Starting phenix.real_space_refine on Thu May 1 03:07:19 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8q86_18248/05_2025/8q86_18248.cif Found real_map, /net/cci-nas-00/data/ceres_data/8q86_18248/05_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8q86_18248/05_2025/8q86_18248.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8q86_18248/05_2025/8q86_18248.map" model { file = "/net/cci-nas-00/data/ceres_data/8q86_18248/05_2025/8q86_18248.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8q86_18248/05_2025/8q86_18248.cif" } resolution = 3.69 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/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: 6.84, per 1000 atoms: 0.66 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: 3.59 Conformation dependent library (CDL) restraints added in 1.0 seconds 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: 1.15 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: 3.07 Time building geometry restraints manager: 4.01 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: 28.060 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.480 Check model and map are aligned: 0.070 Set scattering table: 0.110 Process input model: 28.440 Find NCS groups from input model: 0.450 Set up NCS constraints: 0.060 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:3.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 61.200 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.91 (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 HIS 0.004 0.001 HIS E 64 PHE 0.016 0.002 PHE E 221 TYR 0.019 0.001 TYR F 79 ARG 0.005 0.001 ARG E 28 Details of bonding type rmsd hydrogen bonds : bond 0.22654 ( 407) hydrogen bonds : angle 7.40874 ( 1218) covalent geometry : bond 0.01037 (10426) covalent geometry : angle 1.28929 (13956) *********************** 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 : 1.426 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: 0.2919 time to fit residues: 144.5517 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 : 1.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 102 optimal weight: 10.0000 chunk 91 optimal weight: 0.8980 chunk 50 optimal weight: 0.7980 chunk 31 optimal weight: 5.9990 chunk 61 optimal weight: 2.9990 chunk 48 optimal weight: 2.9990 chunk 94 optimal weight: 0.8980 chunk 36 optimal weight: 1.9990 chunk 57 optimal weight: 1.9990 chunk 70 optimal weight: 0.6980 chunk 109 optimal weight: 0.9980 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 = 0.144564 restraints weight = 15026.667| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.144701 restraints weight = 10579.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.145616 restraints weight = 9873.265| |-----------------------------------------------------------------------------| r_work (final): 0.3716 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7871 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.14 (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 HIS 0.005 0.001 HIS H 96 PHE 0.012 0.001 PHE G 105 TYR 0.017 0.001 TYR D 127 ARG 0.006 0.000 ARG G 215 Details of bonding type rmsd hydrogen bonds : bond 0.03768 ( 407) hydrogen bonds : angle 4.52599 ( 1218) covalent geometry : bond 0.00254 (10426) covalent geometry : angle 0.50470 (13956) *********************** 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 : 1.425 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: 0.6962 (tpt90) cc_final: 0.6072 (tpt90) REVERT: C 65 ASN cc_start: 0.8179 (t0) cc_final: 0.7899 (m-40) REVERT: D 86 GLU cc_start: 0.6625 (tp30) cc_final: 0.6153 (pp20) REVERT: D 183 ILE cc_start: 0.8823 (tp) cc_final: 0.8558 (tt) REVERT: E 4 ASN cc_start: 0.8841 (p0) cc_final: 0.8378 (p0) REVERT: E 169 PHE cc_start: 0.7907 (t80) cc_final: 0.7648 (t80) REVERT: E 174 GLN cc_start: 0.8415 (tm-30) cc_final: 0.8042 (tm-30) REVERT: E 182 GLU cc_start: 0.8152 (tp30) cc_final: 0.7861 (tp30) REVERT: F 117 GLN cc_start: 0.8653 (pp30) cc_final: 0.8288 (pm20) REVERT: F 174 GLN cc_start: 0.8457 (tm-30) cc_final: 0.7858 (tm-30) REVERT: G 32 THR cc_start: 0.9060 (t) cc_final: 0.8859 (t) REVERT: G 211 GLN cc_start: 0.8349 (tt0) cc_final: 0.8118 (tt0) REVERT: G 215 ARG cc_start: 0.8174 (ttm110) cc_final: 0.7879 (ttm110) REVERT: H 4 ASN cc_start: 0.8908 (OUTLIER) cc_final: 0.8652 (p0) REVERT: H 169 PHE cc_start: 0.6250 (m-80) cc_final: 0.5836 (m-80) outliers start: 20 outliers final: 10 residues processed: 239 average time/residue: 0.2674 time to fit residues: 90.7134 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 : 1.950 ------------------------------------------------------------------------------- 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 108 optimal weight: 3.9990 chunk 119 optimal weight: 6.9990 chunk 110 optimal weight: 0.8980 chunk 99 optimal weight: 3.9990 chunk 102 optimal weight: 7.9990 chunk 13 optimal weight: 0.2980 chunk 89 optimal weight: 2.9990 chunk 118 optimal weight: 6.9990 chunk 69 optimal weight: 0.0980 chunk 21 optimal weight: 0.9980 chunk 44 optimal weight: 0.8980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 = 0.4014 r_free = 0.4014 target = 0.170970 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.137094 restraints weight = 15240.612| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.135490 restraints weight = 11447.122| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.137258 restraints weight = 10213.028| |-----------------------------------------------------------------------------| r_work (final): 0.3602 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7829 moved from start: 0.3409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 10426 Z= 0.093 Angle : 0.440 5.708 13956 Z= 0.240 Chirality : 0.037 0.136 1590 Planarity : 0.003 0.025 1769 Dihedral : 3.467 12.402 1303 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 1.69 % Allowed : 15.95 % Favored : 82.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.42 (0.25), residues: 1170 helix: 2.18 (0.24), residues: 502 sheet: -0.86 (0.34), residues: 247 loop : -1.37 (0.24), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.018 0.001 HIS D 55 PHE 0.012 0.001 PHE G 105 TYR 0.018 0.001 TYR G 53 ARG 0.004 0.000 ARG G 215 Details of bonding type rmsd hydrogen bonds : bond 0.02995 ( 407) hydrogen bonds : angle 4.04520 ( 1218) covalent geometry : bond 0.00205 (10426) covalent geometry : angle 0.43964 (13956) *********************** 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 230 residues out of total 1185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 210 time to evaluate : 1.510 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: 0.6915 (tpt90) cc_final: 0.6033 (tpt90) REVERT: C 65 ASN cc_start: 0.8178 (t0) cc_final: 0.7871 (m-40) REVERT: C 175 LYS cc_start: 0.8635 (mttt) cc_final: 0.8416 (mttm) REVERT: D 183 ILE cc_start: 0.8832 (tp) cc_final: 0.8490 (tt) REVERT: E 169 PHE cc_start: 0.7888 (t80) cc_final: 0.7649 (t80) REVERT: E 174 GLN cc_start: 0.8387 (tm-30) cc_final: 0.8157 (tm-30) REVERT: E 182 GLU cc_start: 0.8232 (tp30) cc_final: 0.7960 (tp30) REVERT: F 117 GLN cc_start: 0.8681 (pp30) cc_final: 0.8273 (pm20) REVERT: F 137 GLN cc_start: 0.6273 (mm-40) cc_final: 0.6051 (mm-40) REVERT: F 169 PHE cc_start: 0.8026 (t80) cc_final: 0.7458 (t80) REVERT: F 174 GLN cc_start: 0.8396 (tm-30) cc_final: 0.7961 (tm-30) REVERT: G 211 GLN cc_start: 0.8350 (tt0) cc_final: 0.8100 (tt0) outliers start: 20 outliers final: 13 residues processed: 225 average time/residue: 0.3427 time to fit residues: 110.4997 Evaluate side-chains 205 residues out of total 1185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 192 time to evaluate : 1.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 144 ILE 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 37 optimal weight: 3.9990 chunk 65 optimal weight: 0.9980 chunk 78 optimal weight: 2.9990 chunk 90 optimal weight: 0.0050 chunk 3 optimal weight: 0.0370 chunk 101 optimal weight: 0.5980 chunk 115 optimal weight: 20.0000 chunk 62 optimal weight: 0.8980 chunk 30 optimal weight: 0.0470 chunk 108 optimal weight: 1.9990 chunk 59 optimal weight: 3.9990 overall best weight: 0.3170 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 146 ASN D 55 HIS ** D 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 115 ASN E 115 ASN F 115 ASN H 146 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.173699 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.139444 restraints weight = 15195.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.138343 restraints weight = 10667.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.139626 restraints weight = 11121.054| |-----------------------------------------------------------------------------| r_work (final): 0.3635 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7743 moved from start: 0.3745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 10426 Z= 0.082 Angle : 0.407 6.544 13956 Z= 0.223 Chirality : 0.036 0.132 1590 Planarity : 0.002 0.026 1769 Dihedral : 3.286 12.210 1303 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.03 % Favored : 98.97 % Rotamer: Outliers : 1.69 % Allowed : 17.30 % Favored : 81.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.55 (0.25), residues: 1170 helix: 2.29 (0.25), residues: 499 sheet: -0.77 (0.35), residues: 247 loop : -1.28 (0.24), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.015 0.001 HIS G 55 PHE 0.011 0.001 PHE G 105 TYR 0.022 0.001 TYR G 127 ARG 0.004 0.000 ARG G 116 Details of bonding type rmsd hydrogen bonds : bond 0.02513 ( 407) hydrogen bonds : angle 3.77950 ( 1218) covalent geometry : bond 0.00180 (10426) covalent geometry : angle 0.40740 (13956) *********************** 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 232 residues out of total 1185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 212 time to evaluate : 1.239 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: symmetry clash REVERT: A 19 ARG cc_start: 0.6837 (tpt90) cc_final: 0.6004 (tpt90) REVERT: C 65 ASN cc_start: 0.8169 (t0) cc_final: 0.7599 (m-40) REVERT: C 175 LYS cc_start: 0.8626 (mttt) cc_final: 0.8381 (mttm) REVERT: D 86 GLU cc_start: 0.6735 (tp30) cc_final: 0.6344 (pp20) REVERT: E 40 GLU cc_start: 0.8510 (mm-30) cc_final: 0.8246 (tp30) REVERT: E 174 GLN cc_start: 0.8400 (tm-30) cc_final: 0.8145 (tm-30) REVERT: E 182 GLU cc_start: 0.8235 (tp30) cc_final: 0.7925 (tp30) REVERT: F 117 GLN cc_start: 0.8665 (pp30) cc_final: 0.8167 (pm20) REVERT: F 174 GLN cc_start: 0.8420 (tm-30) cc_final: 0.8074 (tm-30) REVERT: H 146 ASN cc_start: 0.6224 (t0) cc_final: 0.4815 (m110) outliers start: 20 outliers final: 13 residues processed: 225 average time/residue: 0.2191 time to fit residues: 68.9908 Evaluate side-chains 206 residues out of total 1185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 193 time to evaluate : 0.944 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 144 ILE Chi-restraints excluded: chain D residue 55 HIS Chi-restraints excluded: chain D residue 64 HIS Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain D residue 114 ASP Chi-restraints excluded: chain D residue 185 VAL Chi-restraints excluded: chain F residue 111 VAL 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 124 ASP Chi-restraints excluded: chain G residue 168 LEU Chi-restraints excluded: chain G residue 191 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 73 optimal weight: 10.0000 chunk 65 optimal weight: 4.9990 chunk 118 optimal weight: 3.9990 chunk 5 optimal weight: 8.9990 chunk 92 optimal weight: 1.9990 chunk 40 optimal weight: 0.9980 chunk 120 optimal weight: 30.0000 chunk 91 optimal weight: 0.9990 chunk 41 optimal weight: 10.0000 chunk 33 optimal weight: 2.9990 chunk 39 optimal weight: 0.9980 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 55 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.167968 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.134078 restraints weight = 15155.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.132898 restraints weight = 10675.413| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.134022 restraints weight = 11574.385| |-----------------------------------------------------------------------------| r_work (final): 0.3572 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7883 moved from start: 0.3890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10426 Z= 0.123 Angle : 0.464 7.831 13956 Z= 0.247 Chirality : 0.037 0.135 1590 Planarity : 0.002 0.026 1769 Dihedral : 3.440 13.781 1303 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 1.86 % Allowed : 18.65 % Favored : 79.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.58 (0.25), residues: 1170 helix: 2.28 (0.25), residues: 501 sheet: -0.65 (0.35), residues: 252 loop : -1.33 (0.25), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.020 0.001 HIS D 55 PHE 0.013 0.001 PHE E 105 TYR 0.011 0.001 TYR F 127 ARG 0.011 0.000 ARG D 116 Details of bonding type rmsd hydrogen bonds : bond 0.03465 ( 407) hydrogen bonds : angle 3.81999 ( 1218) covalent geometry : bond 0.00297 (10426) covalent geometry : angle 0.46399 (13956) *********************** 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 212 residues out of total 1185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 190 time to evaluate : 1.135 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: 0.6934 (tpt90) cc_final: 0.6072 (tpt90) REVERT: C 65 ASN cc_start: 0.8239 (t0) cc_final: 0.7719 (m-40) REVERT: D 93 ASN cc_start: 0.8150 (OUTLIER) cc_final: 0.7947 (t0) REVERT: D 169 PHE cc_start: 0.8305 (t80) cc_final: 0.7688 (t80) REVERT: E 169 PHE cc_start: 0.8054 (t80) cc_final: 0.7684 (t80) REVERT: E 174 GLN cc_start: 0.8466 (tm-30) cc_final: 0.8000 (tm-30) REVERT: E 182 GLU cc_start: 0.8263 (tp30) cc_final: 0.7962 (tp30) REVERT: F 117 GLN cc_start: 0.8686 (pp30) cc_final: 0.8109 (pm20) REVERT: F 169 PHE cc_start: 0.8143 (t80) cc_final: 0.7923 (t80) REVERT: F 174 GLN cc_start: 0.8627 (tm-30) cc_final: 0.8023 (tm-30) REVERT: G 174 GLN cc_start: 0.8784 (tm-30) cc_final: 0.8505 (tm-30) REVERT: G 215 ARG cc_start: 0.8110 (ttm110) cc_final: 0.7856 (ttm170) REVERT: H 112 GLU cc_start: 0.7376 (mt-10) cc_final: 0.6806 (mp0) outliers start: 22 outliers final: 18 residues processed: 205 average time/residue: 0.2191 time to fit residues: 62.7853 Evaluate side-chains 201 residues out of total 1185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 182 time to evaluate : 1.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 184 ILE Chi-restraints excluded: chain D residue 220 ILE 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 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 124 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 24 optimal weight: 2.9990 chunk 100 optimal weight: 0.7980 chunk 99 optimal weight: 0.8980 chunk 67 optimal weight: 0.8980 chunk 53 optimal weight: 0.9980 chunk 80 optimal weight: 4.9990 chunk 43 optimal weight: 0.2980 chunk 36 optimal weight: 7.9990 chunk 115 optimal weight: 20.0000 chunk 68 optimal weight: 0.8980 chunk 62 optimal weight: 6.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 55 HIS ** D 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 115 ASN F 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 = 0.4142 r_free = 0.4142 target = 0.179505 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.144385 restraints weight = 14928.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.143821 restraints weight = 10744.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.144828 restraints weight = 9956.082| |-----------------------------------------------------------------------------| r_work (final): 0.3725 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7899 moved from start: 0.4066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 10426 Z= 0.091 Angle : 0.435 6.610 13956 Z= 0.233 Chirality : 0.036 0.132 1590 Planarity : 0.002 0.026 1769 Dihedral : 3.340 13.225 1303 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 1.60 % Allowed : 19.16 % Favored : 79.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.64 (0.25), residues: 1170 helix: 2.33 (0.25), residues: 498 sheet: -0.56 (0.35), residues: 247 loop : -1.30 (0.24), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.012 0.001 HIS G 55 PHE 0.012 0.001 PHE G 105 TYR 0.025 0.001 TYR G 127 ARG 0.004 0.000 ARG G 13 Details of bonding type rmsd hydrogen bonds : bond 0.02771 ( 407) hydrogen bonds : angle 3.70663 ( 1218) covalent geometry : bond 0.00213 (10426) covalent geometry : angle 0.43516 (13956) *********************** 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 218 residues out of total 1185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 199 time to evaluate : 1.197 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: A 19 ARG cc_start: 0.6939 (tpt90) cc_final: 0.6144 (tpt90) REVERT: C 65 ASN cc_start: 0.8305 (t0) cc_final: 0.7789 (m-40) REVERT: D 86 GLU cc_start: 0.6802 (tp30) cc_final: 0.6252 (pp20) REVERT: D 169 PHE cc_start: 0.8213 (t80) cc_final: 0.7597 (t80) REVERT: E 40 GLU cc_start: 0.8326 (mm-30) cc_final: 0.8089 (tp30) REVERT: E 169 PHE cc_start: 0.7889 (t80) cc_final: 0.7564 (t80) REVERT: E 174 GLN cc_start: 0.8360 (tm-30) cc_final: 0.7989 (tm-30) REVERT: E 182 GLU cc_start: 0.8166 (tp30) cc_final: 0.7930 (tp30) REVERT: F 117 GLN cc_start: 0.8670 (pp30) cc_final: 0.8277 (pm20) REVERT: F 174 GLN cc_start: 0.8588 (tm-30) cc_final: 0.8181 (tm-30) REVERT: G 174 GLN cc_start: 0.8727 (tm-30) cc_final: 0.8474 (tm-30) REVERT: G 215 ARG cc_start: 0.8085 (ttm110) cc_final: 0.7827 (ttm170) REVERT: H 112 GLU cc_start: 0.7465 (mt-10) cc_final: 0.7040 (mp0) outliers start: 19 outliers final: 15 residues processed: 213 average time/residue: 0.2212 time to fit residues: 65.9789 Evaluate side-chains 196 residues out of total 1185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 181 time to evaluate : 1.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 173 ASN Chi-restraints excluded: chain D residue 55 HIS 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 111 VAL Chi-restraints excluded: chain F residue 177 SER Chi-restraints excluded: chain G residue 94 ILE Chi-restraints excluded: chain G residue 106 GLU 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 68 optimal weight: 0.5980 chunk 14 optimal weight: 6.9990 chunk 96 optimal weight: 0.5980 chunk 114 optimal weight: 20.0000 chunk 78 optimal weight: 5.9990 chunk 25 optimal weight: 5.9990 chunk 52 optimal weight: 20.0000 chunk 36 optimal weight: 5.9990 chunk 57 optimal weight: 3.9990 chunk 72 optimal weight: 1.9990 chunk 39 optimal weight: 3.9990 overall best weight: 2.2386 ------------------------------------------------------------------------------- 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 ** G 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4095 r_free = 0.4095 target = 0.174750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.139185 restraints weight = 15331.929| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.138943 restraints weight = 11194.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.140110 restraints weight = 10457.017| |-----------------------------------------------------------------------------| r_work (final): 0.3650 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.4260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 10426 Z= 0.160 Angle : 0.507 6.610 13956 Z= 0.268 Chirality : 0.038 0.137 1590 Planarity : 0.003 0.025 1769 Dihedral : 3.679 17.436 1303 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 1.69 % Allowed : 19.92 % Favored : 78.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.55 (0.25), residues: 1170 helix: 2.15 (0.25), residues: 498 sheet: -0.45 (0.35), residues: 261 loop : -1.33 (0.24), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.014 0.001 HIS D 55 PHE 0.015 0.001 PHE E 105 TYR 0.019 0.002 TYR G 127 ARG 0.004 0.000 ARG E 19 Details of bonding type rmsd hydrogen bonds : bond 0.03974 ( 407) hydrogen bonds : angle 3.90982 ( 1218) covalent geometry : bond 0.00391 (10426) covalent geometry : angle 0.50713 (13956) *********************** 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 205 residues out of total 1185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 185 time to evaluate : 1.245 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: 0.7029 (tpt90) cc_final: 0.6219 (tpt90) REVERT: C 65 ASN cc_start: 0.8313 (t0) cc_final: 0.7801 (m-40) REVERT: D 93 ASN cc_start: 0.8119 (OUTLIER) cc_final: 0.7584 (t0) REVERT: D 169 PHE cc_start: 0.8322 (t80) cc_final: 0.7686 (t80) REVERT: D 208 GLU cc_start: 0.7506 (tp30) cc_final: 0.7176 (tp30) REVERT: E 137 GLN cc_start: 0.6573 (mm110) cc_final: 0.6345 (mm110) REVERT: E 169 PHE cc_start: 0.8110 (t80) cc_final: 0.7810 (t80) REVERT: E 174 GLN cc_start: 0.8496 (tm-30) cc_final: 0.8188 (tm-30) REVERT: E 182 GLU cc_start: 0.8183 (tp30) cc_final: 0.7915 (tp30) REVERT: F 117 GLN cc_start: 0.8728 (pp30) cc_final: 0.8205 (pm20) REVERT: F 169 PHE cc_start: 0.8046 (t80) cc_final: 0.7670 (t80) REVERT: F 174 GLN cc_start: 0.8617 (tm-30) cc_final: 0.8038 (tm-30) REVERT: G 174 GLN cc_start: 0.8801 (tm-30) cc_final: 0.8601 (tm-30) REVERT: G 215 ARG cc_start: 0.8136 (ttm110) cc_final: 0.7886 (ttm170) outliers start: 20 outliers final: 16 residues processed: 199 average time/residue: 0.2194 time to fit residues: 61.4160 Evaluate side-chains 194 residues out of total 1185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 177 time to evaluate : 1.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 55 HIS Chi-restraints excluded: chain D residue 93 ASN 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 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 191 ILE Chi-restraints excluded: chain G residue 214 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 74 optimal weight: 2.9990 chunk 15 optimal weight: 4.9990 chunk 13 optimal weight: 2.9990 chunk 27 optimal weight: 0.7980 chunk 53 optimal weight: 0.9990 chunk 9 optimal weight: 5.9990 chunk 58 optimal weight: 2.9990 chunk 10 optimal weight: 0.0060 chunk 45 optimal weight: 0.9990 chunk 87 optimal weight: 10.0000 chunk 5 optimal weight: 20.0000 overall best weight: 1.1602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 55 HIS E 115 ASN G 55 HIS ** G 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 146 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 = 0.3970 r_free = 0.3970 target = 0.166891 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.132378 restraints weight = 15391.196| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.132208 restraints weight = 10767.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.132766 restraints weight = 11467.918| |-----------------------------------------------------------------------------| r_work (final): 0.3548 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7909 moved from start: 0.4387 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= 0.107 Angle : 0.462 9.035 13956 Z= 0.245 Chirality : 0.037 0.134 1590 Planarity : 0.002 0.025 1769 Dihedral : 3.529 12.838 1303 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 1.43 % Allowed : 20.59 % Favored : 77.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.59 (0.25), residues: 1170 helix: 2.17 (0.25), residues: 499 sheet: -0.40 (0.35), residues: 261 loop : -1.31 (0.25), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.009 0.001 HIS G 55 PHE 0.014 0.001 PHE G 169 TYR 0.025 0.001 TYR G 127 ARG 0.007 0.000 ARG D 13 Details of bonding type rmsd hydrogen bonds : bond 0.03173 ( 407) hydrogen bonds : angle 3.75813 ( 1218) covalent geometry : bond 0.00259 (10426) covalent geometry : angle 0.46203 (13956) *********************** 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 197 residues out of total 1185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 180 time to evaluate : 1.118 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: 0.6971 (tpt90) cc_final: 0.6145 (tpt90) REVERT: C 65 ASN cc_start: 0.8299 (t0) cc_final: 0.7796 (m-40) REVERT: D 169 PHE cc_start: 0.8268 (t80) cc_final: 0.7629 (t80) REVERT: D 208 GLU cc_start: 0.7536 (tp30) cc_final: 0.7189 (tp30) REVERT: E 169 PHE cc_start: 0.8027 (t80) cc_final: 0.7652 (t80) REVERT: E 174 GLN cc_start: 0.8446 (tm-30) cc_final: 0.8087 (tm-30) REVERT: E 182 GLU cc_start: 0.8234 (tp30) cc_final: 0.7893 (tp30) REVERT: F 117 GLN cc_start: 0.8721 (pp30) cc_final: 0.8108 (pm20) REVERT: F 169 PHE cc_start: 0.7978 (t80) cc_final: 0.7563 (t80) REVERT: F 174 GLN cc_start: 0.8582 (tm-30) cc_final: 0.7954 (tm-30) REVERT: G 60 GLU cc_start: 0.8092 (pt0) cc_final: 0.7830 (pm20) REVERT: G 174 GLN cc_start: 0.8896 (tm-30) cc_final: 0.8643 (tm-30) REVERT: G 215 ARG cc_start: 0.8056 (ttm110) cc_final: 0.7838 (ttm170) outliers start: 17 outliers final: 16 residues processed: 191 average time/residue: 0.2273 time to fit residues: 61.1276 Evaluate side-chains 195 residues out of total 1185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 179 time to evaluate : 1.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 55 HIS 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 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 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 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 64 optimal weight: 0.5980 chunk 20 optimal weight: 5.9990 chunk 17 optimal weight: 0.9990 chunk 89 optimal weight: 1.9990 chunk 119 optimal weight: 9.9990 chunk 33 optimal weight: 2.9990 chunk 53 optimal weight: 0.9980 chunk 19 optimal weight: 7.9990 chunk 12 optimal weight: 0.8980 chunk 7 optimal weight: 2.9990 chunk 58 optimal weight: 0.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 55 HIS ** D 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 115 ASN E 137 GLN G 55 HIS ** G 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 173 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.167803 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.133324 restraints weight = 15564.865| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.132357 restraints weight = 10946.619| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.133404 restraints weight = 11245.294| |-----------------------------------------------------------------------------| r_work (final): 0.3554 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7901 moved from start: 0.4477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 10426 Z= 0.098 Angle : 0.459 8.775 13956 Z= 0.244 Chirality : 0.036 0.132 1590 Planarity : 0.002 0.027 1769 Dihedral : 3.434 12.858 1303 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 1.60 % Allowed : 20.59 % Favored : 77.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.25), residues: 1170 helix: 2.17 (0.25), residues: 499 sheet: -0.37 (0.34), residues: 261 loop : -1.31 (0.25), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.018 0.001 HIS D 55 PHE 0.014 0.001 PHE G 169 TYR 0.026 0.001 TYR G 127 ARG 0.007 0.000 ARG D 13 Details of bonding type rmsd hydrogen bonds : bond 0.02890 ( 407) hydrogen bonds : angle 3.70292 ( 1218) covalent geometry : bond 0.00233 (10426) covalent geometry : angle 0.45914 (13956) *********************** 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 201 residues out of total 1185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 182 time to evaluate : 1.128 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: 0.6944 (tpt90) cc_final: 0.6127 (tpt90) REVERT: C 65 ASN cc_start: 0.8301 (t0) cc_final: 0.7794 (m-40) REVERT: C 139 ARG cc_start: 0.6779 (mmt90) cc_final: 0.6564 (tpt-90) REVERT: D 169 PHE cc_start: 0.8241 (t80) cc_final: 0.7593 (t80) REVERT: D 208 GLU cc_start: 0.7604 (tp30) cc_final: 0.7239 (tp30) REVERT: E 137 GLN cc_start: 0.6596 (mm-40) cc_final: 0.6285 (mm110) REVERT: E 169 PHE cc_start: 0.7994 (t80) cc_final: 0.7645 (t80) REVERT: E 174 GLN cc_start: 0.8407 (tm-30) cc_final: 0.8056 (tm-30) REVERT: E 182 GLU cc_start: 0.8212 (tp30) cc_final: 0.7892 (tp30) REVERT: F 117 GLN cc_start: 0.8716 (pp30) cc_final: 0.8168 (pm20) REVERT: F 169 PHE cc_start: 0.7938 (t80) cc_final: 0.7536 (t80) REVERT: F 174 GLN cc_start: 0.8545 (tm-30) cc_final: 0.8077 (tm-30) REVERT: G 25 LYS cc_start: 0.8946 (tptp) cc_final: 0.8702 (tppt) REVERT: G 174 GLN cc_start: 0.8885 (tm-30) cc_final: 0.8644 (tm-30) REVERT: G 215 ARG cc_start: 0.8022 (ttm110) cc_final: 0.7820 (ttm170) outliers start: 19 outliers final: 18 residues processed: 196 average time/residue: 0.2161 time to fit residues: 59.7663 Evaluate side-chains 192 residues out of total 1185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 174 time to evaluate : 1.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 173 ASN Chi-restraints excluded: chain D residue 55 HIS Chi-restraints excluded: chain D residue 100 ILE 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 220 ILE 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 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 102 optimal weight: 10.0000 chunk 100 optimal weight: 1.9990 chunk 23 optimal weight: 5.9990 chunk 76 optimal weight: 0.9990 chunk 94 optimal weight: 7.9990 chunk 50 optimal weight: 0.9980 chunk 31 optimal weight: 9.9990 chunk 48 optimal weight: 0.1980 chunk 89 optimal weight: 0.9990 chunk 87 optimal weight: 5.9990 chunk 11 optimal weight: 0.9990 overall best weight: 0.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 55 HIS ** D 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 115 ASN G 55 HIS ** G 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4086 r_free = 0.4086 target = 0.176688 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.142757 restraints weight = 15236.684| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.142219 restraints weight = 10477.982| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.143489 restraints weight = 10057.720| |-----------------------------------------------------------------------------| r_work (final): 0.3631 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7909 moved from start: 0.4577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 10426 Z= 0.098 Angle : 0.472 9.344 13956 Z= 0.249 Chirality : 0.037 0.182 1590 Planarity : 0.002 0.028 1769 Dihedral : 3.418 17.696 1303 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 1.60 % Allowed : 20.84 % Favored : 77.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.62 (0.25), residues: 1170 helix: 2.23 (0.25), residues: 494 sheet: -0.37 (0.34), residues: 261 loop : -1.33 (0.24), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.016 0.001 HIS D 55 PHE 0.013 0.001 PHE G 169 TYR 0.026 0.001 TYR G 127 ARG 0.007 0.000 ARG D 13 Details of bonding type rmsd hydrogen bonds : bond 0.02806 ( 407) hydrogen bonds : angle 3.67925 ( 1218) covalent geometry : bond 0.00230 (10426) covalent geometry : angle 0.47191 (13956) ********************** 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 197 residues out of total 1185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 178 time to evaluate : 1.235 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: A 19 ARG cc_start: 0.6941 (tpt90) cc_final: 0.6173 (tpt90) REVERT: C 65 ASN cc_start: 0.8324 (t0) cc_final: 0.7834 (m-40) REVERT: C 139 ARG cc_start: 0.6819 (mmt90) cc_final: 0.6596 (tpt-90) REVERT: D 169 PHE cc_start: 0.8215 (t80) cc_final: 0.7583 (t80) REVERT: D 208 GLU cc_start: 0.7596 (tp30) cc_final: 0.7253 (tp30) REVERT: E 40 GLU cc_start: 0.8368 (mm-30) cc_final: 0.8015 (tp30) REVERT: E 137 GLN cc_start: 0.6565 (mm-40) cc_final: 0.6297 (mm110) REVERT: E 169 PHE cc_start: 0.7951 (t80) cc_final: 0.7629 (t80) REVERT: E 174 GLN cc_start: 0.8373 (tm-30) cc_final: 0.8021 (tm-30) REVERT: E 182 GLU cc_start: 0.8165 (tp30) cc_final: 0.7885 (tp30) REVERT: F 117 GLN cc_start: 0.8688 (pp30) cc_final: 0.8231 (pm20) REVERT: F 169 PHE cc_start: 0.7889 (t80) cc_final: 0.7511 (t80) REVERT: F 174 GLN cc_start: 0.8490 (tm-30) cc_final: 0.8025 (tm-30) REVERT: G 25 LYS cc_start: 0.8970 (tptp) cc_final: 0.8705 (tppt) REVERT: G 174 GLN cc_start: 0.8830 (tm-30) cc_final: 0.8606 (tm-30) REVERT: G 215 ARG cc_start: 0.8026 (ttm110) cc_final: 0.7803 (ttm170) outliers start: 19 outliers final: 17 residues processed: 191 average time/residue: 0.2313 time to fit residues: 62.0427 Evaluate side-chains 191 residues out of total 1185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 174 time to evaluate : 1.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 173 ASN Chi-restraints excluded: chain D residue 55 HIS Chi-restraints excluded: chain D residue 100 ILE 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 214 SER Chi-restraints excluded: chain E residue 177 SER Chi-restraints excluded: chain F residue 111 VAL 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 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 107 optimal weight: 2.9990 chunk 48 optimal weight: 0.0980 chunk 96 optimal weight: 0.9980 chunk 22 optimal weight: 8.9990 chunk 18 optimal weight: 4.9990 chunk 30 optimal weight: 0.8980 chunk 44 optimal weight: 0.0570 chunk 36 optimal weight: 8.9990 chunk 120 optimal weight: 6.9990 chunk 62 optimal weight: 0.0270 chunk 74 optimal weight: 0.8980 overall best weight: 0.3956 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 55 HIS D 138 HIS 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 = 0.4106 r_free = 0.4106 target = 0.178571 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.144774 restraints weight = 15029.975| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.143820 restraints weight = 10296.422| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.145269 restraints weight = 9977.836| |-----------------------------------------------------------------------------| r_work (final): 0.3650 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7876 moved from start: 0.4656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 10426 Z= 0.089 Angle : 0.466 9.327 13956 Z= 0.245 Chirality : 0.036 0.170 1590 Planarity : 0.002 0.040 1769 Dihedral : 3.337 23.268 1303 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 1.18 % Allowed : 21.27 % Favored : 77.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.59 (0.25), residues: 1170 helix: 2.25 (0.25), residues: 494 sheet: -0.44 (0.35), residues: 249 loop : -1.33 (0.24), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.018 0.001 HIS D 55 PHE 0.029 0.001 PHE D 61 TYR 0.027 0.001 TYR G 127 ARG 0.009 0.000 ARG D 13 Details of bonding type rmsd hydrogen bonds : bond 0.02469 ( 407) hydrogen bonds : angle 3.59393 ( 1218) covalent geometry : bond 0.00201 (10426) covalent geometry : angle 0.46584 (13956) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3625.48 seconds wall clock time: 65 minutes 31.16 seconds (3931.16 seconds total)