cannot create tardy model for: "GLU C 8 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ARG D 3 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash REVERT: A 19 ARG cc_start: 0.6937 (tpt90) cc_final: 0.6151 (tpt90) REVERT: C 65 ASN cc_start: 0.8307 (t0) cc_final: 0.7795 (m-40) REVERT: D 93 ASN cc_start: 0.7859 (OUTLIER) cc_final: 0.7574 (t0) REVERT: D 169 PHE cc_start: 0.8255 (t80) cc_final: 0.7660 (t80) REVERT: D 208 GLU cc_start: 0.7574 (tp30) cc_final: 0.7243 (tp30) REVERT: E 169 PHE cc_start: 0.8008 (t80) cc_final: 0.7664 (t80) REVERT: E 174 GLN cc_start: 0.8409 (tm-30) cc_final: 0.8084 (tm-30) REVERT: E 182 GLU cc_start: 0.8176 (tp30) cc_final: 0.7904 (tp30) REVERT: F 117 GLN cc_start: 0.8703 (pp30) cc_final: 0.8243 (pm20) REVERT: F 169 PHE cc_start: 0.8050 (t80) cc_final: 0.7624 (t80) REVERT: F 174 GLN cc_start: 0.8573 (tm-30) cc_final: 0.7976 (tm-30) REVERT: G 174 GLN cc_start: 0.8857 (tm-30) cc_final: 0.8610 (tm-30) outliers start: 25 outliers final: 20 residues processed: 205 average time/residue: 0.1097 time to fit residues: 31.5828 Evaluate side-chains 197 residues out of total 1185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 176 time to evaluate : 0.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain D residue 55 HIS Chi-restraints excluded: chain D residue 93 ASN Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain D residue 114 ASP Chi-restraints excluded: chain D residue 147 GLU Chi-restraints excluded: chain D residue 177 SER Chi-restraints excluded: chain D residue 184 ILE Chi-restraints excluded: chain D residue 185 VAL Chi-restraints excluded: chain E residue 177 SER Chi-restraints excluded: chain F residue 111 VAL Chi-restraints excluded: chain F residue 133 ILE Chi-restraints excluded: chain F residue 177 SER Chi-restraints excluded: chain G residue 55 HIS Chi-restraints excluded: chain G residue 94 ILE Chi-restraints excluded: chain G residue 109 VAL Chi-restraints excluded: chain G residue 114 ASP Chi-restraints excluded: chain G residue 177 SER Chi-restraints excluded: chain G residue 191 ILE Chi-restraints excluded: chain G residue 214 SER Chi-restraints excluded: chain H residue 64 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 87 optimal weight: 6.9990 chunk 59 optimal weight: 1.9990 chunk 99 optimal weight: 6.9990 chunk 112 optimal weight: 10.0000 chunk 11 optimal weight: 0.9980 chunk 10 optimal weight: 4.9990 chunk 49 optimal weight: 0.7980 chunk 0 optimal weight: 20.0000 chunk 62 optimal weight: 9.9990 chunk 13 optimal weight: 0.9980 chunk 100 optimal weight: 2.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 55 HIS D 93 ASN E 115 ASN E 137 GLN E 211 GLN F 115 ASN G 55 HIS ** G 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 146 ASN H 173 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.172878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.138891 restraints weight = 15448.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.138280 restraints weight = 10819.186| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.139579 restraints weight = 10309.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.140057 restraints weight = 6502.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.140793 restraints weight = 5965.928| |-----------------------------------------------------------------------------| r_work (final): 0.3632 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 moved from start: 0.4472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10426 Z= 0.123 Angle : 0.461 7.642 13956 Z= 0.247 Chirality : 0.037 0.137 1590 Planarity : 0.002 0.026 1769 Dihedral : 3.590 17.942 1303 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 2.28 % Allowed : 20.34 % Favored : 77.38 % 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: 0.52 (0.25), residues: 1170 helix: 2.13 (0.25), residues: 498 sheet: -0.43 (0.35), residues: 261 loop : -1.38 (0.25), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 13 TYR 0.012 0.001 TYR G 53 PHE 0.012 0.001 PHE E 105 HIS 0.008 0.001 HIS D 55 Details of bonding type rmsd covalent geometry : bond 0.00298 (10426) covalent geometry : angle 0.46080 (13956) hydrogen bonds : bond 0.03297 ( 407) hydrogen bonds : angle 3.88370 ( 1218) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 176 time to evaluate : 0.469 Fit side-chains TARDY: cannot create tardy model for: "GLU C 8 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ARG D 3 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash REVERT: A 19 ARG cc_start: 0.6929 (tpt90) cc_final: 0.6158 (tpt90) REVERT: C 65 ASN cc_start: 0.8320 (t0) cc_final: 0.7800 (m-40) REVERT: D 93 ASN cc_start: 0.8000 (OUTLIER) cc_final: 0.7566 (t0) REVERT: D 169 PHE cc_start: 0.8300 (t80) cc_final: 0.7675 (t80) REVERT: D 208 GLU cc_start: 0.7615 (tp30) cc_final: 0.7300 (tp30) REVERT: E 169 PHE cc_start: 0.8061 (t80) cc_final: 0.7725 (t80) REVERT: E 174 GLN cc_start: 0.8430 (tm-30) cc_final: 0.8099 (tm-30) REVERT: E 182 GLU cc_start: 0.8186 (tp30) cc_final: 0.7919 (tp30) REVERT: F 117 GLN cc_start: 0.8720 (pp30) cc_final: 0.8254 (pm20) REVERT: F 169 PHE cc_start: 0.8091 (t80) cc_final: 0.7648 (t80) REVERT: F 174 GLN cc_start: 0.8570 (tm-30) cc_final: 0.7972 (tm-30) REVERT: G 174 GLN cc_start: 0.8852 (tm-30) cc_final: 0.8610 (tm-30) outliers start: 27 outliers final: 25 residues processed: 198 average time/residue: 0.1053 time to fit residues: 29.6510 Evaluate side-chains 194 residues out of total 1185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 168 time to evaluate : 0.505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain C residue 173 ASN Chi-restraints excluded: chain D residue 55 HIS Chi-restraints excluded: chain D residue 93 ASN Chi-restraints excluded: chain D residue 100 ILE Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain D residue 114 ASP Chi-restraints excluded: chain D residue 147 GLU Chi-restraints excluded: chain D residue 177 SER Chi-restraints excluded: chain D residue 184 ILE Chi-restraints excluded: chain D residue 185 VAL Chi-restraints excluded: chain E residue 177 SER Chi-restraints excluded: chain E residue 180 VAL Chi-restraints excluded: chain F residue 111 VAL Chi-restraints excluded: chain F residue 133 ILE Chi-restraints excluded: chain F residue 177 SER Chi-restraints excluded: chain G residue 55 HIS Chi-restraints excluded: chain G residue 94 ILE Chi-restraints excluded: chain G residue 109 VAL Chi-restraints excluded: chain G residue 114 ASP Chi-restraints excluded: chain G residue 124 ASP Chi-restraints excluded: chain G residue 177 SER Chi-restraints excluded: chain G residue 191 ILE Chi-restraints excluded: chain G residue 214 SER Chi-restraints excluded: chain H residue 64 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 36 optimal weight: 4.9990 chunk 76 optimal weight: 0.7980 chunk 104 optimal weight: 0.0270 chunk 63 optimal weight: 0.0870 chunk 32 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 chunk 83 optimal weight: 5.9990 chunk 64 optimal weight: 0.5980 chunk 23 optimal weight: 6.9990 chunk 43 optimal weight: 0.0870 chunk 91 optimal weight: 1.9990 overall best weight: 0.3194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 55 HIS D 93 ASN E 115 ASN G 55 HIS ** G 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4085 r_free = 0.4085 target = 0.176462 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.142455 restraints weight = 15337.882| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.141891 restraints weight = 10869.330| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.143348 restraints weight = 10022.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.143624 restraints weight = 6404.211| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.144330 restraints weight = 5954.449| |-----------------------------------------------------------------------------| r_work (final): 0.3651 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7886 moved from start: 0.4621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 10426 Z= 0.089 Angle : 0.455 9.661 13956 Z= 0.244 Chirality : 0.036 0.136 1590 Planarity : 0.002 0.029 1769 Dihedral : 3.391 16.171 1303 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 1.43 % Allowed : 21.10 % Favored : 77.47 % 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: 0.62 (0.25), residues: 1170 helix: 2.17 (0.25), residues: 497 sheet: -0.36 (0.34), residues: 261 loop : -1.27 (0.25), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 13 TYR 0.028 0.001 TYR D 53 PHE 0.012 0.001 PHE G 105 HIS 0.019 0.001 HIS D 55 Details of bonding type rmsd covalent geometry : bond 0.00201 (10426) covalent geometry : angle 0.45481 (13956) hydrogen bonds : bond 0.02497 ( 407) hydrogen bonds : angle 3.71715 ( 1218) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 183 time to evaluate : 0.296 Fit side-chains TARDY: cannot create tardy model for: "GLU C 8 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ARG D 3 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 19 ARG cc_start: 0.6933 (tpt90) cc_final: 0.6152 (tpt90) REVERT: C 65 ASN cc_start: 0.8299 (t0) cc_final: 0.7783 (m-40) REVERT: D 169 PHE cc_start: 0.8213 (t80) cc_final: 0.7603 (t80) REVERT: D 208 GLU cc_start: 0.7641 (tp30) cc_final: 0.7323 (tp30) REVERT: E 40 GLU cc_start: 0.8415 (mm-30) cc_final: 0.8088 (tp30) REVERT: E 137 GLN cc_start: 0.6695 (mm110) cc_final: 0.6331 (mm110) REVERT: E 169 PHE cc_start: 0.7920 (t80) cc_final: 0.7583 (t80) REVERT: E 174 GLN cc_start: 0.8306 (tm-30) cc_final: 0.7942 (tm-30) REVERT: E 182 GLU cc_start: 0.8178 (tp30) cc_final: 0.7926 (tp30) REVERT: F 117 GLN cc_start: 0.8674 (pp30) cc_final: 0.8217 (pm20) REVERT: F 169 PHE cc_start: 0.7931 (t80) cc_final: 0.7528 (t80) REVERT: F 174 GLN cc_start: 0.8497 (tm-30) cc_final: 0.8069 (tm-30) REVERT: G 174 GLN cc_start: 0.8848 (tm-30) cc_final: 0.8609 (tm-30) outliers start: 17 outliers final: 13 residues processed: 195 average time/residue: 0.1078 time to fit residues: 29.7932 Evaluate side-chains 186 residues out of total 1185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 173 time to evaluate : 0.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain C residue 173 ASN Chi-restraints excluded: chain D residue 114 ASP Chi-restraints excluded: chain D residue 177 SER Chi-restraints excluded: chain D residue 185 VAL Chi-restraints excluded: chain F residue 111 VAL Chi-restraints excluded: chain F residue 133 ILE Chi-restraints excluded: chain G residue 55 HIS Chi-restraints excluded: chain G residue 94 ILE Chi-restraints excluded: chain G residue 109 VAL Chi-restraints excluded: chain G residue 114 ASP Chi-restraints excluded: chain G residue 124 ASP Chi-restraints excluded: chain G residue 177 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 64 optimal weight: 0.6980 chunk 119 optimal weight: 10.0000 chunk 20 optimal weight: 6.9990 chunk 114 optimal weight: 20.0000 chunk 69 optimal weight: 0.9990 chunk 92 optimal weight: 0.0270 chunk 56 optimal weight: 0.5980 chunk 49 optimal weight: 1.9990 chunk 50 optimal weight: 5.9990 chunk 84 optimal weight: 5.9990 chunk 106 optimal weight: 3.9990 overall best weight: 0.8642 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 115 ASN G 55 HIS ** G 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.175554 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.141406 restraints weight = 15235.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.140400 restraints weight = 10782.680| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.141756 restraints weight = 9916.958| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.142639 restraints weight = 6463.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.143169 restraints weight = 5819.585| |-----------------------------------------------------------------------------| r_work (final): 0.3635 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7912 moved from start: 0.4674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 10426 Z= 0.096 Angle : 0.464 12.007 13956 Z= 0.245 Chirality : 0.036 0.136 1590 Planarity : 0.002 0.029 1769 Dihedral : 3.383 15.864 1303 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 1.27 % Allowed : 21.35 % Favored : 77.38 % 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: 0.62 (0.25), residues: 1170 helix: 2.20 (0.25), residues: 494 sheet: -0.30 (0.35), residues: 259 loop : -1.34 (0.24), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 13 TYR 0.010 0.001 TYR F 127 PHE 0.030 0.001 PHE D 61 HIS 0.009 0.001 HIS G 55 Details of bonding type rmsd covalent geometry : bond 0.00226 (10426) covalent geometry : angle 0.46371 (13956) hydrogen bonds : bond 0.02740 ( 407) hydrogen bonds : angle 3.71996 ( 1218) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 173 time to evaluate : 0.486 Fit side-chains TARDY: cannot create tardy model for: "GLU C 8 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ARG D 3 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 19 ARG cc_start: 0.6924 (tpt90) cc_final: 0.6144 (tpt90) REVERT: C 65 ASN cc_start: 0.8295 (t0) cc_final: 0.7785 (m-40) REVERT: D 169 PHE cc_start: 0.8247 (t80) cc_final: 0.7627 (t80) REVERT: D 208 GLU cc_start: 0.7620 (tp30) cc_final: 0.7288 (tp30) REVERT: E 40 GLU cc_start: 0.8418 (mm-30) cc_final: 0.8093 (tp30) REVERT: E 137 GLN cc_start: 0.6762 (mm110) cc_final: 0.6488 (mm110) REVERT: E 169 PHE cc_start: 0.7970 (t80) cc_final: 0.7620 (t80) REVERT: E 174 GLN cc_start: 0.8345 (tm-30) cc_final: 0.7986 (tm-30) REVERT: E 182 GLU cc_start: 0.8176 (tp30) cc_final: 0.7919 (tp30) REVERT: F 117 GLN cc_start: 0.8691 (pp30) cc_final: 0.8244 (pm20) REVERT: F 169 PHE cc_start: 0.8010 (t80) cc_final: 0.7576 (t80) REVERT: F 174 GLN cc_start: 0.8555 (tm-30) cc_final: 0.8132 (tm-30) REVERT: G 174 GLN cc_start: 0.8862 (tm-30) cc_final: 0.8643 (tm-30) outliers start: 15 outliers final: 15 residues processed: 186 average time/residue: 0.1022 time to fit residues: 27.3320 Evaluate side-chains 187 residues out of total 1185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 172 time to evaluate : 0.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain C residue 173 ASN Chi-restraints excluded: chain D residue 100 ILE Chi-restraints excluded: chain D residue 114 ASP Chi-restraints excluded: chain D residue 177 SER Chi-restraints excluded: chain D residue 185 VAL Chi-restraints excluded: chain F residue 111 VAL Chi-restraints excluded: chain F residue 133 ILE Chi-restraints excluded: chain G residue 55 HIS Chi-restraints excluded: chain G residue 94 ILE Chi-restraints excluded: chain G residue 109 VAL Chi-restraints excluded: chain G residue 114 ASP Chi-restraints excluded: chain G residue 124 ASP Chi-restraints excluded: chain G residue 177 SER Chi-restraints excluded: chain G residue 191 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 74 optimal weight: 0.9990 chunk 120 optimal weight: 20.0000 chunk 49 optimal weight: 1.9990 chunk 103 optimal weight: 1.9990 chunk 71 optimal weight: 0.9980 chunk 75 optimal weight: 4.9990 chunk 87 optimal weight: 3.9990 chunk 117 optimal weight: 8.9990 chunk 33 optimal weight: 3.9990 chunk 97 optimal weight: 5.9990 chunk 0 optimal weight: 20.0000 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 115 ASN G 55 HIS ** G 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 146 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.164386 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.130085 restraints weight = 15540.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.128888 restraints weight = 10916.434| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.130018 restraints weight = 11395.119| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.130682 restraints weight = 7321.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.131613 restraints weight = 6508.425| |-----------------------------------------------------------------------------| r_work (final): 0.3549 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7893 moved from start: 0.4707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 10426 Z= 0.148 Angle : 0.517 11.702 13956 Z= 0.270 Chirality : 0.038 0.139 1590 Planarity : 0.003 0.030 1769 Dihedral : 3.638 14.748 1303 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 1.52 % Allowed : 21.52 % Favored : 76.96 % 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: 0.51 (0.25), residues: 1170 helix: 2.08 (0.25), residues: 499 sheet: -0.32 (0.35), residues: 259 loop : -1.41 (0.25), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F 19 TYR 0.018 0.001 TYR G 53 PHE 0.030 0.001 PHE D 61 HIS 0.005 0.001 HIS G 55 Details of bonding type rmsd covalent geometry : bond 0.00363 (10426) covalent geometry : angle 0.51656 (13956) hydrogen bonds : bond 0.03704 ( 407) hydrogen bonds : angle 3.91105 ( 1218) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1775.93 seconds wall clock time: 31 minutes 35.26 seconds (1895.26 seconds total)