Starting phenix.real_space_refine on Sat Sep 12 12:06:03 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7ku7_23035/09_2026/7ku7_23035.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ku7_23035/09_2026/7ku7_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 { model { file = "/net/cci-nas-00/data/ceres_data/7ku7_23035/09_2026/7ku7_23035.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ku7_23035/09_2026/7ku7_23035.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7ku7_23035/09_2026/7ku7_23035.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7ku7_23035/09_2026/7ku7_23035.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7ku7_23035/09_2026/7ku7_23035.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ku7_23035/09_2026/7ku7_23035.map" } 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-2.2.1-6174/lib/python3.11/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: 3.46, per 1000 atoms: 0.22 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: 1.35 Conformation dependent library (CDL) restraints added in 594.2 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: 1.78 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: 2.57 Time building geometry restraints manager: 1.77 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: 2121 0.071 - 0.143: 324 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: 3.870 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: 0.280 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 17.600 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6524 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 : 0.006 0.183 16193 Z= 0.334 Angle : 0.997 48.291 22262 Z= 0.492 Chirality : 0.048 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/Z covalent geometry : bond 0.00568 / 0.33 (16185) covalent geometry : angle 0.99546 / 0.49 (22259) hydrogen bonds : bond 0.22562 / 15.40 ( 664) hydrogen bonds : angle 7.71108 / 5.49 ( 1884) metal coordination : bond 0.00796 / 0.53 ( 8) metal coordination : angle 4.15780 / 2.30 ( 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 : 0.570 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: 0.5640 (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: 0.7140 (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: -0.1315 (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: -0.2886 (mtt) outliers start: 0 outliers final: 0 residues processed: 343 average time/residue: 0.1535 time to fit residues: 73.6303 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 : 0.534 ------------------------------------------------------------------------------- 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: 1.9990 chunk 149 optimal weight: 4.9990 overall best weight: 1.3396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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** B 238 ASN 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** ** F 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 62 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4587 r_free = 0.4587 target = 0.165404 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.114079 restraints weight = 45984.984| |-----------------------------------------------------------------------------| r_work (start): 0.3778 rms_B_bonded: 6.30 r_work: 0.3525 rms_B_bonded: 5.97 restraints_weight: 2.0000 r_work (final): 0.3525 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7051 moved from start: 0.2751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 16193 Z= 0.199 Angle : 0.759 12.948 22262 Z= 0.399 Chirality : 0.050 0.200 2450 Planarity : 0.006 0.057 2577 Dihedral : 18.907 126.236 2776 Min Nonbonded Distance : 1.868 Molprobity Statistics. All-atom Clashscore : 15.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.11 % Favored : 93.89 % Rotamer: Outliers : 2.68 % Allowed : 12.18 % Favored : 85.14 % 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: -1.44 (0.19), residues: 1783 helix: 0.25 (0.20), residues: 628 sheet: -1.20 (0.24), residues: 402 loop : -1.80 (0.23), residues: 753 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 17 TYR 0.028 0.003 TYR D 246 PHE 0.022 0.002 PHE B 176 TRP 0.027 0.002 TRP F 134 HIS 0.006 0.001 HIS E 13 Details of bonding type rmsd/Z covalent geometry : bond 0.00418 / 0.20 (16185) covalent geometry : angle 0.75362 / 0.40 (22259) hydrogen bonds : bond 0.06384 / 4.39 ( 664) hydrogen bonds : angle 6.07470 / 4.31 ( 1884) metal coordination : bond 0.02070 / 1.43 ( 8) metal coordination : angle 7.67051 / 4.14 ( 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 228 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 188 time to evaluate : 0.581 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 HIS cc_start: 0.6916 (OUTLIER) cc_final: 0.6693 (m-70) REVERT: A 135 LEU cc_start: 0.8724 (OUTLIER) cc_final: 0.8458 (mm) REVERT: B 61 TRP cc_start: 0.7094 (m-10) cc_final: 0.6634 (m-10) REVERT: B 101 VAL cc_start: 0.4825 (OUTLIER) cc_final: 0.4211 (t) REVERT: B 105 TRP cc_start: 0.6494 (m-90) cc_final: 0.6215 (m-10) REVERT: B 126 PHE cc_start: 0.5994 (m-80) cc_final: 0.5699 (m-10) REVERT: B 176 PHE cc_start: 0.8354 (m-80) cc_final: 0.7764 (m-80) REVERT: B 232 GLU cc_start: 0.8035 (pp20) cc_final: 0.7195 (mp0) REVERT: E 187 GLU cc_start: 0.8540 (tm-30) cc_final: 0.8283 (tm-30) REVERT: E 193 MET cc_start: 0.7487 (mmp) cc_final: 0.7020 (mtm) REVERT: F 238 ASN cc_start: 0.7240 (p0) cc_final: 0.6909 (p0) outliers start: 40 outliers final: 19 residues processed: 211 average time/residue: 0.1153 time to fit residues: 38.0637 Evaluate side-chains 179 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 157 time to evaluate : 0.520 ------------------------------------------------------------------------------- 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 135 LEU 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 101 VAL Chi-restraints excluded: chain B residue 135 LEU 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 34 VAL Chi-restraints excluded: chain E residue 77 LEU Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 99 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 219 THR Chi-restraints excluded: chain G residue 188 LEU 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: 20.0000 chunk 134 optimal weight: 9.9990 chunk 53 optimal weight: 0.9980 chunk 125 optimal weight: 0.8980 chunk 75 optimal weight: 20.0000 chunk 130 optimal weight: 0.2980 chunk 167 optimal weight: 9.9990 chunk 120 optimal weight: 0.9990 chunk 62 optimal weight: 7.9990 chunk 24 optimal weight: 5.9990 overall best weight: 1.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 35 GLN A 160 ASN ** A 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 62 GLN ** C 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 93 HIS 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** H 238 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4557 r_free = 0.4557 target = 0.163303 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.117535 restraints weight = 47539.570| |-----------------------------------------------------------------------------| r_work (start): 0.3817 rms_B_bonded: 7.03 r_work (final): 0.3817 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7202 moved from start: 0.4682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.189 16193 Z= 0.237 Angle : 0.788 12.906 22262 Z= 0.415 Chirality : 0.049 0.290 2450 Planarity : 0.006 0.076 2577 Dihedral : 18.969 133.874 2776 Min Nonbonded Distance : 1.777 Molprobity Statistics. All-atom Clashscore : 15.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.06 % Favored : 93.94 % Rotamer: Outliers : 4.08 % Allowed : 15.06 % Favored : 80.86 % 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: -1.33 (0.19), residues: 1783 helix: 0.34 (0.20), residues: 633 sheet: -0.95 (0.24), residues: 410 loop : -1.88 (0.23), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG E 263 TYR 0.026 0.003 TYR D 246 PHE 0.020 0.002 PHE F 176 TRP 0.033 0.002 TRP C 259 HIS 0.012 0.002 HIS B 198 Details of bonding type rmsd/Z covalent geometry : bond 0.00530 / 0.24 (16185) covalent geometry : angle 0.78308 / 0.42 (22259) hydrogen bonds : bond 0.07125 / 4.96 ( 664) hydrogen bonds : angle 5.56899 / 4.02 ( 1884) metal coordination : bond 0.01496 / 0.96 ( 8) metal coordination : angle 7.47596 / 3.95 ( 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 221 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 160 time to evaluate : 0.545 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 THR cc_start: 0.8618 (m) cc_final: 0.8363 (t) REVERT: A 188 LEU cc_start: 0.8534 (mm) cc_final: 0.8292 (mp) REVERT: A 193 MET cc_start: 0.8208 (ttm) cc_final: 0.7964 (ttm) REVERT: B 105 TRP cc_start: 0.6399 (m-90) cc_final: 0.5851 (m-10) REVERT: B 109 ILE cc_start: 0.8478 (OUTLIER) cc_final: 0.8221 (mt) REVERT: B 155 MET cc_start: 0.7601 (mmm) cc_final: 0.7400 (mmp) REVERT: B 246 TYR cc_start: 0.7363 (m-80) cc_final: 0.7086 (m-10) REVERT: C 262 SER cc_start: 0.8880 (m) cc_final: 0.8494 (t) REVERT: D 71 MET cc_start: 0.0194 (ttp) cc_final: -0.3730 (mmt) REVERT: D 177 MET cc_start: 0.2656 (mmp) cc_final: 0.1883 (mpp) REVERT: E 32 GLU cc_start: 0.8049 (OUTLIER) cc_final: 0.7783 (pm20) REVERT: F 238 ASN cc_start: 0.7124 (p0) cc_final: 0.6871 (p0) REVERT: G 228 ILE cc_start: 0.8446 (tp) cc_final: 0.8069 (tp) REVERT: H 92 GLN cc_start: 0.6415 (OUTLIER) cc_final: 0.6126 (tm-30) REVERT: H 246 TYR cc_start: 0.6100 (p90) cc_final: 0.5714 (p90) outliers start: 61 outliers final: 33 residues processed: 204 average time/residue: 0.1159 time to fit residues: 36.4963 Evaluate side-chains 174 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 138 time to evaluate : 0.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 ILE Chi-restraints excluded: chain A residue 35 GLN Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 258 ILE Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 103 HIS Chi-restraints excluded: chain B residue 109 ILE Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 194 TYR Chi-restraints excluded: chain B residue 209 ILE Chi-restraints excluded: chain C residue 226 ILE Chi-restraints excluded: chain D residue 143 THR Chi-restraints excluded: chain D residue 241 VAL 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 149 ASN Chi-restraints excluded: chain E residue 153 GLN Chi-restraints excluded: chain E residue 177 MET Chi-restraints excluded: chain E residue 241 VAL Chi-restraints excluded: chain F residue 90 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 230 THR Chi-restraints excluded: chain H residue 92 GLN Chi-restraints excluded: chain H residue 96 VAL 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: 0.0770 chunk 108 optimal weight: 0.9980 chunk 153 optimal weight: 1.9990 chunk 21 optimal weight: 3.9990 chunk 116 optimal weight: 0.8980 chunk 131 optimal weight: 0.2980 chunk 177 optimal weight: 0.9980 chunk 152 optimal weight: 0.9990 chunk 159 optimal weight: 20.0000 chunk 42 optimal weight: 10.0000 chunk 82 optimal weight: 20.0000 overall best weight: 0.6538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 204 ASN C 197 ASN ** C 212 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** H 62 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4574 r_free = 0.4574 target = 0.164990 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.119289 restraints weight = 46795.150| |-----------------------------------------------------------------------------| r_work (start): 0.3825 rms_B_bonded: 6.23 r_work (final): 0.3825 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7190 moved from start: 0.4993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 16193 Z= 0.133 Angle : 0.615 9.220 22262 Z= 0.330 Chirality : 0.045 0.175 2450 Planarity : 0.005 0.083 2577 Dihedral : 18.804 123.321 2776 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 12.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 3.48 % Allowed : 16.93 % Favored : 79.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.96 (0.20), residues: 1783 helix: 0.66 (0.20), residues: 634 sheet: -0.74 (0.24), residues: 404 loop : -1.69 (0.23), residues: 745 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 244 TYR 0.018 0.002 TYR D 246 PHE 0.017 0.001 PHE B 65 TRP 0.020 0.001 TRP H 242 HIS 0.004 0.001 HIS E 198 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.13 (16185) covalent geometry : angle 0.61162 / 0.33 (22259) hydrogen bonds : bond 0.04840 / 3.43 ( 664) hydrogen bonds : angle 5.27445 / 3.81 ( 1884) metal coordination : bond 0.01594 / 1.09 ( 8) metal coordination : angle 5.70189 / 3.17 ( 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 215 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 163 time to evaluate : 0.689 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 THR cc_start: 0.8671 (m) cc_final: 0.8443 (p) REVERT: A 41 ASN cc_start: 0.7927 (t0) cc_final: 0.7649 (t0) REVERT: A 188 LEU cc_start: 0.8495 (mm) cc_final: 0.8262 (mt) REVERT: B 105 TRP cc_start: 0.6480 (m-90) cc_final: 0.6188 (m-10) REVERT: B 155 MET cc_start: 0.7456 (mmm) cc_final: 0.7196 (mmm) REVERT: B 163 LEU cc_start: 0.9083 (tp) cc_final: 0.8872 (tt) REVERT: B 187 GLU cc_start: 0.8052 (mm-30) cc_final: 0.7414 (mm-30) REVERT: B 232 GLU cc_start: 0.7920 (pp20) cc_final: 0.7382 (mp0) REVERT: B 246 TYR cc_start: 0.7316 (m-80) cc_final: 0.7043 (m-10) REVERT: C 262 SER cc_start: 0.8838 (m) cc_final: 0.8480 (t) REVERT: D 71 MET cc_start: -0.0366 (ttp) cc_final: -0.4599 (mmt) REVERT: D 244 ARG cc_start: 0.4358 (mmp-170) cc_final: 0.3108 (mmm160) REVERT: F 232 GLU cc_start: 0.8025 (mp0) cc_final: 0.7748 (mp0) REVERT: G 228 ILE cc_start: 0.8240 (OUTLIER) cc_final: 0.7878 (tp) outliers start: 52 outliers final: 28 residues processed: 196 average time/residue: 0.1241 time to fit residues: 37.2118 Evaluate side-chains 175 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 146 time to evaluate : 0.564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 HIS Chi-restraints excluded: chain A residue 80 THR 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 258 ILE Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 103 HIS Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 194 TYR Chi-restraints excluded: chain C residue 241 VAL 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 146 ILE Chi-restraints excluded: chain E residue 153 GLN Chi-restraints excluded: chain E residue 207 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 71 MET Chi-restraints excluded: chain G residue 81 VAL Chi-restraints excluded: chain G residue 228 ILE Chi-restraints excluded: chain G residue 230 THR 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 230 THR 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: 0.8980 chunk 137 optimal weight: 20.0000 chunk 57 optimal weight: 1.9990 chunk 41 optimal weight: 0.0170 chunk 99 optimal weight: 0.9980 chunk 124 optimal weight: 7.9990 chunk 138 optimal weight: 0.3980 chunk 150 optimal weight: 9.9990 chunk 110 optimal weight: 4.9990 chunk 117 optimal weight: 7.9990 chunk 21 optimal weight: 2.9990 overall best weight: 0.8620 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 210 GLN ** B 92 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** ** 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** ** H 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4571 r_free = 0.4571 target = 0.164350 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.114685 restraints weight = 46818.053| |-----------------------------------------------------------------------------| r_work (start): 0.3731 rms_B_bonded: 6.56 r_work: 0.3525 rms_B_bonded: 5.26 restraints_weight: 2.0000 r_work (final): 0.3525 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7651 moved from start: 0.5300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 16193 Z= 0.135 Angle : 0.609 9.288 22262 Z= 0.323 Chirality : 0.044 0.281 2450 Planarity : 0.005 0.062 2577 Dihedral : 18.807 151.059 2776 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 13.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 3.75 % Allowed : 17.94 % Favored : 78.31 % 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: -0.83 (0.19), residues: 1783 helix: 0.82 (0.20), residues: 633 sheet: -0.69 (0.24), residues: 405 loop : -1.64 (0.23), residues: 745 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 95 TYR 0.027 0.002 TYR H 246 PHE 0.015 0.001 PHE B 176 TRP 0.032 0.001 TRP C 259 HIS 0.005 0.001 HIS E 198 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.13 (16185) covalent geometry : angle 0.60614 / 0.32 (22259) hydrogen bonds : bond 0.04720 / 3.33 ( 664) hydrogen bonds : angle 5.13662 / 3.71 ( 1884) metal coordination : bond 0.01241 / 0.84 ( 8) metal coordination : angle 5.24228 / 2.91 ( 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 209 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 153 time to evaluate : 0.544 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 THR cc_start: 0.9099 (m) cc_final: 0.8847 (p) REVERT: A 41 ASN cc_start: 0.8072 (t0) cc_final: 0.7811 (t0) REVERT: A 62 GLN cc_start: 0.8904 (OUTLIER) cc_final: 0.7050 (mp10) REVERT: A 71 MET cc_start: 0.8142 (mmt) cc_final: 0.7924 (mmt) REVERT: B 105 TRP cc_start: 0.7125 (m-90) cc_final: 0.6596 (m-10) REVERT: B 155 MET cc_start: 0.7679 (mmm) cc_final: 0.7462 (mmm) REVERT: B 163 LEU cc_start: 0.9199 (tp) cc_final: 0.8922 (tt) REVERT: B 187 GLU cc_start: 0.8083 (OUTLIER) cc_final: 0.7265 (mm-30) REVERT: B 246 TYR cc_start: 0.7653 (m-80) cc_final: 0.7166 (m-10) REVERT: C 262 SER cc_start: 0.9134 (m) cc_final: 0.8856 (t) REVERT: D 71 MET cc_start: 0.2498 (ttp) cc_final: -0.2626 (mmt) REVERT: D 244 ARG cc_start: 0.4093 (mmp-170) cc_final: 0.2541 (mmm160) REVERT: E 210 GLN cc_start: 0.7439 (OUTLIER) cc_final: 0.7042 (pp30) REVERT: F 232 GLU cc_start: 0.7737 (mp0) cc_final: 0.7226 (mp0) REVERT: G 228 ILE cc_start: 0.8505 (OUTLIER) cc_final: 0.7835 (tp) outliers start: 56 outliers final: 33 residues processed: 189 average time/residue: 0.1212 time to fit residues: 35.2988 Evaluate side-chains 178 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 141 time to evaluate : 0.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 HIS Chi-restraints excluded: chain A residue 62 GLN Chi-restraints excluded: chain A residue 80 THR 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 258 ILE Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 103 HIS Chi-restraints excluded: chain B residue 187 GLU Chi-restraints excluded: chain B residue 194 TYR Chi-restraints excluded: chain B residue 199 PHE Chi-restraints excluded: chain C residue 260 VAL Chi-restraints excluded: chain D residue 177 MET Chi-restraints excluded: chain D residue 241 VAL Chi-restraints excluded: chain D residue 257 VAL Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 140 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 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 155 MET Chi-restraints excluded: chain F residue 169 VAL Chi-restraints excluded: chain G residue 71 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 228 ILE Chi-restraints excluded: chain G residue 241 VAL Chi-restraints excluded: chain H residue 90 VAL Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 254 THR 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: 10.0000 chunk 40 optimal weight: 4.9990 chunk 105 optimal weight: 2.9990 chunk 82 optimal weight: 20.0000 chunk 62 optimal weight: 8.9990 chunk 48 optimal weight: 0.9990 chunk 50 optimal weight: 0.9990 chunk 176 optimal weight: 0.7980 chunk 101 optimal weight: 0.0970 chunk 172 optimal weight: 6.9990 chunk 87 optimal weight: 0.0050 overall best weight: 0.5796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 210 GLN ** B 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 185 GLN ** 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** ** H 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4583 r_free = 0.4583 target = 0.165097 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.102542 restraints weight = 45001.209| |-----------------------------------------------------------------------------| r_work (start): 0.3736 rms_B_bonded: 3.70 r_work: 0.3570 rms_B_bonded: 4.21 restraints_weight: 0.5000 r_work (final): 0.3570 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7790 moved from start: 0.5502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 16193 Z= 0.123 Angle : 0.606 10.628 22262 Z= 0.321 Chirality : 0.045 0.303 2450 Planarity : 0.005 0.058 2577 Dihedral : 18.769 154.614 2776 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 12.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 3.88 % Allowed : 18.14 % 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: -0.73 (0.20), residues: 1783 helix: 0.96 (0.20), residues: 627 sheet: -0.66 (0.24), residues: 410 loop : -1.63 (0.23), residues: 746 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 95 TYR 0.029 0.002 TYR H 246 PHE 0.009 0.001 PHE B 65 TRP 0.020 0.001 TRP C 259 HIS 0.005 0.001 HIS E 198 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.12 (16185) covalent geometry : angle 0.60365 / 0.32 (22259) hydrogen bonds : bond 0.04616 / 3.26 ( 664) hydrogen bonds : angle 5.03704 / 3.64 ( 1884) metal coordination : bond 0.01317 / 0.90 ( 8) metal coordination : angle 4.49771 / 2.54 ( 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 203 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 145 time to evaluate : 0.568 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 THR cc_start: 0.9053 (m) cc_final: 0.8817 (p) REVERT: A 40 CYS cc_start: 0.9351 (OUTLIER) cc_final: 0.8816 (m) REVERT: A 41 ASN cc_start: 0.7973 (t0) cc_final: 0.7426 (m-40) REVERT: A 62 GLN cc_start: 0.8937 (OUTLIER) cc_final: 0.7121 (mp10) REVERT: A 112 LEU cc_start: 0.8982 (OUTLIER) cc_final: 0.8475 (mm) REVERT: B 105 TRP cc_start: 0.6978 (m-90) cc_final: 0.6579 (m-10) REVERT: B 163 LEU cc_start: 0.9171 (tp) cc_final: 0.8952 (tt) REVERT: B 187 GLU cc_start: 0.7909 (OUTLIER) cc_final: 0.7287 (mm-30) REVERT: B 246 TYR cc_start: 0.7618 (m-80) cc_final: 0.7158 (m-10) REVERT: C 262 SER cc_start: 0.9031 (m) cc_final: 0.8768 (t) REVERT: D 71 MET cc_start: 0.3885 (ttp) cc_final: 0.1126 (mmt) REVERT: E 210 GLN cc_start: 0.7205 (OUTLIER) cc_final: 0.6905 (pp30) REVERT: F 172 GLU cc_start: 0.8658 (OUTLIER) cc_final: 0.8436 (mm-30) REVERT: F 232 GLU cc_start: 0.8078 (mp0) cc_final: 0.7797 (mp0) REVERT: F 250 LYS cc_start: 0.7621 (OUTLIER) cc_final: 0.7286 (mtpp) outliers start: 58 outliers final: 38 residues processed: 186 average time/residue: 0.1238 time to fit residues: 35.1346 Evaluate side-chains 185 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 140 time to evaluate : 0.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 HIS Chi-restraints excluded: chain A residue 40 CYS Chi-restraints excluded: chain A residue 62 GLN Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 210 GLN Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 258 ILE Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 77 LEU Chi-restraints excluded: chain B residue 103 HIS Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 187 GLU Chi-restraints excluded: chain C residue 241 VAL Chi-restraints excluded: chain C residue 260 VAL Chi-restraints excluded: chain D residue 177 MET Chi-restraints excluded: chain D residue 241 VAL Chi-restraints excluded: chain D residue 257 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 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 155 MET Chi-restraints excluded: chain F residue 169 VAL Chi-restraints excluded: chain F residue 172 GLU Chi-restraints excluded: chain F residue 250 LYS Chi-restraints excluded: chain G residue 71 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 241 VAL Chi-restraints excluded: chain H residue 90 VAL Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 254 THR Chi-restraints excluded: chain H residue 260 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 130 optimal weight: 0.0000 chunk 86 optimal weight: 0.3980 chunk 177 optimal weight: 0.0570 chunk 109 optimal weight: 0.0980 chunk 160 optimal weight: 3.9990 chunk 125 optimal weight: 0.8980 chunk 38 optimal weight: 0.5980 chunk 178 optimal weight: 10.0000 chunk 21 optimal weight: 0.0270 chunk 28 optimal weight: 3.9990 chunk 141 optimal weight: 6.9990 overall best weight: 0.1160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 210 GLN ** B 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 185 GLN ** 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** ** H 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4593 r_free = 0.4593 target = 0.165467 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.121440 restraints weight = 45147.649| |-----------------------------------------------------------------------------| r_work (start): 0.3865 rms_B_bonded: 5.73 r_work (final): 0.3865 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7197 moved from start: 0.5600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 16193 Z= 0.116 Angle : 0.600 11.411 22262 Z= 0.318 Chirality : 0.044 0.315 2450 Planarity : 0.005 0.055 2577 Dihedral : 18.733 157.780 2776 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 11.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 3.35 % Allowed : 18.81 % Favored : 77.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.56 (0.20), residues: 1783 helix: 1.12 (0.20), residues: 625 sheet: -0.51 (0.25), residues: 401 loop : -1.56 (0.23), residues: 757 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 95 TYR 0.017 0.001 TYR D 246 PHE 0.007 0.001 PHE B 65 TRP 0.020 0.001 TRP D 134 HIS 0.004 0.001 HIS G 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00236 / 0.12 (16185) covalent geometry : angle 0.59838 / 0.32 (22259) hydrogen bonds : bond 0.04506 / 3.18 ( 664) hydrogen bonds : angle 4.96755 / 3.59 ( 1884) metal coordination : bond 0.01001 / 0.66 ( 8) metal coordination : angle 4.18797 / 2.39 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 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 201 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 151 time to evaluate : 0.578 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 THR cc_start: 0.8615 (m) cc_final: 0.8400 (p) REVERT: A 62 GLN cc_start: 0.8794 (OUTLIER) cc_final: 0.6828 (mp10) REVERT: B 105 TRP cc_start: 0.6797 (m-90) cc_final: 0.6528 (m-10) REVERT: B 109 ILE cc_start: 0.8385 (mm) cc_final: 0.7975 (mm) REVERT: B 163 LEU cc_start: 0.9171 (tp) cc_final: 0.8956 (tt) REVERT: B 187 GLU cc_start: 0.8008 (OUTLIER) cc_final: 0.7421 (mm-30) REVERT: B 193 MET cc_start: 0.7567 (mmm) cc_final: 0.7122 (mmm) REVERT: B 246 TYR cc_start: 0.7327 (m-80) cc_final: 0.7005 (m-10) REVERT: D 71 MET cc_start: -0.0272 (ttp) cc_final: -0.4336 (mmt) REVERT: E 210 GLN cc_start: 0.7054 (OUTLIER) cc_final: 0.6699 (pp30) REVERT: F 172 GLU cc_start: 0.8589 (OUTLIER) cc_final: 0.8367 (mm-30) REVERT: F 232 GLU cc_start: 0.7801 (mp0) cc_final: 0.7485 (mp0) outliers start: 50 outliers final: 39 residues processed: 185 average time/residue: 0.1214 time to fit residues: 34.5946 Evaluate side-chains 181 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 138 time to evaluate : 0.569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 140 ILE Chi-restraints excluded: chain A residue 210 GLN Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 258 ILE Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 77 LEU Chi-restraints excluded: chain B residue 103 HIS Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 187 GLU Chi-restraints excluded: chain C residue 241 VAL Chi-restraints excluded: chain C residue 260 VAL Chi-restraints excluded: chain D residue 143 THR Chi-restraints excluded: chain D residue 177 MET Chi-restraints excluded: chain D residue 241 VAL Chi-restraints excluded: chain D residue 257 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 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 155 MET Chi-restraints excluded: chain F residue 169 VAL Chi-restraints excluded: chain F residue 172 GLU Chi-restraints excluded: chain G residue 71 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 188 LEU Chi-restraints excluded: chain G residue 241 VAL Chi-restraints excluded: chain H residue 90 VAL Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 254 THR Chi-restraints excluded: chain H residue 260 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 91 optimal weight: 8.9990 chunk 179 optimal weight: 30.0000 chunk 34 optimal weight: 0.7980 chunk 129 optimal weight: 7.9990 chunk 69 optimal weight: 5.9990 chunk 98 optimal weight: 0.2980 chunk 144 optimal weight: 4.9990 chunk 57 optimal weight: 7.9990 chunk 43 optimal weight: 10.0000 chunk 169 optimal weight: 10.0000 chunk 41 optimal weight: 4.9990 overall best weight: 3.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 160 ASN ** A 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 149 ASN ** 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** ** 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** ** H 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 198 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4502 r_free = 0.4502 target = 0.159416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.103085 restraints weight = 46546.873| |-----------------------------------------------------------------------------| r_work (start): 0.3592 rms_B_bonded: 6.92 r_work: 0.3434 rms_B_bonded: 5.76 restraints_weight: 2.0000 r_work (final): 0.3434 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8012 moved from start: 0.6753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.170 16193 Z= 0.296 Angle : 0.783 17.068 22262 Z= 0.418 Chirality : 0.050 0.442 2450 Planarity : 0.007 0.062 2577 Dihedral : 19.069 165.278 2776 Min Nonbonded Distance : 1.796 Molprobity Statistics. All-atom Clashscore : 16.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.34 % Favored : 93.66 % Rotamer: Outliers : 3.61 % Allowed : 19.21 % Favored : 77.18 % 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: -0.90 (0.20), residues: 1783 helix: 0.75 (0.20), residues: 632 sheet: -0.66 (0.25), residues: 408 loop : -1.72 (0.23), residues: 743 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 17 TYR 0.014 0.003 TYR D 246 PHE 0.018 0.002 PHE B 199 TRP 0.032 0.002 TRP F 237 HIS 0.015 0.002 HIS E 212 Details of bonding type rmsd/Z covalent geometry : bond 0.00637 / 0.29 (16185) covalent geometry : angle 0.77215 / 0.42 (22259) hydrogen bonds : bond 0.05573 / 3.88 ( 664) hydrogen bonds : angle 5.36544 / 3.88 ( 1884) metal coordination : bond 0.04454 / 2.39 ( 8) metal coordination : angle 11.19961 / 7.08 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 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: 54 poor density : 128 time to evaluate : 0.588 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 THR cc_start: 0.9181 (m) cc_final: 0.8980 (p) REVERT: A 21 LYS cc_start: 0.9303 (mmpt) cc_final: 0.8873 (mptt) REVERT: A 51 ASN cc_start: 0.8038 (OUTLIER) cc_final: 0.7836 (m-40) REVERT: A 62 GLN cc_start: 0.9180 (OUTLIER) cc_final: 0.7736 (mt0) REVERT: A 112 LEU cc_start: 0.9176 (OUTLIER) cc_final: 0.8732 (mm) REVERT: B 187 GLU cc_start: 0.8460 (OUTLIER) cc_final: 0.8011 (mp0) REVERT: D 71 MET cc_start: 0.3781 (ttp) cc_final: 0.0301 (mmt) REVERT: D 244 ARG cc_start: 0.4677 (mmp-170) cc_final: 0.3348 (mmm160) REVERT: F 92 GLN cc_start: 0.8530 (pt0) cc_final: 0.8312 (pt0) REVERT: F 232 GLU cc_start: 0.8195 (mp0) cc_final: 0.7968 (mp0) REVERT: F 234 GLU cc_start: 0.6644 (OUTLIER) cc_final: 0.5818 (pm20) outliers start: 54 outliers final: 34 residues processed: 170 average time/residue: 0.1328 time to fit residues: 33.9677 Evaluate side-chains 148 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 109 time to evaluate : 0.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 HIS Chi-restraints excluded: chain A residue 51 ASN Chi-restraints excluded: chain A residue 62 GLN Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 122 ASN 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 241 VAL Chi-restraints excluded: chain C residue 265 VAL Chi-restraints excluded: chain D residue 143 THR Chi-restraints excluded: chain D residue 177 MET 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 207 THR Chi-restraints excluded: chain E residue 210 GLN Chi-restraints excluded: chain E residue 241 VAL Chi-restraints excluded: chain F residue 103 HIS Chi-restraints excluded: chain F residue 105 TRP Chi-restraints excluded: chain F residue 188 LEU Chi-restraints excluded: chain F residue 234 GLU 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 H residue 90 VAL Chi-restraints excluded: chain H residue 92 GLN Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 254 THR Chi-restraints excluded: chain H residue 258 ILE Chi-restraints excluded: chain H residue 260 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 149 optimal weight: 1.9990 chunk 130 optimal weight: 0.7980 chunk 72 optimal weight: 30.0000 chunk 98 optimal weight: 0.5980 chunk 29 optimal weight: 3.9990 chunk 14 optimal weight: 1.9990 chunk 121 optimal weight: 0.9980 chunk 165 optimal weight: 8.9990 chunk 24 optimal weight: 2.9990 chunk 76 optimal weight: 6.9990 chunk 97 optimal weight: 0.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 122 ASN C 197 ASN ** C 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 185 GLN ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4534 r_free = 0.4534 target = 0.162218 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.118384 restraints weight = 46225.840| |-----------------------------------------------------------------------------| r_work (start): 0.3815 rms_B_bonded: 5.55 r_work (final): 0.3815 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7353 moved from start: 0.6963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 16193 Z= 0.144 Angle : 0.660 12.189 22262 Z= 0.346 Chirality : 0.045 0.323 2450 Planarity : 0.005 0.071 2577 Dihedral : 18.883 156.790 2776 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 12.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 2.48 % Allowed : 20.35 % Favored : 77.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.65 (0.20), residues: 1783 helix: 1.00 (0.20), residues: 631 sheet: -0.47 (0.24), residues: 413 loop : -1.65 (0.23), residues: 739 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG E 95 TYR 0.028 0.002 TYR C 246 PHE 0.014 0.001 PHE B 65 TRP 0.027 0.001 TRP B 105 HIS 0.007 0.001 HIS A 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.14 (16185) covalent geometry : angle 0.65513 / 0.35 (22259) hydrogen bonds : bond 0.04690 / 3.35 ( 664) hydrogen bonds : angle 5.04990 / 3.64 ( 1884) metal coordination : bond 0.01167 / 0.69 ( 8) metal coordination : angle 7.25234 / 4.37 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 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 161 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 124 time to evaluate : 0.585 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 LYS cc_start: 0.8863 (mmpt) cc_final: 0.8628 (mptt) REVERT: A 62 GLN cc_start: 0.8679 (OUTLIER) cc_final: 0.7163 (mt0) REVERT: B 187 GLU cc_start: 0.8518 (OUTLIER) cc_final: 0.7627 (mp0) REVERT: B 193 MET cc_start: 0.7865 (ttm) cc_final: 0.7654 (ttm) REVERT: D 71 MET cc_start: -0.0659 (ttp) cc_final: -0.4476 (mmt) REVERT: D 244 ARG cc_start: 0.4349 (mmp-170) cc_final: 0.3297 (mmm160) REVERT: E 210 GLN cc_start: 0.7857 (OUTLIER) cc_final: 0.7322 (pp30) REVERT: F 232 GLU cc_start: 0.8070 (mp0) cc_final: 0.7777 (mp0) REVERT: F 234 GLU cc_start: 0.6432 (OUTLIER) cc_final: 0.5672 (pm20) REVERT: G 255 ASP cc_start: 0.8463 (t0) cc_final: 0.7927 (m-30) outliers start: 37 outliers final: 28 residues processed: 154 average time/residue: 0.1259 time to fit residues: 29.3779 Evaluate side-chains 143 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 111 time to evaluate : 0.552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 GLN Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 153 GLN Chi-restraints excluded: chain B residue 187 GLU Chi-restraints excluded: chain C residue 226 ILE Chi-restraints excluded: chain D residue 143 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 149 ASN 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 207 THR Chi-restraints excluded: chain E residue 210 GLN Chi-restraints excluded: chain E residue 241 VAL Chi-restraints excluded: chain F residue 155 MET Chi-restraints excluded: chain F residue 188 LEU Chi-restraints excluded: chain F residue 234 GLU 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 H residue 90 VAL Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 254 THR Chi-restraints excluded: chain H residue 260 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 104 optimal weight: 5.9990 chunk 47 optimal weight: 7.9990 chunk 174 optimal weight: 3.9990 chunk 40 optimal weight: 0.8980 chunk 34 optimal weight: 0.9990 chunk 129 optimal weight: 2.9990 chunk 96 optimal weight: 0.3980 chunk 123 optimal weight: 4.9990 chunk 75 optimal weight: 10.0000 chunk 13 optimal weight: 2.9990 chunk 70 optimal weight: 10.0000 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 92 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4518 r_free = 0.4518 target = 0.161059 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.115743 restraints weight = 46125.882| |-----------------------------------------------------------------------------| r_work (start): 0.3764 rms_B_bonded: 7.64 r_work: 0.3372 rms_B_bonded: 7.26 restraints_weight: 2.0000 r_work (final): 0.3372 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 moved from start: 0.7252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 16193 Z= 0.173 Angle : 0.665 13.013 22262 Z= 0.348 Chirality : 0.045 0.322 2450 Planarity : 0.005 0.059 2577 Dihedral : 18.898 156.596 2776 Min Nonbonded Distance : 1.881 Molprobity Statistics. All-atom Clashscore : 13.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer: Outliers : 2.54 % Allowed : 20.21 % Favored : 77.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.67 (0.20), residues: 1783 helix: 0.98 (0.20), residues: 632 sheet: -0.52 (0.24), residues: 403 loop : -1.63 (0.23), residues: 748 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG E 95 TYR 0.015 0.002 TYR C 246 PHE 0.010 0.001 PHE B 199 TRP 0.022 0.001 TRP B 105 HIS 0.014 0.001 HIS A 104 Details of bonding type rmsd/Z covalent geometry : bond 0.00380 / 0.17 (16185) covalent geometry : angle 0.66053 / 0.35 (22259) hydrogen bonds : bond 0.04739 / 3.35 ( 664) hydrogen bonds : angle 5.04530 / 3.63 ( 1884) metal coordination : bond 0.01371 / 0.82 ( 8) metal coordination : angle 6.67445 / 4.16 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 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 156 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 118 time to evaluate : 0.581 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 LYS cc_start: 0.9370 (mmpt) cc_final: 0.8875 (mmtm) REVERT: A 41 ASN cc_start: 0.7831 (t0) cc_final: 0.7578 (t0) REVERT: A 62 GLN cc_start: 0.9168 (OUTLIER) cc_final: 0.7722 (mt0) REVERT: B 187 GLU cc_start: 0.8632 (OUTLIER) cc_final: 0.8200 (mp0) REVERT: D 71 MET cc_start: 0.2565 (ttp) cc_final: -0.1450 (mmt) REVERT: D 244 ARG cc_start: 0.4802 (mmp-170) cc_final: 0.3745 (mmm160) REVERT: E 27 MET cc_start: 0.7927 (mmp) cc_final: 0.7599 (mmp) REVERT: E 210 GLN cc_start: 0.8205 (OUTLIER) cc_final: 0.7584 (pp30) REVERT: F 232 GLU cc_start: 0.8285 (mp0) cc_final: 0.8017 (mp0) REVERT: F 234 GLU cc_start: 0.6571 (OUTLIER) cc_final: 0.5729 (pm20) REVERT: F 246 TYR cc_start: 0.8646 (m-80) cc_final: 0.8163 (m-80) outliers start: 38 outliers final: 28 residues processed: 150 average time/residue: 0.1298 time to fit residues: 29.5069 Evaluate side-chains 147 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 115 time to evaluate : 0.661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 HIS Chi-restraints excluded: chain A residue 62 GLN Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain B residue 81 VAL 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 D residue 143 THR Chi-restraints excluded: chain D residue 241 VAL Chi-restraints excluded: chain D residue 257 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 149 ASN 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 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 188 LEU Chi-restraints excluded: chain F residue 234 GLU 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 H residue 90 VAL Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 254 THR Chi-restraints excluded: chain H residue 260 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 18 optimal weight: 0.7980 chunk 101 optimal weight: 6.9990 chunk 56 optimal weight: 7.9990 chunk 27 optimal weight: 3.9990 chunk 92 optimal weight: 0.0000 chunk 5 optimal weight: 2.9990 chunk 180 optimal weight: 8.9990 chunk 160 optimal weight: 0.9980 chunk 60 optimal weight: 5.9990 chunk 146 optimal weight: 10.0000 chunk 85 optimal weight: 8.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 92 GLN ** 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** ** H 62 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 = 0.4510 r_free = 0.4510 target = 0.160648 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.116042 restraints weight = 45639.630| |-----------------------------------------------------------------------------| r_work (start): 0.3755 rms_B_bonded: 6.81 r_work (final): 0.3755 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7495 moved from start: 0.7559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.090 16193 Z= 0.173 Angle : 0.670 13.316 22262 Z= 0.350 Chirality : 0.045 0.316 2450 Planarity : 0.005 0.061 2577 Dihedral : 18.886 152.697 2776 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 13.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 2.34 % Allowed : 20.48 % Favored : 77.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.69 (0.20), residues: 1783 helix: 0.94 (0.20), residues: 634 sheet: -0.54 (0.24), residues: 405 loop : -1.63 (0.23), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG E 95 TYR 0.016 0.002 TYR C 246 PHE 0.011 0.001 PHE F 65 TRP 0.024 0.001 TRP B 105 HIS 0.008 0.001 HIS A 104 Details of bonding type rmsd/Z covalent geometry : bond 0.00381 / 0.17 (16185) covalent geometry : angle 0.66565 / 0.35 (22259) hydrogen bonds : bond 0.04713 / 3.33 ( 664) hydrogen bonds : angle 5.02252 / 3.62 ( 1884) metal coordination : bond 0.01601 / 1.01 ( 8) metal coordination : angle 6.48269 / 4.15 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5347.16 seconds wall clock time: 92 minutes 14.44 seconds (5534.44 seconds total)