Starting phenix.real_space_refine on Tue Nov 18 16:55:48 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ku7_23035/11_2025/7ku7_23035.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ku7_23035/11_2025/7ku7_23035.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7ku7_23035/11_2025/7ku7_23035.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ku7_23035/11_2025/7ku7_23035.map" model { file = "/net/cci-nas-00/data/ceres_data/7ku7_23035/11_2025/7ku7_23035.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ku7_23035/11_2025/7ku7_23035.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.060 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: 9 Type Number sf(0) Gaussians Zn 2 6.06 5 P 64 5.49 5 Mg 4 5.21 5 S 48 5.16 5 Cl 2 4.86 5 C 9707 2.51 5 N 2932 2.21 5 O 2905 1.98 5 F 2 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 15666 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 2099 Number of conformers: 1 Conformer: "" Number of residues, atoms: 269, 2099 Classifications: {'peptide': 269} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 252} Chain: "B" Number of atoms: 1687 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1687 Classifications: {'peptide': 213} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 201} Chain: "C" Number of atoms: 1658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 210, 1658 Classifications: {'peptide': 210} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 198} Chain breaks: 1 Chain: "D" Number of atoms: 1676 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1676 Classifications: {'peptide': 212} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 200} Chain breaks: 1 Chain: "E" Number of atoms: 2099 Number of conformers: 1 Conformer: "" Number of residues, atoms: 269, 2099 Classifications: {'peptide': 269} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 252} Chain: "F" Number of atoms: 1691 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1691 Classifications: {'peptide': 214} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 201} Chain: "G" Number of atoms: 1651 Number of conformers: 1 Conformer: "" Number of residues, atoms: 210, 1651 Classifications: {'peptide': 210} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 198} Chain breaks: 1 Chain: "H" Number of atoms: 1651 Number of conformers: 1 Conformer: "" Number of residues, atoms: 210, 1651 Classifications: {'peptide': 210} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 198} Chain breaks: 1 Chain: "I" Number of atoms: 366 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 366 Classifications: {'DNA': 18} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 17} Chain: "J" Number of atoms: 326 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 326 Classifications: {'DNA': 16} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 15} Chain: "K" Number of atoms: 366 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 366 Classifications: {'DNA': 18} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 17} Chain: "L" Number of atoms: 326 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 326 Classifications: {'DNA': 16} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 15} Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 2, ' ZN': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 2, ' ZN': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "J" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'ZZX': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'ZZX': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 283 SG CYS A 37 63.203 103.901 50.908 1.00146.57 S ATOM 306 SG CYS A 40 64.442 100.194 51.131 1.00167.11 S ATOM 7403 SG CYS E 37 57.256 59.151 87.803 1.00157.49 S ATOM 7426 SG CYS E 40 60.025 61.807 87.401 1.00173.77 S Time building chain proxies: 4.23, per 1000 atoms: 0.27 Number of scatterers: 15666 At special positions: 0 Unit cell: (110, 172.7, 139.7, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 9 Type Number sf(0) Zn 2 29.99 Cl 2 17.00 S 48 16.00 P 64 15.00 Mg 4 11.99 F 2 9.00 O 2905 8.00 N 2932 7.00 C 9707 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.47 Conformation dependent library (CDL) restraints added in 951.9 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 301 " pdb="ZN ZN A 301 " - pdb=" ND1 HIS A 13 " pdb="ZN ZN A 301 " - pdb=" NE2 HIS A 9 " pdb="ZN ZN A 301 " - pdb=" SG CYS A 40 " pdb="ZN ZN A 301 " - pdb=" SG CYS A 37 " pdb=" ZN E 301 " pdb="ZN ZN E 301 " - pdb=" NE2 HIS E 9 " pdb="ZN ZN E 301 " - pdb=" ND1 HIS E 13 " pdb="ZN ZN E 301 " - pdb=" SG CYS E 37 " pdb="ZN ZN E 301 " - pdb=" SG CYS E 40 " Number of angles added : 3 3566 Ramachandran restraints generated. 1783 Oldfield, 0 Emsley, 1783 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3324 Finding SS restraints... Secondary structure from input PDB file: 56 helices and 17 sheets defined 37.8% alpha, 18.3% beta 24 base pairs and 37 stacking pairs defined. Time for finding SS restraints: 2.02 Creating SS restraints... Processing helix chain 'A' and resid 2 through 13 Processing helix chain 'A' and resid 15 through 23 Processing helix chain 'A' and resid 26 through 35 Processing helix chain 'A' and resid 37 through 41 Processing helix chain 'A' and resid 69 through 72 removed outlier: 3.526A pdb=" N ALA A 72 " --> pdb=" O PRO A 69 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 69 through 72' Processing helix chain 'A' and resid 97 through 113 removed outlier: 3.683A pdb=" N VAL A 101 " --> pdb=" O THR A 97 " (cutoff:3.500A) Processing helix chain 'A' and resid 128 through 139 Processing helix chain 'A' and resid 153 through 174 Processing helix chain 'A' and resid 181 through 183 No H-bonds generated for 'chain 'A' and resid 181 through 183' Processing helix chain 'A' and resid 184 through 198 Processing helix chain 'A' and resid 207 through 214 Processing helix chain 'B' and resid 97 through 113 removed outlier: 4.166A pdb=" N TRP B 105 " --> pdb=" O VAL B 101 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ALA B 106 " --> pdb=" O GLN B 102 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N THR B 107 " --> pdb=" O HIS B 103 " (cutoff:3.500A) Processing helix chain 'B' and resid 128 through 139 Processing helix chain 'B' and resid 154 through 174 removed outlier: 4.657A pdb=" N ARG B 158 " --> pdb=" O ALA B 154 " (cutoff:3.500A) Processing helix chain 'B' and resid 181 through 183 No H-bonds generated for 'chain 'B' and resid 181 through 183' Processing helix chain 'B' and resid 184 through 199 removed outlier: 3.534A pdb=" N LEU B 188 " --> pdb=" O LYS B 184 " (cutoff:3.500A) Processing helix chain 'B' and resid 207 through 214 Processing helix chain 'C' and resid 69 through 72 removed outlier: 3.818A pdb=" N ALA C 72 " --> pdb=" O PRO C 69 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 69 through 72' Processing helix chain 'C' and resid 97 through 112 Processing helix chain 'C' and resid 128 through 139 Processing helix chain 'C' and resid 154 through 175 Processing helix chain 'C' and resid 184 through 198 removed outlier: 3.566A pdb=" N HIS C 198 " --> pdb=" O TYR C 194 " (cutoff:3.500A) Processing helix chain 'D' and resid 97 through 112 Processing helix chain 'D' and resid 128 through 139 Processing helix chain 'D' and resid 153 through 175 Processing helix chain 'D' and resid 184 through 198 Processing helix chain 'E' and resid 2 through 13 Processing helix chain 'E' and resid 15 through 23 Processing helix chain 'E' and resid 26 through 35 Processing helix chain 'E' and resid 37 through 41 removed outlier: 3.806A pdb=" N ASN E 41 " --> pdb=" O PRO E 38 " (cutoff:3.500A) Processing helix chain 'E' and resid 69 through 72 Processing helix chain 'E' and resid 97 through 113 removed outlier: 3.805A pdb=" N ALA E 106 " --> pdb=" O GLN E 102 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N THR E 107 " --> pdb=" O HIS E 103 " (cutoff:3.500A) Processing helix chain 'E' and resid 128 through 139 Processing helix chain 'E' and resid 153 through 173 Processing helix chain 'E' and resid 184 through 198 Processing helix chain 'E' and resid 207 through 214 Processing helix chain 'F' and resid 69 through 72 removed outlier: 3.652A pdb=" N ALA F 72 " --> pdb=" O PRO F 69 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 69 through 72' Processing helix chain 'F' and resid 97 through 113 removed outlier: 3.890A pdb=" N VAL F 101 " --> pdb=" O THR F 97 " (cutoff:3.500A) Processing helix chain 'F' and resid 128 through 139 Processing helix chain 'F' and resid 155 through 174 removed outlier: 3.597A pdb=" N ARG F 168 " --> pdb=" O LYS F 164 " (cutoff:3.500A) Processing helix chain 'F' and resid 184 through 199 removed outlier: 3.651A pdb=" N PHE F 199 " --> pdb=" O ALA F 195 " (cutoff:3.500A) Processing helix chain 'F' and resid 207 through 213 Processing helix chain 'G' and resid 69 through 72 Processing helix chain 'G' and resid 97 through 113 removed outlier: 3.676A pdb=" N VAL G 101 " --> pdb=" O THR G 97 " (cutoff:3.500A) Processing helix chain 'G' and resid 123 through 127 Processing helix chain 'G' and resid 128 through 139 Processing helix chain 'G' and resid 155 through 175 Processing helix chain 'G' and resid 184 through 198 Processing helix chain 'G' and resid 207 through 212 Processing helix chain 'H' and resid 68 through 72 removed outlier: 3.506A pdb=" N ALA H 72 " --> pdb=" O PRO H 69 " (cutoff:3.500A) Processing helix chain 'H' and resid 97 through 113 removed outlier: 3.775A pdb=" N ALA H 110 " --> pdb=" O ALA H 106 " (cutoff:3.500A) Processing helix chain 'H' and resid 128 through 138 Processing helix chain 'H' and resid 149 through 175 removed outlier: 3.913A pdb=" N ALA H 154 " --> pdb=" O SER H 150 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N MET H 155 " --> pdb=" O GLN H 151 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N VAL H 156 " --> pdb=" O GLY H 152 " (cutoff:3.500A) Processing helix chain 'H' and resid 181 through 196 removed outlier: 4.601A pdb=" N GLY H 186 " --> pdb=" O THR H 182 " (cutoff:3.500A) removed outlier: 4.948A pdb=" N GLU H 187 " --> pdb=" O SER H 183 " (cutoff:3.500A) Processing helix chain 'H' and resid 207 through 212 Processing helix chain 'H' and resid 261 through 263 No H-bonds generated for 'chain 'H' and resid 261 through 263' Processing sheet with id=AA1, first strand: chain 'A' and resid 88 through 92 removed outlier: 6.052A pdb=" N TRP A 61 " --> pdb=" O LYS A 119 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N ILE A 118 " --> pdb=" O THR A 143 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 257 through 261 removed outlier: 6.454A pdb=" N TYR A 246 " --> pdb=" O TRP A 242 " (cutoff:3.500A) removed outlier: 4.944A pdb=" N TRP A 242 " --> pdb=" O TYR A 246 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N ALA A 248 " --> pdb=" O LEU A 240 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N GLY A 236 " --> pdb=" O VAL A 224 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N VAL A 224 " --> pdb=" O GLY A 236 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 88 through 93 removed outlier: 3.586A pdb=" N ASP B 64 " --> pdb=" O VAL B 79 " (cutoff:3.500A) removed outlier: 5.971A pdb=" N TRP B 61 " --> pdb=" O LYS B 119 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 257 through 261 removed outlier: 6.890A pdb=" N TYR B 246 " --> pdb=" O TRP B 242 " (cutoff:3.500A) removed outlier: 5.167A pdb=" N TRP B 242 " --> pdb=" O TYR B 246 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N ALA B 248 " --> pdb=" O LEU B 240 " (cutoff:3.500A) removed outlier: 5.820A pdb=" N LYS B 235 " --> pdb=" O ILE B 226 " (cutoff:3.500A) removed outlier: 6.073A pdb=" N ILE B 226 " --> pdb=" O LYS B 235 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 88 through 92 removed outlier: 3.608A pdb=" N ALA C 78 " --> pdb=" O THR C 91 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N THR C 66 " --> pdb=" O LEU C 77 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N TRP C 61 " --> pdb=" O LYS C 119 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 233 through 234 Processing sheet with id=AA7, first strand: chain 'C' and resid 237 through 242 removed outlier: 7.055A pdb=" N ALA C 248 " --> pdb=" O LEU C 240 " (cutoff:3.500A) removed outlier: 5.203A pdb=" N TRP C 242 " --> pdb=" O TYR C 246 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N TYR C 246 " --> pdb=" O TRP C 242 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 88 through 90 removed outlier: 3.524A pdb=" N VAL D 89 " --> pdb=" O THR D 80 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N THR D 80 " --> pdb=" O VAL D 89 " (cutoff:3.500A) removed outlier: 5.807A pdb=" N TRP D 61 " --> pdb=" O LYS D 119 " (cutoff:3.500A) removed outlier: 7.912A pdb=" N ASP D 121 " --> pdb=" O TRP D 61 " (cutoff:3.500A) removed outlier: 8.200A pdb=" N THR D 63 " --> pdb=" O ASP D 121 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ILE D 118 " --> pdb=" O ALA D 141 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N THR D 143 " --> pdb=" O ILE D 118 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N THR D 120 " --> pdb=" O THR D 143 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N GLY D 145 " --> pdb=" O THR D 120 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 257 through 261 Processing sheet with id=AB1, first strand: chain 'E' and resid 88 through 93 removed outlier: 6.122A pdb=" N TRP E 61 " --> pdb=" O LYS E 119 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N THR E 143 " --> pdb=" O ILE E 118 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 257 through 261 removed outlier: 6.415A pdb=" N TYR E 246 " --> pdb=" O TRP E 242 " (cutoff:3.500A) removed outlier: 5.020A pdb=" N TRP E 242 " --> pdb=" O TYR E 246 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N ALA E 248 " --> pdb=" O LEU E 240 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N GLY E 236 " --> pdb=" O VAL E 224 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N VAL E 224 " --> pdb=" O GLY E 236 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 88 through 93 Processing sheet with id=AB4, first strand: chain 'F' and resid 257 through 261 removed outlier: 6.685A pdb=" N ALA F 248 " --> pdb=" O LEU F 240 " (cutoff:3.500A) removed outlier: 4.984A pdb=" N LYS F 235 " --> pdb=" O ILE F 226 " (cutoff:3.500A) removed outlier: 5.674A pdb=" N ILE F 226 " --> pdb=" O LYS F 235 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N TRP F 237 " --> pdb=" O VAL F 224 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'G' and resid 88 through 90 removed outlier: 3.963A pdb=" N ASP G 64 " --> pdb=" O VAL G 79 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N LYS G 119 " --> pdb=" O TRP G 61 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N THR G 63 " --> pdb=" O LYS G 119 " (cutoff:3.500A) removed outlier: 7.204A pdb=" N ILE G 118 " --> pdb=" O THR G 143 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'G' and resid 257 through 261 removed outlier: 6.750A pdb=" N TYR G 246 " --> pdb=" O TRP G 242 " (cutoff:3.500A) removed outlier: 5.248A pdb=" N TRP G 242 " --> pdb=" O TYR G 246 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N ALA G 248 " --> pdb=" O LEU G 240 " (cutoff:3.500A) removed outlier: 5.798A pdb=" N LYS G 235 " --> pdb=" O ILE G 226 " (cutoff:3.500A) removed outlier: 7.340A pdb=" N ILE G 226 " --> pdb=" O LYS G 235 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N TRP G 237 " --> pdb=" O VAL G 224 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'H' and resid 88 through 89 removed outlier: 6.337A pdb=" N TRP H 61 " --> pdb=" O LYS H 119 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'H' and resid 257 through 260 removed outlier: 6.402A pdb=" N LYS H 250 " --> pdb=" O VAL H 239 " (cutoff:3.500A) removed outlier: 5.277A pdb=" N VAL H 239 " --> pdb=" O LYS H 250 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N GLY H 236 " --> pdb=" O VAL H 224 " (cutoff:3.500A) removed outlier: 7.076A pdb=" N VAL H 224 " --> pdb=" O GLY H 236 " (cutoff:3.500A) 613 hydrogen bonds defined for protein. 1794 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 51 hydrogen bonds 90 hydrogen bond angles 0 basepair planarities 24 basepair parallelities 37 stacking parallelities Total time for adding SS restraints: 2.79 Time building geometry restraints manager: 1.93 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 4577 1.34 - 1.46: 3351 1.46 - 1.58: 8043 1.58 - 1.70: 130 1.70 - 1.82: 84 Bond restraints: 16185 Sorted by residual: bond pdb=" CBC ZZX L 401 " pdb=" NBF ZZX L 401 " ideal model delta sigma weight residual 1.468 1.651 -0.183 2.00e-02 2.50e+03 8.35e+01 bond pdb=" CAO ZZX L 401 " pdb=" CBC ZZX L 401 " ideal model delta sigma weight residual 1.521 1.345 0.176 2.00e-02 2.50e+03 7.76e+01 bond pdb=" CAO ZZX J 401 " pdb=" CBC ZZX J 401 " ideal model delta sigma weight residual 1.521 1.351 0.170 2.00e-02 2.50e+03 7.19e+01 bond pdb=" CBC ZZX J 401 " pdb=" NBF ZZX J 401 " ideal model delta sigma weight residual 1.468 1.630 -0.162 2.00e-02 2.50e+03 6.59e+01 bond pdb=" CAO ZZX J 401 " pdb=" NBD ZZX J 401 " ideal model delta sigma weight residual 1.461 1.325 0.136 2.00e-02 2.50e+03 4.65e+01 ... (remaining 16180 not shown) Histogram of bond angle deviations from ideal: 0.00 - 9.66: 22249 9.66 - 19.32: 4 19.32 - 28.97: 0 28.97 - 38.63: 4 38.63 - 48.29: 2 Bond angle restraints: 22259 Sorted by residual: angle pdb=" CBC ZZX J 401 " pdb=" CAO ZZX J 401 " pdb=" NBD ZZX J 401 " ideal model delta sigma weight residual 112.49 160.78 -48.29 3.00e+00 1.11e-01 2.59e+02 angle pdb=" CBC ZZX L 401 " pdb=" CAO ZZX L 401 " pdb=" NBD ZZX L 401 " ideal model delta sigma weight residual 112.49 159.79 -47.30 3.00e+00 1.11e-01 2.49e+02 angle pdb=" CAO ZZX L 401 " pdb=" CBC ZZX L 401 " pdb=" NBF ZZX L 401 " ideal model delta sigma weight residual 106.81 70.95 35.86 3.00e+00 1.11e-01 1.43e+02 angle pdb=" CAO ZZX J 401 " pdb=" NBD ZZX J 401 " pdb=" CAS ZZX J 401 " ideal model delta sigma weight residual 121.21 85.53 35.68 3.00e+00 1.11e-01 1.41e+02 angle pdb=" CAO ZZX L 401 " pdb=" NBD ZZX L 401 " pdb=" CAS ZZX L 401 " ideal model delta sigma weight residual 121.21 85.85 35.36 3.00e+00 1.11e-01 1.39e+02 ... (remaining 22254 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.84: 8826 29.84 - 59.68: 660 59.68 - 89.52: 35 89.52 - 119.36: 1 119.36 - 149.20: 9 Dihedral angle restraints: 9531 sinusoidal: 4396 harmonic: 5135 Sorted by residual: dihedral pdb=" CA ALA E 43 " pdb=" C ALA E 43 " pdb=" N PRO E 44 " pdb=" CA PRO E 44 " ideal model delta harmonic sigma weight residual -180.00 -145.48 -34.52 0 5.00e+00 4.00e-02 4.77e+01 dihedral pdb=" CA ALA A 43 " pdb=" C ALA A 43 " pdb=" N PRO A 44 " pdb=" CA PRO A 44 " ideal model delta harmonic sigma weight residual -180.00 -147.81 -32.19 0 5.00e+00 4.00e-02 4.14e+01 dihedral pdb=" CAM ZZX J 401 " pdb=" CAO ZZX J 401 " pdb=" NBD ZZX J 401 " pdb=" CBC ZZX J 401 " ideal model delta sinusoidal sigma weight residual 146.26 -2.94 149.20 1 3.00e+01 1.11e-03 1.98e+01 ... (remaining 9528 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.071: 2177 0.071 - 0.143: 268 0.143 - 0.214: 3 0.214 - 0.286: 0 0.286 - 0.357: 2 Chirality restraints: 2450 Sorted by residual: chirality pdb=" CBC ZZX L 401 " pdb=" CAC ZZX L 401 " pdb=" CAO ZZX L 401 " pdb=" NBF ZZX L 401 " both_signs ideal model delta sigma weight residual False -2.51 -2.87 0.36 2.00e-01 2.50e+01 3.19e+00 chirality pdb=" CBC ZZX J 401 " pdb=" CAC ZZX J 401 " pdb=" CAO ZZX J 401 " pdb=" NBF ZZX J 401 " both_signs ideal model delta sigma weight residual False -2.51 -2.87 0.36 2.00e-01 2.50e+01 3.18e+00 chirality pdb=" CB ILE G 226 " pdb=" CA ILE G 226 " pdb=" CG1 ILE G 226 " pdb=" CG2 ILE G 226 " both_signs ideal model delta sigma weight residual False 2.64 2.83 -0.19 2.00e-01 2.50e+01 8.86e-01 ... (remaining 2447 not shown) Planarity restraints: 2577 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CAS ZZX L 401 " -0.016 2.00e-02 2.50e+03 3.02e-02 2.29e+01 pdb=" CAW ZZX L 401 " 0.000 2.00e-02 2.50e+03 pdb=" CAX ZZX L 401 " -0.063 2.00e-02 2.50e+03 pdb=" CAY ZZX L 401 " -0.008 2.00e-02 2.50e+03 pdb=" CAZ ZZX L 401 " 0.010 2.00e-02 2.50e+03 pdb=" CBA ZZX L 401 " 0.008 2.00e-02 2.50e+03 pdb=" CBB ZZX L 401 " 0.067 2.00e-02 2.50e+03 pdb=" CBC ZZX L 401 " 0.011 2.00e-02 2.50e+03 pdb=" NBF ZZX L 401 " 0.000 2.00e-02 2.50e+03 pdb=" OAG ZZX L 401 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CAS ZZX J 401 " -0.007 2.00e-02 2.50e+03 2.24e-02 1.26e+01 pdb=" CAW ZZX J 401 " -0.000 2.00e-02 2.50e+03 pdb=" CAX ZZX J 401 " -0.046 2.00e-02 2.50e+03 pdb=" CAY ZZX J 401 " -0.004 2.00e-02 2.50e+03 pdb=" CAZ ZZX J 401 " 0.009 2.00e-02 2.50e+03 pdb=" CBA ZZX J 401 " 0.006 2.00e-02 2.50e+03 pdb=" CBB ZZX J 401 " 0.051 2.00e-02 2.50e+03 pdb=" CBC ZZX J 401 " 0.005 2.00e-02 2.50e+03 pdb=" NBF ZZX J 401 " -0.001 2.00e-02 2.50e+03 pdb=" OAG ZZX J 401 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CAB ZZX J 401 " 0.028 2.00e-02 2.50e+03 3.03e-02 1.15e+01 pdb=" CAR ZZX J 401 " -0.040 2.00e-02 2.50e+03 pdb=" CAX ZZX J 401 " 0.006 2.00e-02 2.50e+03 pdb=" NAQ ZZX J 401 " -0.030 2.00e-02 2.50e+03 pdb=" OAD ZZX J 401 " 0.036 2.00e-02 2.50e+03 ... (remaining 2574 not shown) Histogram of nonbonded interaction distances: 1.91 - 2.51: 168 2.51 - 3.11: 11773 3.11 - 3.70: 26701 3.70 - 4.30: 35533 4.30 - 4.90: 56283 Nonbonded interactions: 130458 Sorted by model distance: nonbonded pdb="MG MG A 302 " pdb=" OAG ZZX J 401 " model vdw 1.912 2.170 nonbonded pdb=" OE2 GLU A 157 " pdb="MG MG A 302 " model vdw 1.916 2.170 nonbonded pdb="MG MG A 302 " pdb=" OAF ZZX J 401 " model vdw 1.918 2.170 nonbonded pdb=" CAO ZZX L 401 " pdb=" CAY ZZX L 401 " model vdw 1.934 2.792 nonbonded pdb="MG MG E 303 " pdb=" OAG ZZX L 401 " model vdw 1.934 2.170 ... (remaining 130453 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'E' } ncs_group { reference = (chain 'B' and (resid 57 through 212 or resid 221 through 269)) selection = (chain 'C' and (resid 57 through 212 or resid 221 through 269)) selection = (chain 'D' and (resid 57 through 212 or resid 221 through 269)) selection = (chain 'F' and (resid 57 through 212 or resid 221 through 269)) selection = (chain 'G' and resid 57 through 269) selection = (chain 'H' and resid 57 through 269) } ncs_group { reference = chain 'I' selection = chain 'K' } ncs_group { reference = chain 'J' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.530 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.300 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 19.650 Find NCS groups from input model: 0.330 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6536 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.183 16193 Z= 0.260 Angle : 0.974 48.291 22262 Z= 0.423 Chirality : 0.045 0.357 2450 Planarity : 0.005 0.058 2577 Dihedral : 18.717 149.197 6207 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 19.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.40 % Favored : 92.60 % Rotamer: Outliers : 0.00 % Allowed : 0.27 % Favored : 99.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 2.02 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.44 (0.20), residues: 1783 helix: 0.33 (0.21), residues: 610 sheet: -1.22 (0.25), residues: 395 loop : -1.82 (0.22), residues: 778 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 244 TYR 0.030 0.002 TYR A 246 PHE 0.011 0.001 PHE B 126 TRP 0.041 0.002 TRP B 134 HIS 0.007 0.001 HIS D 93 Details of bonding type rmsd covalent geometry : bond 0.00540 (16185) covalent geometry : angle 0.97274 (22259) hydrogen bonds : bond 0.22562 ( 664) hydrogen bonds : angle 7.71108 ( 1884) metal coordination : bond 0.00796 ( 8) metal coordination : angle 4.15780 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3566 Ramachandran restraints generated. 1783 Oldfield, 0 Emsley, 1783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3566 Ramachandran restraints generated. 1783 Oldfield, 0 Emsley, 1783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 343 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 343 time to evaluate : 0.563 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 ILE cc_start: 0.8096 (mm) cc_final: 0.7786 (mm) REVERT: A 76 TRP cc_start: 0.7251 (m100) cc_final: 0.6760 (m100) REVERT: A 134 TRP cc_start: 0.6850 (t60) cc_final: 0.6574 (t60) REVERT: A 209 ILE cc_start: 0.7309 (mm) cc_final: 0.6396 (mm) REVERT: B 61 TRP cc_start: 0.6686 (m-10) cc_final: 0.6182 (m-10) REVERT: B 91 THR cc_start: 0.5980 (p) cc_final: 0.5639 (p) REVERT: B 126 PHE cc_start: 0.6552 (m-80) cc_final: 0.5338 (m-10) REVERT: B 176 PHE cc_start: 0.8181 (m-80) cc_final: 0.7141 (m-80) REVERT: C 81 VAL cc_start: 0.4182 (t) cc_final: 0.3561 (p) REVERT: C 83 THR cc_start: -0.0713 (m) cc_final: -0.1049 (p) REVERT: C 244 ARG cc_start: 0.6270 (mtp180) cc_final: 0.5834 (tpp80) REVERT: D 71 MET cc_start: -0.0945 (mmt) cc_final: -0.1317 (mmt) REVERT: E 91 THR cc_start: 0.7681 (m) cc_final: 0.7412 (p) REVERT: E 199 PHE cc_start: 0.6773 (m-80) cc_final: 0.5818 (m-80) REVERT: E 238 ASN cc_start: 0.7142 (m-40) cc_final: 0.6584 (m110) REVERT: F 76 TRP cc_start: 0.7975 (m100) cc_final: 0.7662 (m100) REVERT: F 131 THR cc_start: 0.8467 (m) cc_final: 0.8183 (p) REVERT: F 176 PHE cc_start: 0.6800 (m-10) cc_final: 0.6395 (m-80) REVERT: G 71 MET cc_start: -0.2635 (ttt) cc_final: -0.2887 (mtt) outliers start: 0 outliers final: 0 residues processed: 343 average time/residue: 0.1687 time to fit residues: 79.8945 Evaluate side-chains 193 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 193 time to evaluate : 0.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 6.9990 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 0.6980 chunk 77 optimal weight: 0.0030 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 0.0470 chunk 149 optimal weight: 4.9990 overall best weight: 0.9492 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 198 HIS B 92 GLN ** B 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 92 GLN ** C 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 238 ASN ** D 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 210 GLN ** F 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4596 r_free = 0.4596 target = 0.166446 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.120862 restraints weight = 45385.917| |-----------------------------------------------------------------------------| r_work (start): 0.3863 rms_B_bonded: 6.26 r_work (final): 0.3863 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6625 moved from start: 0.2940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 16193 Z= 0.179 Angle : 0.707 13.007 22262 Z= 0.371 Chirality : 0.047 0.170 2450 Planarity : 0.006 0.057 2577 Dihedral : 18.711 116.567 2776 Min Nonbonded Distance : 1.882 Molprobity Statistics. All-atom Clashscore : 14.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 1.87 % Allowed : 12.58 % Favored : 85.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 1.01 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.29 (0.20), residues: 1783 helix: 0.39 (0.20), residues: 626 sheet: -1.18 (0.24), residues: 400 loop : -1.67 (0.23), residues: 757 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG B 74 TYR 0.027 0.003 TYR D 246 PHE 0.010 0.001 PHE B 199 TRP 0.031 0.002 TRP E 105 HIS 0.008 0.001 HIS B 198 Details of bonding type rmsd covalent geometry : bond 0.00388 (16185) covalent geometry : angle 0.70067 (22259) hydrogen bonds : bond 0.05994 ( 664) hydrogen bonds : angle 5.82610 ( 1884) metal coordination : bond 0.01963 ( 8) metal coordination : angle 7.97234 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3566 Ramachandran restraints generated. 1783 Oldfield, 0 Emsley, 1783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3566 Ramachandran restraints generated. 1783 Oldfield, 0 Emsley, 1783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 186 time to evaluate : 0.581 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 HIS cc_start: 0.7052 (OUTLIER) cc_final: 0.6806 (m-70) REVERT: A 135 LEU cc_start: 0.8450 (mm) cc_final: 0.8149 (mm) REVERT: A 193 MET cc_start: 0.7962 (ttm) cc_final: 0.7551 (ttm) REVERT: B 61 TRP cc_start: 0.6937 (m-10) cc_final: 0.6531 (m-10) REVERT: B 176 PHE cc_start: 0.8439 (m-80) cc_final: 0.7858 (m-80) REVERT: B 232 GLU cc_start: 0.7895 (pp20) cc_final: 0.7408 (mp0) REVERT: E 193 MET cc_start: 0.7199 (mmp) cc_final: 0.6951 (mtm) REVERT: F 172 GLU cc_start: 0.8531 (mp0) cc_final: 0.8325 (mp0) REVERT: F 174 ASP cc_start: 0.7774 (p0) cc_final: 0.7387 (t70) REVERT: F 238 ASN cc_start: 0.6749 (p0) cc_final: 0.6424 (p0) REVERT: H 246 TYR cc_start: 0.5715 (p90) cc_final: 0.5181 (p90) outliers start: 28 outliers final: 17 residues processed: 204 average time/residue: 0.1236 time to fit residues: 38.5870 Evaluate side-chains 170 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 152 time to evaluate : 0.569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 HIS Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 258 ILE Chi-restraints excluded: chain B residue 77 LEU Chi-restraints excluded: chain B residue 103 HIS Chi-restraints excluded: chain B residue 199 PHE Chi-restraints excluded: chain C residue 226 ILE Chi-restraints excluded: chain C residue 241 VAL Chi-restraints excluded: chain C residue 262 SER Chi-restraints excluded: chain D residue 241 VAL Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 140 ILE Chi-restraints excluded: chain E residue 149 ASN Chi-restraints excluded: chain E residue 153 GLN Chi-restraints excluded: chain F residue 90 VAL Chi-restraints excluded: chain F residue 155 MET Chi-restraints excluded: chain G residue 268 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 154 optimal weight: 5.9990 chunk 61 optimal weight: 9.9990 chunk 134 optimal weight: 3.9990 chunk 53 optimal weight: 6.9990 chunk 125 optimal weight: 0.3980 chunk 75 optimal weight: 20.0000 chunk 130 optimal weight: 3.9990 chunk 167 optimal weight: 8.9990 chunk 120 optimal weight: 0.7980 chunk 62 optimal weight: 6.9990 chunk 24 optimal weight: 4.9990 overall best weight: 2.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 210 GLN ** B 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 62 GLN ** C 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 93 HIS E 210 GLN ** F 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 185 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 = 0.4533 r_free = 0.4533 target = 0.161370 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.120557 restraints weight = 48226.336| |-----------------------------------------------------------------------------| r_work (start): 0.3869 rms_B_bonded: 4.98 r_work (final): 0.3869 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7248 moved from start: 0.6220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.069 16193 Z= 0.296 Angle : 0.849 14.346 22262 Z= 0.450 Chirality : 0.051 0.275 2450 Planarity : 0.007 0.084 2577 Dihedral : 19.035 127.296 2776 Min Nonbonded Distance : 1.713 Molprobity Statistics. All-atom Clashscore : 17.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.95 % Favored : 93.05 % Rotamer: Outliers : 4.69 % Allowed : 16.20 % Favored : 79.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 1.01 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.60 (0.19), residues: 1783 helix: 0.07 (0.19), residues: 631 sheet: -1.07 (0.24), residues: 434 loop : -2.02 (0.23), residues: 718 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG E 227 TYR 0.028 0.003 TYR H 246 PHE 0.018 0.002 PHE B 126 TRP 0.024 0.002 TRP C 242 HIS 0.013 0.002 HIS E 212 Details of bonding type rmsd covalent geometry : bond 0.00649 (16185) covalent geometry : angle 0.84378 (22259) hydrogen bonds : bond 0.07282 ( 664) hydrogen bonds : angle 5.75782 ( 1884) metal coordination : bond 0.01968 ( 8) metal coordination : angle 8.30840 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3566 Ramachandran restraints generated. 1783 Oldfield, 0 Emsley, 1783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3566 Ramachandran restraints generated. 1783 Oldfield, 0 Emsley, 1783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 156 time to evaluate : 0.605 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 176 PHE cc_start: 0.8272 (m-80) cc_final: 0.7684 (m-80) REVERT: D 71 MET cc_start: -0.1572 (ttp) cc_final: -0.4446 (mmt) REVERT: E 2 LEU cc_start: 0.6919 (pt) cc_final: 0.6663 (mp) REVERT: E 27 MET cc_start: 0.7125 (OUTLIER) cc_final: 0.6735 (mtm) REVERT: E 32 GLU cc_start: 0.8148 (OUTLIER) cc_final: 0.7928 (pm20) REVERT: F 174 ASP cc_start: 0.7792 (p0) cc_final: 0.7574 (t0) REVERT: F 232 GLU cc_start: 0.7752 (mp0) cc_final: 0.7283 (mp0) REVERT: F 238 ASN cc_start: 0.7231 (p0) cc_final: 0.7027 (p0) REVERT: H 92 GLN cc_start: 0.6852 (OUTLIER) cc_final: 0.6455 (tm-30) outliers start: 70 outliers final: 28 residues processed: 215 average time/residue: 0.1392 time to fit residues: 43.9885 Evaluate side-chains 155 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 124 time to evaluate : 0.584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 203 GLU Chi-restraints excluded: chain D residue 143 THR Chi-restraints excluded: chain D residue 241 VAL Chi-restraints excluded: chain E residue 27 MET Chi-restraints excluded: chain E residue 32 GLU Chi-restraints excluded: chain E residue 81 VAL Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 146 ILE Chi-restraints excluded: chain E residue 153 GLN Chi-restraints excluded: chain E residue 165 ASP Chi-restraints excluded: chain E residue 207 THR Chi-restraints excluded: chain E residue 210 GLN Chi-restraints excluded: chain E residue 241 VAL Chi-restraints excluded: chain F residue 105 TRP Chi-restraints excluded: chain F residue 155 MET Chi-restraints excluded: chain F residue 219 THR Chi-restraints excluded: chain G residue 96 VAL Chi-restraints excluded: chain G residue 177 MET Chi-restraints excluded: chain G residue 268 ASP Chi-restraints excluded: chain H residue 92 GLN Chi-restraints excluded: chain H residue 230 THR Chi-restraints excluded: chain H residue 239 VAL Chi-restraints excluded: chain H residue 260 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 41 optimal weight: 2.9990 chunk 108 optimal weight: 0.9980 chunk 153 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 116 optimal weight: 1.9990 chunk 131 optimal weight: 0.0010 chunk 177 optimal weight: 1.9990 chunk 152 optimal weight: 1.9990 chunk 159 optimal weight: 7.9990 chunk 42 optimal weight: 6.9990 chunk 82 optimal weight: 20.0000 overall best weight: 1.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 GLN A 210 GLN ** A 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 92 GLN ** B 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 210 GLN E 212 HIS ** F 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4539 r_free = 0.4539 target = 0.162659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.105361 restraints weight = 47225.221| |-----------------------------------------------------------------------------| r_work (start): 0.3662 rms_B_bonded: 6.10 r_work: 0.3485 rms_B_bonded: 5.01 restraints_weight: 2.0000 r_work (final): 0.3485 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 moved from start: 0.6608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 16193 Z= 0.163 Angle : 0.648 10.390 22262 Z= 0.342 Chirality : 0.045 0.194 2450 Planarity : 0.005 0.053 2577 Dihedral : 18.799 110.766 2776 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 12.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 3.61 % Allowed : 17.74 % Favored : 78.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 1.01 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.10 (0.20), residues: 1783 helix: 0.61 (0.20), residues: 632 sheet: -0.90 (0.24), residues: 398 loop : -1.77 (0.23), residues: 753 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 17 TYR 0.017 0.002 TYR D 246 PHE 0.011 0.001 PHE A 176 TRP 0.030 0.001 TRP C 259 HIS 0.007 0.001 HIS E 198 Details of bonding type rmsd covalent geometry : bond 0.00364 (16185) covalent geometry : angle 0.64359 (22259) hydrogen bonds : bond 0.04845 ( 664) hydrogen bonds : angle 5.30497 ( 1884) metal coordination : bond 0.02372 ( 8) metal coordination : angle 6.39838 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3566 Ramachandran restraints generated. 1783 Oldfield, 0 Emsley, 1783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3566 Ramachandran restraints generated. 1783 Oldfield, 0 Emsley, 1783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 140 time to evaluate : 0.604 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 HIS cc_start: 0.8303 (OUTLIER) cc_final: 0.7628 (m-70) REVERT: A 41 ASN cc_start: 0.8022 (t0) cc_final: 0.7700 (m-40) REVERT: A 62 GLN cc_start: 0.8973 (OUTLIER) cc_final: 0.7387 (mt0) REVERT: A 151 GLN cc_start: 0.8605 (OUTLIER) cc_final: 0.7349 (tm-30) REVERT: B 176 PHE cc_start: 0.8012 (m-80) cc_final: 0.7518 (m-80) REVERT: C 227 ARG cc_start: 0.8687 (ttm110) cc_final: 0.8290 (ttm110) REVERT: D 244 ARG cc_start: 0.4425 (mmp-170) cc_final: 0.2922 (mmm160) REVERT: E 187 GLU cc_start: 0.8520 (tm-30) cc_final: 0.8151 (tm-30) REVERT: F 92 GLN cc_start: 0.8387 (pt0) cc_final: 0.7983 (pt0) REVERT: F 232 GLU cc_start: 0.7834 (mp0) cc_final: 0.7308 (mp0) REVERT: F 238 ASN cc_start: 0.7447 (p0) cc_final: 0.7154 (p0) outliers start: 54 outliers final: 30 residues processed: 181 average time/residue: 0.1295 time to fit residues: 35.5400 Evaluate side-chains 155 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 122 time to evaluate : 0.587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 35 GLN Chi-restraints excluded: chain A residue 39 HIS Chi-restraints excluded: chain A residue 62 GLN Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 151 GLN Chi-restraints excluded: chain A residue 210 GLN Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 105 TRP Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain C residue 226 ILE Chi-restraints excluded: chain C residue 260 VAL Chi-restraints excluded: chain D residue 241 VAL Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain E residue 140 ILE Chi-restraints excluded: chain E residue 153 GLN Chi-restraints excluded: chain E residue 205 THR Chi-restraints excluded: chain E residue 210 GLN Chi-restraints excluded: chain F residue 155 MET Chi-restraints excluded: chain F residue 193 MET Chi-restraints excluded: chain G residue 112 LEU Chi-restraints excluded: chain G residue 177 MET Chi-restraints excluded: chain G residue 188 LEU Chi-restraints excluded: chain G residue 262 SER Chi-restraints excluded: chain G residue 268 ASP Chi-restraints excluded: chain H residue 90 VAL Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 230 THR Chi-restraints excluded: chain H residue 239 VAL Chi-restraints excluded: chain H residue 260 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 4 optimal weight: 2.9990 chunk 137 optimal weight: 0.6980 chunk 57 optimal weight: 9.9990 chunk 41 optimal weight: 0.0570 chunk 99 optimal weight: 0.7980 chunk 124 optimal weight: 9.9990 chunk 138 optimal weight: 7.9990 chunk 150 optimal weight: 0.9980 chunk 110 optimal weight: 0.6980 chunk 117 optimal weight: 7.9990 chunk 21 optimal weight: 0.3980 overall best weight: 0.5298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 210 GLN ** F 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4548 r_free = 0.4548 target = 0.163595 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.106498 restraints weight = 46788.723| |-----------------------------------------------------------------------------| r_work (start): 0.3690 rms_B_bonded: 6.25 r_work: 0.3511 rms_B_bonded: 5.21 restraints_weight: 2.0000 r_work (final): 0.3511 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7996 moved from start: 0.6778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 16193 Z= 0.130 Angle : 0.604 9.775 22262 Z= 0.319 Chirality : 0.043 0.153 2450 Planarity : 0.005 0.072 2577 Dihedral : 18.622 109.631 2776 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 12.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 3.48 % Allowed : 18.54 % Favored : 77.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 1.01 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.84 (0.20), residues: 1783 helix: 0.83 (0.20), residues: 634 sheet: -0.62 (0.25), residues: 399 loop : -1.72 (0.23), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG H 263 TYR 0.017 0.002 TYR D 246 PHE 0.009 0.001 PHE B 65 TRP 0.022 0.001 TRP C 259 HIS 0.005 0.001 HIS E 198 Details of bonding type rmsd covalent geometry : bond 0.00289 (16185) covalent geometry : angle 0.59986 (22259) hydrogen bonds : bond 0.04554 ( 664) hydrogen bonds : angle 5.08817 ( 1884) metal coordination : bond 0.01412 ( 8) metal coordination : angle 6.23541 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3566 Ramachandran restraints generated. 1783 Oldfield, 0 Emsley, 1783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3566 Ramachandran restraints generated. 1783 Oldfield, 0 Emsley, 1783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 137 time to evaluate : 0.583 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 HIS cc_start: 0.8316 (OUTLIER) cc_final: 0.7875 (m-70) REVERT: A 41 ASN cc_start: 0.7821 (t0) cc_final: 0.7554 (m-40) REVERT: A 62 GLN cc_start: 0.8965 (OUTLIER) cc_final: 0.7347 (mt0) REVERT: A 135 LEU cc_start: 0.9208 (OUTLIER) cc_final: 0.8946 (mm) REVERT: A 151 GLN cc_start: 0.8389 (OUTLIER) cc_final: 0.7086 (tm-30) REVERT: B 176 PHE cc_start: 0.7673 (m-80) cc_final: 0.7349 (m-80) REVERT: B 187 GLU cc_start: 0.8418 (OUTLIER) cc_final: 0.7674 (mp0) REVERT: D 71 MET cc_start: 0.0597 (ttt) cc_final: -0.1906 (mmt) REVERT: D 244 ARG cc_start: 0.4525 (mmp-170) cc_final: 0.3071 (mmm160) REVERT: E 187 GLU cc_start: 0.8523 (tm-30) cc_final: 0.8261 (tm-30) REVERT: E 210 GLN cc_start: 0.8110 (OUTLIER) cc_final: 0.7602 (pp30) REVERT: F 92 GLN cc_start: 0.8284 (pt0) cc_final: 0.7941 (pt0) REVERT: F 238 ASN cc_start: 0.7370 (p0) cc_final: 0.7053 (p0) outliers start: 52 outliers final: 28 residues processed: 176 average time/residue: 0.1339 time to fit residues: 35.3140 Evaluate side-chains 157 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 123 time to evaluate : 0.579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 39 HIS Chi-restraints excluded: chain A residue 62 GLN Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 151 GLN Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 103 HIS Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 187 GLU Chi-restraints excluded: chain C residue 226 ILE Chi-restraints excluded: chain C residue 254 THR Chi-restraints excluded: chain D residue 241 VAL Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 140 ILE Chi-restraints excluded: chain E residue 146 ILE Chi-restraints excluded: chain E residue 153 GLN Chi-restraints excluded: chain E residue 177 MET Chi-restraints excluded: chain E residue 205 THR Chi-restraints excluded: chain E residue 210 GLN Chi-restraints excluded: chain E residue 260 VAL Chi-restraints excluded: chain F residue 155 MET Chi-restraints excluded: chain G residue 81 VAL Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 112 LEU Chi-restraints excluded: chain G residue 177 MET Chi-restraints excluded: chain G residue 241 VAL Chi-restraints excluded: chain G residue 268 ASP Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 155 MET Chi-restraints excluded: chain H residue 230 THR Chi-restraints excluded: chain H residue 239 VAL Chi-restraints excluded: chain H residue 260 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 147 optimal weight: 8.9990 chunk 40 optimal weight: 1.9990 chunk 105 optimal weight: 0.6980 chunk 82 optimal weight: 7.9990 chunk 62 optimal weight: 0.0770 chunk 48 optimal weight: 0.5980 chunk 50 optimal weight: 9.9990 chunk 176 optimal weight: 5.9990 chunk 101 optimal weight: 2.9990 chunk 172 optimal weight: 8.9990 chunk 87 optimal weight: 0.0980 overall best weight: 0.6940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 210 GLN ** F 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4546 r_free = 0.4546 target = 0.163312 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.121011 restraints weight = 46770.749| |-----------------------------------------------------------------------------| r_work (start): 0.3863 rms_B_bonded: 5.51 r_work (final): 0.3863 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7302 moved from start: 0.6971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 16193 Z= 0.129 Angle : 0.601 9.196 22262 Z= 0.317 Chirality : 0.043 0.197 2450 Planarity : 0.005 0.055 2577 Dihedral : 18.562 108.882 2776 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 11.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 3.75 % Allowed : 19.14 % Favored : 77.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 1.01 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.70 (0.20), residues: 1783 helix: 0.94 (0.20), residues: 635 sheet: -0.50 (0.25), residues: 407 loop : -1.67 (0.23), residues: 741 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 95 TYR 0.015 0.002 TYR D 246 PHE 0.009 0.001 PHE B 65 TRP 0.020 0.001 TRP D 134 HIS 0.004 0.001 HIS E 198 Details of bonding type rmsd covalent geometry : bond 0.00286 (16185) covalent geometry : angle 0.59722 (22259) hydrogen bonds : bond 0.04471 ( 664) hydrogen bonds : angle 5.01130 ( 1884) metal coordination : bond 0.01555 ( 8) metal coordination : angle 5.78909 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3566 Ramachandran restraints generated. 1783 Oldfield, 0 Emsley, 1783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3566 Ramachandran restraints generated. 1783 Oldfield, 0 Emsley, 1783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 126 time to evaluate : 0.586 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 HIS cc_start: 0.8142 (OUTLIER) cc_final: 0.7791 (m-70) REVERT: A 62 GLN cc_start: 0.8831 (OUTLIER) cc_final: 0.6801 (mp10) REVERT: A 135 LEU cc_start: 0.8970 (OUTLIER) cc_final: 0.8688 (mm) REVERT: A 151 GLN cc_start: 0.8091 (OUTLIER) cc_final: 0.6574 (tm-30) REVERT: B 176 PHE cc_start: 0.8326 (m-80) cc_final: 0.7704 (m-80) REVERT: B 187 GLU cc_start: 0.8340 (OUTLIER) cc_final: 0.7576 (mp0) REVERT: D 71 MET cc_start: -0.2991 (ttt) cc_final: -0.5738 (mmt) REVERT: D 244 ARG cc_start: 0.4235 (mmp-170) cc_final: 0.2764 (mmm160) REVERT: E 187 GLU cc_start: 0.7862 (tm-30) cc_final: 0.7379 (tm-30) REVERT: E 210 GLN cc_start: 0.8088 (OUTLIER) cc_final: 0.7429 (pp30) REVERT: F 92 GLN cc_start: 0.7993 (pt0) cc_final: 0.7683 (pt0) REVERT: F 155 MET cc_start: 0.8081 (OUTLIER) cc_final: 0.7814 (mtt) REVERT: F 238 ASN cc_start: 0.7074 (p0) cc_final: 0.6799 (p0) outliers start: 56 outliers final: 33 residues processed: 168 average time/residue: 0.1293 time to fit residues: 33.2353 Evaluate side-chains 156 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 116 time to evaluate : 0.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 35 GLN Chi-restraints excluded: chain A residue 39 HIS Chi-restraints excluded: chain A residue 62 GLN Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 151 GLN Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 187 GLU Chi-restraints excluded: chain B residue 199 PHE Chi-restraints excluded: chain C residue 226 ILE Chi-restraints excluded: chain C residue 241 VAL Chi-restraints excluded: chain C residue 254 THR Chi-restraints excluded: chain D residue 143 THR Chi-restraints excluded: chain D residue 241 VAL Chi-restraints excluded: chain E residue 146 ILE Chi-restraints excluded: chain E residue 149 ASN Chi-restraints excluded: chain E residue 153 GLN Chi-restraints excluded: chain E residue 205 THR Chi-restraints excluded: chain E residue 207 THR Chi-restraints excluded: chain E residue 210 GLN Chi-restraints excluded: chain E residue 241 VAL Chi-restraints excluded: chain E residue 260 VAL Chi-restraints excluded: chain F residue 105 TRP Chi-restraints excluded: chain F residue 155 MET Chi-restraints excluded: chain G residue 81 VAL Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 96 VAL Chi-restraints excluded: chain G residue 112 LEU Chi-restraints excluded: chain G residue 177 MET Chi-restraints excluded: chain G residue 241 VAL Chi-restraints excluded: chain G residue 268 ASP Chi-restraints excluded: chain H residue 90 VAL Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 155 MET Chi-restraints excluded: chain H residue 239 VAL Chi-restraints excluded: chain H residue 260 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/iotbx/cli_parser.py", line 999, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1588, in energies_sites pair_proxies = self.pair_proxies( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1491, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1372, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 56.1517 > 50: distance: 37 - 62: 13.619 distance: 44 - 71: 9.206 distance: 47 - 53: 19.578 distance: 48 - 81: 26.124 distance: 53 - 54: 17.298 distance: 54 - 55: 13.216 distance: 54 - 57: 24.377 distance: 55 - 56: 10.950 distance: 55 - 62: 7.526 distance: 56 - 95: 23.101 distance: 57 - 58: 34.255 distance: 58 - 59: 20.860 distance: 59 - 60: 24.407 distance: 59 - 61: 18.787 distance: 62 - 63: 10.707 distance: 63 - 64: 10.655 distance: 63 - 66: 13.244 distance: 64 - 65: 34.986 distance: 64 - 71: 5.971 distance: 66 - 67: 17.022 distance: 67 - 68: 12.492 distance: 68 - 69: 32.386 distance: 69 - 70: 22.899 distance: 71 - 72: 11.492 distance: 72 - 73: 31.497 distance: 72 - 75: 19.374 distance: 73 - 74: 31.638 distance: 73 - 81: 9.244 distance: 75 - 76: 12.508 distance: 76 - 77: 16.862 distance: 76 - 78: 14.971 distance: 77 - 79: 30.258 distance: 78 - 80: 7.968 distance: 79 - 80: 9.461 distance: 81 - 82: 15.177 distance: 82 - 83: 12.724 distance: 82 - 85: 24.658 distance: 83 - 84: 14.762 distance: 83 - 95: 13.490 distance: 85 - 86: 11.221 distance: 86 - 87: 15.859 distance: 86 - 88: 16.258 distance: 87 - 89: 14.831 distance: 88 - 90: 13.466 distance: 88 - 91: 4.490 distance: 89 - 90: 9.257 distance: 90 - 92: 9.922 distance: 91 - 93: 6.669 distance: 92 - 94: 13.792 distance: 93 - 94: 6.538 distance: 95 - 96: 6.520 distance: 96 - 97: 19.082 distance: 96 - 99: 10.908 distance: 97 - 98: 9.392 distance: 97 - 106: 14.376 distance: 99 - 100: 5.178 distance: 100 - 101: 8.325 distance: 101 - 102: 10.097 distance: 102 - 103: 4.143 distance: 103 - 104: 5.315 distance: 103 - 105: 7.097 distance: 106 - 107: 4.167 distance: 106 - 112: 15.287 distance: 107 - 108: 10.009 distance: 107 - 110: 15.908 distance: 108 - 113: 10.321 distance: 110 - 111: 9.578 distance: 111 - 112: 8.621 distance: 113 - 114: 13.167 distance: 114 - 115: 20.246 distance: 114 - 117: 9.479 distance: 115 - 116: 55.973 distance: 115 - 120: 15.299 distance: 117 - 118: 24.896 distance: 117 - 119: 13.301 distance: 120 - 121: 30.560 distance: 121 - 122: 19.537 distance: 121 - 124: 14.648 distance: 122 - 123: 18.302 distance: 122 - 127: 28.183 distance: 124 - 125: 21.486 distance: 124 - 126: 31.872 distance: 127 - 128: 9.435 distance: 128 - 129: 6.512 distance: 128 - 131: 12.568 distance: 129 - 130: 11.673 distance: 129 - 135: 17.011 distance: 131 - 132: 13.342 distance: 132 - 133: 18.108 distance: 132 - 134: 16.285 distance: 135 - 136: 18.480 distance: 136 - 137: 7.189 distance: 136 - 139: 10.951 distance: 137 - 138: 21.652 distance: 137 - 142: 5.550 distance: 139 - 141: 22.369